Interallelic and intergenic conversion events could induce differential evolution of the two rabbit immunoglobulin kappa light chain genes.

Contrary to the situation in humans or mice, where the constant region (C) of the Immunoglobulin (Ig) kappa (kappa) light chain is encoded by a single gene, the rabbit possesses two C kappa genes: C kappa 1 and C kappa 2. However, in domestic rabbits, the vast majority of the immunoglobulins have a light chain of the kappa 1 isotype, which is expressed under four complex, highly divergent allelic forms: b4, b5, b6 and b9. In previous papers, we have shown that this high level of divergence was due, at least partly, to conversion events of the kappa 1 by the kappa 2 locus. Up to now, little was known about the evolution of the C kappa 2 gene. Here, we report sequences of the C kappa 2 genes in three different haplotypes, and show that, in contrast to the situation in the kappa 1 locus, the three analysed C kappa 2 alleles are identical (or only differing by one silent substitution). This suggests that intergenic conversion, which introduced most of the divergence in the kappa 1 locus, is not reciprocal and is unidirectional from kappa 2 towards kappa 1. To explain the small number of silent substitutions in the C kappa 2 gene and its remarkable conservation, we propose an extended model of multigenic family evolution, which postulates that gene conversion events occur between linked genes as well as between alleles.     

Complex allotypes of the rabbit immunoglobulin kappa light chains are encoded by structural alleles.

We have isolated the rabbit immunoglobulin b9 Ck light chain gene and compared its nucleotide sequence with the b4, b4var , b5 and bas Ck sequences. In spite of the high number of substitutions found between the different rabbit Ck coding regions, only very few changes are silent. Furthermore, the nucleotide changes are clustered in segments which correlate with the bends and helical regions found in the tertiary structure of the Ck domain of the protein. The flanking regions present a higher degree of conservation than the coding regions. The two genomic EcoRI fragments hybridizing to a b4cDNA probe have been correlated with the two distinct loci, Ck1 and Ck2 : one encodes for the nominal b9 Ck allotype and the other contains the information for the bas Ck region. The b allotypes are true alleles which could have evolved by intergenic conversion.     

Involvement of the alternative oxidase in respiration of Yarrowia lipolytica mitochondria is controlled by the activity of the cytochrome pathway

The degree of involvement of cyanide-resistant alternative oxidase in the respiration of Yarrowia lipolytica mitochondria was evaluated by comparing the rate of oxygen consumption in the presence of cyanide, which shows the activity of the cyanide-resistant alternative oxidase, and the oxidation rate of cytochrome c by ferricyanide, which shows the activity of the main cytochrome pathway. The oxidation of succinate by mitochondria in the presence of ferricyanide and cyanide was associated with oxygen consumption due to the functioning of the alternative oxidase. The subsequent addition of ADP or FCCP (an uncoupler of oxidative phosphorylation) completely inhibited oxygen consumption by the mitochondria. Under these conditions, the inhibition of the alternative oxidase by benzohydroxamic acid (BHA) failed to affect the reduction of ferricyanide at the level of cytochrome c. BHA did not influence the rate of ferricyanide reduction by the cytochrome pathway occurring in controlled state 4, nor could it change the phosphorylation quotient ATP/O upon the oxidation of various substrates. These data indicate that the alternative system is unable to compete with the cytochrome respiratory chain for electrons. The alternative oxidase only transfers the electrons that are superfluous for the cytochrome respiratory chain.     

