Bayesian phylogenetic analysis reveals two-domain topology of S-adenosylhomocysteine hydrolase protein sequences

S-Adenosylhomocysteine hydrolase (SahH) is involved in the degradation of the compound which inhibits methylation reactions. Using a Bayesian approach and other methods, we reconstructed a phylogenetic tree of amino acid sequences of this protein originating from all three major domains of living organisms. The SahH sequences formed two major branches: one composed mainly of Archaea and the other of eukaryotes and majority of bacteria, clearly contradicting the three-domain topology shown by small subunit rRNA gene. This topology suggests the occurrence of lateral transfer of this gene between the domains. Poor resolution of eukaryotes and bacteria excluded an ultimate conclusion in which out of the two domains this gene appeared first, however, the congruence of the secondary branches with SS rRNA and/or concatenated ribosomal protein datasets phylogenies suggested an "early" acquisition by some bacterial and eukaryotic phyla. Similarly, the branching pattern of Archaea reflected the phylogenies shown by SS rRNA and ribosomal proteins. SahH is widespread in Eucarya, albeit, due to reductive evolution, it is missing in the intracellular parasite Encephalitozoon cuniculi. On the other hand, the lack of affinity to the sequences from the alpha-Proteobacteria and cyanobacteria excludes a possibility of its acquisition in the course of mitochondrial or chloroplast endosymbioses. Unlike Archaea, most bacteria carry MTA/SAH nucleosidase, an enzyme involved also in metabolism of methylthioadenosine. However, the double function of MTA/SAH nucleosidase may be a barrier to ensure the efficient degradation of S-adenosylhomocysteine, specially when the intensity of methylation processes is high. This would explain the presence of S-adenosylhomocysteine hydrolase in the bacteria that have more complex metabolism. On the other hand, majority of obligate pathogenic bacteria due to simpler metabolism rely entirely on MTA/SAH nucleosidase. This could explain the observed phenetic pattern in which bacteria with larger (>6 Mb-million base pairs) genomes carry SAH hydrolase, whereas bacteria that have undergone reductive evolution usually carry MTA/SAH nucleosidase. This suggests that the presence or acquisition of S-adenosylhomocysteine hydrolase in bacteria may predispose towards higher metabolic, and in consequence, higher genomic complexity. The good examples are the phototrophic bacteria all of which carry this gene, however, the SahH phylogeny shows lack of congruence with SSU rRNA and photosyntethic genes, implying that the acquisition was independent and presumably preceded the acquisition of photosyntethic genes. The majority of cyanobacteria acquired this gene from Archaea, however, in some species the sahH gene was replaced by a copy from the beta- or gamma-Proteobacteria.     

Stress-induced expression and structure of the putative gene hyp-1 for hypericin biosynthesis

The phenolic oxidative coupling protein (Hyp-1) with proposed activity in the biosynthesis of hypericin in Hypericum perforatum shares about 50 % sequence similarity with Bet.v.1-like/PR-10 proteins. In our previous study, we showed that this protein is not a limiting factor in hypericin biosynthesis. To ascertain the role of Hyp-1 in defense mechanisms, we have analyzed some structural features of the hyp-1 gene in 14 Hypericum species with different abilities to synthesise hypericin. We show that the hyp-1 gene possesses characteristics typical for genes encoding plant PR-10 proteins. The coding sequence of the hyp-1 gene is interrupted by a single 86- to 125-bp intron localised strictly in codon 62, which is a typical feature of the dicot PR-10 subfamily. The localisation of the intron is conserved in all 14 tested Hypericum species indicating a common evolutionary history with genes encoding PR-10 proteins. In addition, we report that the hyp-1 gene exhibits a similar response to stress conditions as the PR-10 proteins encoding genes. Following either wounding or infection by Agrobacterium tumefaciens, all analysed Hypericum species exhibited rapid and significant upregulation of hyp-1 gene expression; this was particularly observed in hypericin-producing species. On the other hand, in the presence of high levels of abscisic acid, different levels of gene expression were observed.     

