Evidence from beta-tubulin phylogeny that microsporidia evolved from within the fungi

Microsporidia are obligate intracellular parasites that were thought to be an ancient eukaryotic lineage based on molecular phylogenies using ribosomal RNA and translation elongation factors. However, this ancient origin of microsporidia has been contested recently, as several other molecular phylogenies suggest that microsporidia are closely related to fungi. Most of the protein trees that place microsporidia with fungi are not well sampled, however, and it is impossible to resolve whether microsporidia evolved from a fungus or from a protistan relative of fungi. We have sequenced beta-tubulins from 3 microsporidia, 4 chytrid fungi, and 12 zygomycete fungi, expanding the representation of beta-tubulin to include all four fungal divisions and a wide diversity of microsporidia. In phylogenetic trees including these new sequences, the overall topology of the fungal beta-tubulins generally matched the expected relationships among the four fungal divisions, although the zygomycetes were polyphyletic in some analyses. The microsporidia consistently fell within this fungal diversification, and not as a sister group to fungi. Overall, beta-tubulin phylogeny suggests that microsporidia evolved from a fungus sometime after the divergence of chytrids. We also found that chytrid alpha- and beta-tubulins are much less divergent than are tubulins from other fungi or microsporidia. In trees in which the only fungal representatives were the chytrids, microsporidia still branched with fungi (i.e., with chytrids), suggesting that the affiliation between microsporidian and fungal tubulins is not an artifact of long-branch attraction.     

Biogeochemical evidence that thermophilic archaea mediate the anaerobic oxidation of methane

Distributions and isotopic analyses of lipids from sediment cores at a hydrothermally active site in the Guaymas Basin with a steep sedimentary temperature gradient revealed the presence of archaea that oxidize methane anaerobically. The presence of strongly (13)C-depleted lipids at greater depths in the sediments suggests that microbes involved in anaerobic oxidation of methane are present and presumably active at environmental temperatures of >30 degrees C, indicating that this process can occur not only at cold seeps but also at hydrothermal sites. The distribution of the membrane tetraether lipids of the methanotrophic archaea shows that these organisms have adapted their membrane composition to these high environmental temperatures.     

A revision of brain composition in Onychophora (velvet worms) suggests that the tritocerebrum evolved in arthropods

Background  

The composition of the arthropod head is one of the most contentious issues in animal evolution. In particular, controversy surrounds the homology and innervation of segmental cephalic appendages by the brain. Onychophora (velvet worms) play a crucial role in understanding the evolution of the arthropod brain, because they are close relatives of arthropods and have apparently changed little since the Early Cambrian. However, the segmental origins of their brain neuropils and the number of cephalic appendages innervated by the brain - key issues in clarifying brain composition in the last common ancestor of Onychophora and Arthropoda - remain unclear.     

An evidence of laccases in archaea

Laccases (benzenediol:oxygen oxidoreductase, EC 1.10.3.2) are a diverse group of multicopper oxidases that catalyze the oxidation of a variety of aromatic compounds. Here we present evidence for distribution of laccases among archaea and their probable functions. Putative laccase genes have been found in different archaeal groups that might have branched off early during evolution, e.g. Haloarcula marismortui ATCC 43049, Natronomonas pharaonis DSM2160, Pyrobaculum aerophilum IM2, Candidatus Nitrosopumilus maritimus SCM1, Halorubrum lacusprofundi ATCC 49239. Most of the archaeal multicopper oxidases reported here are of Type 1 and Type 2 whereas type 3 copper-binding domain could be found in Pyrobaculum aerophilum IM2 and Halorubrum lacusprofundi ATCC49239. An analysis of the genome sequence database revealed the presence of novel types of two-domain laccases in archaea. ed using this method. CyMVin the positive samples of Phalaenopsis sp. and Arachnis sp. was confirmed by DNA sequencing and cp gene homeology blast. The results showed that CyMV extracted from the leaves of orchid in Hangzhou, Zhejiang Province, China, could be derived from Kunming city (KM), Yunnan Province, China. This method characterized by high sensitivity, specificity, and precision is suitable for early diagnosis and quantitative detection of CyMV.     