Unique functional properties of a sensory neuronal P2X ATP-gated channel from zebrafish

We report here the structural and functional characterization of an ionotropic P2X ATP receptor from the lower vertebrate zebrafish (Danio rerio). The full-length cDNA encodes a 410-amino acid-long channel subunit zP2X(3), which shares only 54% identity with closest mammalian P2X subunits. When expressed in XENOPUS: oocytes in homomeric form, ATP-gated zP2X(3) channels evoked a unique nonselective cationic current with faster rise time, faster kinetics of desensitization, and slower recovery than any other known P2X channel. Interestingly, the order of agonist potency for this P2X receptor was found similar to that of distantly related P2X(7) receptors, with benzoylbenzoyl ATP (EC(50) = 5 microM) > ATP (EC(50) = 350 microM) = ADP > alpha,beta-methylene ATP (EC(50) = 480 microM). zP2X(3) receptors are highly sensitive to blockade by the antagonist trinitrophenyl ATP (IC(50) < 5 nM) but are weakly sensitive to the noncompetitive antagonist pyridoxal phosphate-6-azophenyl-2',4'-disulfonic acid. zP2X(3) subunit mRNA is exclusively expressed at high levels in trigeminal neurons and Rohon-Beard cells during embryonic development, suggesting that neuronal P2X receptors mediating fast ATP responses were selected early in the vertebrate phylogeny to play an important role in sensory pathways.     

Involvement of the respiratory chain of gram-negative bacteria in the reduction of tellurite

The terminal oxidases of the respiratory chain of seven strains of gram-negative bacteria were shown to be involved in the reduction of tellurite. The rate of tellurite reduction correlated with the intensity of respiration. The inhibitors of terminal oxidases, carbon monoxide and cyanide, inhibited the reduction of tellurite. In Pseudomonas aeruginosa PAO ML4262 and P. aeruginosa PAO ML4262 (pBS 10), the respiratory chain was found to contain three types of cytochrome c, one of which (the carbon monoxide-binding cytochrome c) was involved in the reduction of tellurite. Agrobacterium tumefaciens VKM B-1219, P. aeruginosa IBPM B-13, and Escherichia coli G0-102bd++ cells contained oxidases aa3, bb3, and bd, respectively. The respiratory chain of other strains contained two oxidases: E. coli DH5alpha of bb3- and bd-type, and Erwinia carotovora VKM B-567 of bo3- and bd-type. All the strains under study reduced tellurite with the formation of tellurium crystallites. Depending on the position of the active center of terminal oxidases in the plasma membrane, the crystallites appeared either in the periplasmic space [P. aeruginosa PAO ML4262 and P. aeruginosa PAO ML4262 (pBS10)], or on the outer surface of the membrane (A. tumefaciens VKM B-1219 and P. aeruginosa IBPM B-13), its inner surface (E. coli G0-102bd++), or on both surfaces (E. coli DHaalpha and E. carotovora VKM B-567).     

Novel psychrophilic anaerobic spore-forming bacterium from the overcooled water brine in permafrost: description Clostridium algoriphilum sp. nov.

A gram-positive, motile, strict anaerobic spore-forming bacterium was isolated from the over-cooled brine in the permafrost. The optimal temperature for isolate growth was 5-6 degrees C at pH 6.8-7.2. The bacterium was growing on the medium rich in saccharides and disaccharides. Out of polysaccharides tested, only xylan sustained the growth. Fermentation of the hexoses led to the formation of acetate, butyrate, lactate, H2,CO2 and some formate and ethanol. Cell wall peptidoglycan contained meso-diaminopimelic acid. The major fatty acids of the cell wall were C(14:0) and C(16:1c9). The content of G-C pairs in DNA was 31.4 mol%. As phylogenetic analysis has shown, it is closely linked to the members of cluster 1 of Clostridium. It differs from the other species of the genus by the substrates necessary for the growth, products forming as a result of the fermentation and content of the fatty acids in the cell wall. Thus, it was suggested to describe this strain as a new species named Clostridium algoriphilum. Type strain 14D1 was deposited into the Russian Collection of the Microorganisms VKM B-2271T and German Collection of the Microorganisms DSM 16153T .     

Tracking the genetic imprints of lost Jewish tribes among the gene pool of Kuki-Chin-Mizo population of India

Background  

The Kuki-Chin-Mizo population comprising traditionally endogamous tribal groups residing in the state of Mizoram, India claim their descent from the ten lost tribes of Israel that were exiled by the Assyrians. To ascertain their oral history, we analysed DNA markers comprising 15 autosomal microsatellite markers, 5 biallelic and 20 microsatellite markers on Y-chromosome and the maternally inherited mitochondrial DNA sequence variations on 414 individuals belonging to 5 tribal communities from Mizoram (Hmar, Kuki, Mara, Lai and Lusei). The genetic profiles obtained were compared either with populations sharing Jewish ancestry or with local populations along the probable route of migration of the Jewish ancestry claimant Mizoram tribes.     