The Ecology of Testate Amoebae (Protists) in Sphagnum in North-western Poland in Relation to Peatland Ecology

We studied the relationship between testate amoebae (Protozoa) communities and the depth to the water table (DWT), pH, conductivity, and microhabitat type in Sphagnum dominated peatlands of north-western Poland and built predictive (transfer function) models for inferring DWT and pH based on the testate amoebae community structure. Such models can be used for peatland monitoring and paleoecology. A total of 52 testate amoebae taxa were recorded. In a redundancy analysis, DWT and pH explained 20.1% of the variation in the species data and allowed us to identify three groups of taxa: species that are associated with (1) high DWT and low pH, (2) low DWT and low pH, and (3) high pH and mid-range DWT. Our transfer function models allow DWT and pH to be estimated with mean errors of 9.89 cm and 0.71 pH units. The prediction error of the DWT model and the tolerance of the species both increase with increasing dryness. This pattern mirrors the ecology of Sphagnum mosses: Species growing in wet habitats are more sensitive to change in water table depth than the species growing in drier microhabitats. Our results are consistent with studies of testate amoeba ecology in other regions, and they provide additional support for the use of these organisms in paleoecological and biomonitoring contexts.     

Kin recognition and adjustment of reproductive effort in zebra finches

The differential allocation theory predicts that females should invest more in offspring produced with attractive partners, and a number of studies support this prediction in birds. Females have been shown to increase reproductive investment when mated to males showing elaborated sexual traits. However, mate attractiveness might also depend on the interaction between male and female genotypes. Accordingly, females should invest more in offspring sired by individuals that are genetically dissimilar or carry superior alleles. Here, we show in zebra finches (Taeniopygia guttata) that pairs of unfamiliar genetic brothers and sisters are less likely to reproduce in comparison with randomly mated pairs. Among the brother–sister pairs, those that attempted to breed laid smaller clutches and of lower total clutch mass. Our results provide the first experimental evidence that females adjust their reproductive effort in response to the genetic similarity of their partners. Importantly, these results imply a female ability to assess relatedness of a social mate without prior association.     

The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes

The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation. During sexual genome development, the expressed, somatic macronuclear genome is whittled down to the genic portion of a small fraction (∼5%) of its precursor “silent” germline micronuclear genome by a process of “unscrambling” and fragmentation. The tiny macronuclear “nanochromosomes” typically encode single, protein-coding genes (a small portion, 10%, encode 2–8 genes), have minimal noncoding regions, and are differentially amplified to an average of ∼2,000 copies. We report the high-quality genome assembly of ∼16,000 complete nanochromosomes (∼50 Mb haploid genome size) that vary from 469 bp to 66 kb long (mean ∼3.2 kb) and encode ∼18,500 genes. Alternative DNA fragmentation processes ∼10% of the nanochromosomes into multiple isoforms that usually encode complete genes. Nucleotide diversity in the macronucleus is very high (SNP heterozygosity is ∼4.0%), suggesting that Oxytricha trifallax may have one of the largest known effective population sizes of eukaryotes. Comparison to other ciliates with nonscrambled genomes and long macronuclear chromosomes (on the order of 100 kb) suggests several candidate proteins that could be involved in genome rearrangement, including domesticated MULE and IS1595-like DDE transposases. The assembly of the highly fragmented Oxytricha macronuclear genome is the first completed genome with such an unusual architecture. This genome sequence provides tantalizing glimpses into novel molecular biology and evolution. For example, Oxytricha maintains tens of millions of telomeres per cell and has also evolved an intriguing expansion of telomere end-binding proteins. In conjunction with the micronuclear genome in progress, the O. trifallax macronuclear genome will provide an invaluable resource for investigating programmed genome rearrangements, complementing studies of rearrangements arising during evolution and disease.     

Comparison of different signal peptides for protein secretion in nonlytic insect cell system

Protein expression and secretion in insect cells have been widely studied in the baculovirus-infected insect cell system. In directly transfected insect cells only intracellular expression and purification of recombinant proteins have been studied in detail. To examine multiple recombinant protein variants, easy and fast expression and a purification screening system are required. The aim of this study was to establish an effective and rapid secretion system for human azurocidin using directly transfected insect cells. We also constructed and tested expression vectors possessing heterologous signal peptides derived from human azurocidin, yellow lupin diphosphonucleotide phosphatase/phosphodiesterase (PPD1), and papaya papain IV to secrete yellow lupin and red kidney bean purple acid phosphatases, PPD1, and papain IV. Our results demonstrate that the secretion vectors used here can direct recombinant proteins to the culture medium very effectively, allowing their simple purification on a small/medium scale. Based on secretion and activity analyses it seems that the azurocidin signal peptide is one of the most potent secretion signals.     