Comparison of bacteriophage T4 UvsX and human Rad51 filaments suggests that RecA-like polymers may have evolved independently

The UvsX protein from bacteriophage T4 is a member of the RecA/Rad51/RadA family of recombinases active in homologous genetic recombination. Like RecA, Rad51 and RadA, UvsX forms helical filaments on DNA. We have used electron microscopy and a novel method for image analysis of helical filaments to show that UvsX-DNA filaments exist in two different conformations: an ADP state and an ATP state. As with RecA protein, these two states have a large difference in pitch. Remarkably, even though UvsX is only weakly homologous to RecA, both UvsX filament states are more similar to the RecA crystal structure than are RecA-DNA filaments. We use this similarity to fit the RecA crystal structure into the UvsX filament, and show that two of the three previously described blocks of similarity between UvsX and RecA are involved in the subunit-subunit interface in both the UvsX filament and the RecA crystal filament. Conversely, we show that human Rad51-DNA filaments have a different subunit-subunit interface than is present in the RecA crystal, and this interface involves two blocks of sequence similarity between Rad51 and RecA that do not overlap with those found between UvsX and RecA. This suggests that helical filaments in the RecA/Rad51/RadA family may have arisen from convergent evolution, with a conserved core structure that has assembled into multimeric filaments in a number of different ways.     

Evolutionary evidence suggests that CpG island-associated Alus are frequently unmethylated in human germline

Most Alu elements are considered to belong to the methylated fraction of the genome that has undergone CpG depletion, whereas CpG islands are characteristically unmethylated. By analysing the CpG content of >12,000 autosomal CpG island-Alu Sx pairs we wanted to study what happens when an Alu is situated close to a CpG island. We have found that many Alus located close to CpG islands have retained a high proportion of CpG sites, which is consistent with these Alus being unmethylated in the human germline.     

How humans evolved large brains: Comparative evidence

The human brain is about three times as large as that of our closest living relatives, the great apes. Overall brain size is a good predictor of cognitive performance in a variety of tests in primates. 1 , 2 Therefore, hypotheses explaining the evolution of this remarkable difference have attracted much interest. In this review, we give an overview of the current evidence from comparative studies testing these hypotheses. If cognitive benefits are diverse and ubiquitous, it is possible that most of the variation in relative brain size among extant primates is explained by variation in the ability to avoid the fitness costs of increased brain size (allocation trade‐offs and increased minimum energy needs). This is indeed what we find, suggesting that an energetic perspective helps to complement approaches to explain variation in brain size that postulate cognitive benefits. The expensive brain framework also provides a coherent scenario for how these factors may have shaped early hominin brain expansion.     

Complete DNA sequence of a ColBM plasmid from avian pathogenic Escherichia coli suggests that it evolved from closely related ColV virulence plasmids

Avian pathogenic Escherichia coli (APEC), an extraintestinal pathogenic E. coli causing colibacillosis in birds, is responsible for significant economic losses for the poultry industry. Recently, we reported that the APEC pathotype was characterized by possession of a set of genes contained within a 94-kb cluster linked to a ColV plasmid, pAPEC-O2-ColV. These included sitABCD, genes of the aerobactin operon, hlyF, iss, genes of the salmochelin operon, and the 5' end of cvaB of the ColV operon. However, the results of gene prevalence studies performed among APEC isolates revealed that these traits were not always linked to ColV plasmids. Here, we present the complete sequence of a 174-kb plasmid, pAPEC-O1-ColBM, which contains a putative virulence cluster similar to that of pAPEC-O2-ColV. These two F-type plasmids share remarkable similarity, except that they encode the production of different colicins; pAPEC-O2-ColV contains an intact ColV operon, and pAPEC-O1-ColBM encodes the colicins B and M. Interestingly, remnants of the ColV operon exist in pAPEC-O1-ColBM, hinting that ColBM-type plasmids may have evolved from ColV plasmids. Among APEC isolates, the prevalence of ColBM sequences helps account for the previously observed differences in prevalence between genes of the "conserved" portion of the putative virulence cluster of pAPEC-O2-ColV and those genes within its "variable" portion. These results, in conjunction with Southern blotting and probing of representative ColBM-positive strains, indicate that this "conserved" cluster of putative virulence genes is primarily linked to F-type virulence plasmids among the APEC isolates studied.     