Articles selected by Faculty of 1000: plant comparative mitochondrial genomics; open source proteomics database; identifying disease-associated enzymes; predicting microRNA targets; genome annotation using polymorphisms

Background

Phylogenetic analysis of human complete mitochondrial DNA sequences has largely contributed to resolving phylogenies and antiquity of different lineages belonging to the majorhaplogroups L, N and M (East-Asian lineages). In the absence of whole mtDNA sequence information of M lineages reported in India that exhibits highest diversity within the sub-continent, the present study was undertaken to provide a detailed analysis of this haplogroup to precisely characterize the lineages and unravel their intricate phylogeny.

Results

The phylogenetic tree constructed from sequencing information of twenty four whole mtDNA genome revealed novel substitutions in the previously defined M2a and M6 lineages. The most striking feature of this phylogenetic tree is the formulation of a new lineage M30, distinguished by the presence of 12007 transition, and comprises of the recently defined M18 and a potential new sub-lineage possessing substitution at 16223 and 16300. M30 further branches into M30a sub-lineage, defined by 15431 and 195A substitution. The age of M30 lineage was estimated at 33,042 YBP, indicating a more recent expansion time than M2 (49,686 YBP). Contradictory to earlier reports, the M5 lineage does not always include a 12477 substitution, and is more appropriately defined by a transversion at 10986A. The phylogenetic tree also identifies a potential new lineage M* with HVSI sequence 16223,16325. No new substitutions were found in M25 and the M3 mt DNA genome could only be tentatively rooted by 16126 mutation. M4 and M*(16251, 16267) lineages could not be resolved distinctly.

Conclusions

This study describes seven new basal mutations and fourteen lineages that substantially contribute to the present understanding of superhaplogroup M. The phylogenetic tree supported by median-joining network helps in distinctly identifying the genetic relation between different M lineages that could not be achieved solely by control region sequence information. Although high control region diversity has been reported in the different M lineages distributed in India, complete sequencing of M* and defined lineages suggests that these mt DNA genomes emerged from a limited number of branches arising from the M trunk.     

Intracellular cAMP Content and the Induction of Alternative Oxidase in the Yeast Yarrowia lipolytica

The effect of cyanide, antimycin A, ethanol, and acetate on the induction of alternative oxidase in the yeast Yarrowia lipolytica VKM Y-155 was studied. The aerobic incubation of logarithmic-phase cells, whose respiration is sensitive to cyanide, in the presence of the aforementioned compounds led to the development of cyanide-resistant respiration, which could be suppressed by benzohydroxamic acid, an inhibitor of alternative oxidases. The incubation of cells with cyanide, ethanol, or acetate raised the intracellular pool of cAMP, which attained maximal values after a 2- to 3-min incubation period, then rapidly decreased to the initial value and did not change over the next three hours of incubation. The possible role of cAMP in the induction of alternative oxidase in yeast cells is discussed.     

Interaction Specificity of Benzimidazol Group Compounds with AT-Containing Polynucleotides

Abstract

The interaction between polynucleotides: poly(dA)-poly(dT), poly(dA-dT), poly(am2dA- dT), and the AT-specific compounds of benzimidazol group has been studied. It is been shown that these compounds bind to poly(dA)-poly(dT) and poly(dA-dT) at low and high salt concentration in solution. Poly(am2dA-dT) interacts with AT-specific compounds only at low salt, where this polynucleotide is in a B-form, but not at high salt when the polynucleotide converts to another conformation. Thus, the interaction specificity of the groove-binding ligands is influenced not only by the minor groove substituents, but the peculiarities of the secondary structure of polynucleotides.