The origin of ovarian neuropeptide Y (NPY)-immunoreactive nerve fibres from the inferior mesenteric ganglion in the pig

Summary Applying a double-immunofluorescence technique, the porcine ovary is demonstrated to receive two populations of NPY-immunoreactive nerve fibres originating from the inferior mesenteric ganglion: one with colocalized tyrosine hydroxylase and supplying predominantly the ovarian vasculature, and a second, solely NPY-immunoreactive and almost exclusively associated with growing follicles. A third group of tyrosine hydroxylase-and dopamine--hydroxylase-positive, but NPY-negative nerve fibres is associated with ovarian blood vessels and, to a minor extent, with ovarian follicles. As revealed by retrograde tracing, the vast majority of postganglionic neurons projecting to the ovary is located in a discrete area of the ganglion, suggesting a somatotopic organization of the porcine inferior mesenteric ganglion. Moreover, the finding indicate that three subpopulations of postganglionic sympathetic neurons with different chemical codes supply different target components of the porcine ovary. The physiological relevance of the described neurons in the nervous control of ovarian functions remains to be elucidated.A portion of these results has been presented in abstract form (Majewski et al. 1991)     

Costs of immune response in cold-stressed laboratory mice selected for high and low basal metabolism rates

To study whether mounting an immune response is energetically costly, mice from two lines divergently selected for high (H-BMR) and low (L-BMR) basal metabolic rate (BMR) were immunized with sheep red blood cells. Their energy budgets were then additionally burdened by sudden transfer from an ambient temperature of 23 degrees C to 5 degrees C. We found that the immune response of H-BMR mice was lower than that of L-BMR mice. However, the interaction between line affiliation and ambient temperature was not significant and cold exposure did not result in immunosuppression in either line. At 23 degrees C the animals of both lines seemed to cover the costs of immune response by increasing food consumption and digestive efficiency. This was not observed at 5 degrees C, so these costs must have been covered at the expense of other components of the energy budget. Cold exposure itself elicited a considerable increase in food intake and the mass of internal organs, which were also heavier in H-BMR than in L-BMR mice. However, irrespective of the temperature or line affiliation, immunized mice had smaller intestines, while cold-exposed immunized mice had smaller hearts. Furthermore, the observed larger mass of the liver and kidneys in immunized mice of both lines kept at 23 degrees C was not observed at 5 degrees C. Hence, immunization compromised upregulation of the function of metabolically active internal organs, essential for meeting the energetic demands of cold. We conclude that the difficulties with a straightforward demonstration of the energetic costs of immune responses in these animals stem from the extreme flexibility of their energy budgets.     

The evolution of brood parasitism: the role of facultative parasitism

The hypothesis that facultative brood parasitism may serve asan intermediate step in the evolutionary transition from purelyparental reproduction to obligate parasitism was investigated.The population dynamics of a host-parasite complex were computer-simulatedin a model that incorporated different intensities of parasitismand host defense and considered a simplified semelparous birdspecies living in a homogeneous habitat The individuals usetwo different breeding strategies: provide parental care orparasitize the nest of those providing parental care. Underobligate parasitism, the parasites appeared unsuccessful, drovethe host population to extinction, or coexisted with the hostin stable or oscillating proportions. The behavior of the systemdepended on both the effectiveness of the parasite and the defenseof the host. Under facultative parasitism (making the best ofa bad job), the parasites reduced host numbers but did not reducethe population size below the number of breeding sites. Thus,facultative parasitism provides a better opportunity for thedevelopment of defense in the host. The population of a hostthat shows a certain level of defense can be more successfullyinvaded by obligate parasites so that stable coexistence ofhosts and parasites is possible.     

Quercetin metabolites inhibit copper ion-induced lipid peroxidation in rat plasma

The oxidative susceptibility of plasma obtained from rats after intragastric administration of quercetin was studied to know whether or not quercetin acts as an in vivo antioxidant after metabolic conversion. Quercetin was raised in the rat blood plasma essentially as glucuronide and/or sulfate conjugates. The plasma obtained from rats after quercetin administration was more resistant against copper sulfate-induced lipid peroxidation than the control plasma on the basis of the accumulation of cholesteryl ester hydroperoxides and the consumption of α-tocopherol. The results strongly suggest that some conjugated metabolites of quercetin act as effective antioxidants when plasma is subject to metal ion-induced lipid peroxidation.