Further evidence that there is more than one adrenal 21-hydroxylase system

The 21-hydroxylase activity of microsomes isolated from bovine adrenal cortex have been assayed using [21-3H]17-hydroxypregnenolone and [1,2-3H]17-hydroxyprogesterone as substrates. When the assays are performed in the presence of an NADH regenerating system, to inhibit steroid 3 beta-hydroxy isomerase-dehydrogenase activity, the microsomes oxidize the 3 beta-hydroxy-5-ene steroid at a rate of 0.37 nmol/min.nmol cytochrome P-450 and the 3-keto-4-ene steroid at a rate of 6.4 nmol/min.nmol. When the microsomes are solubilized with Triton CF-54 they lose the ability to oxidize the 3-hydroxy-5-ene steroid, while the specific activity of the microsomes for the 3-keto-4-ene steroid is enhanced 3-fold. In contrast, when the microsomes are solubilized with sodium cholate, their specific activity towards the 4-ene steroid is decreased by 50% while the specific activity for a low concentration of the 5-ene steroid, 1 microM, is unchanged. In addition, when the oxidations of the labeled steroids (at 1 microM) by the microsomes, are examined in the presence of unlabeled 17-hydroxyprogesterone (at 20 microM) the oxidation of the 3-keto-4-ene steroid is inhibited by 92% while the oxidation of the 3 beta-hydroxy-5-ene steroid is only inhibited by 20%. These results all suggest that there are at least two 21-hydroxylases in bovine adrenal tissue, one of which can utilize the 3-keto-4-ene steroids only, the other of which, in addition, can utilize the 3 beta-hydroxy-5-ene steroids as substrates.     

Molecular evidence that deep-branching fungi are major fungal components in deep-sea methane cold-seep sediments

The motile cells of chytrids were once believed to be relics from the time before the colonization of land by fungi. However, the majority of chytrids had not been found in marine but freshwater environments. We investigated fungal diversity by a fungal-specific PCR-based analysis of environmental DNA in deep-sea methane cold-seep sediments, identifying a total of 35 phylotypes, 12 of which were early diverging fungi (basal fungi, ex 'lower fungi'). The basal fungi occupied a major portion of fungal clones. These were phylogenetically placed into a deep-branching clade of fungi and the LKM11 clade that was a divergent group comprised of only environmental clones from aquatic environments. As suggested by Lara and colleagues, species of the endoparasitic genus Rozella, being recently considered of the earliest branching taxa of fungi, were nested within the LKM11 clade. In the remaining 23 phylotypes identified as the Dikarya, the majority of which were similar to those which appeared in previously deep-sea studies, but also highly novel lineages associated with Soil Clone Group I (SCGI), Entorrhiza sp. and the agaricomycetous fungi were recorded. The fungi of the Dikarya may play a role in the biodegradation of lignin and lignin-derived materials in deep-sea, because the characterized fungal species related to the frequent phylotypes within the Dikarya have been reported to possess an ability to degrade lignin.     

DNA is present in the nucleomorph of cryptomonads: Further evidence that the chloroplast evolved from a eukaryotic endosymbiont

Summary The nucleomorph is a unique self-replicating organelle which is invariably present in the periplastidal compartment of cryptomonads. The nucleomorph ofCryptomonas abbreviata is located in a groove on the inner face of the pyrenoid. When JB-4-embedded sections ofC. abbreviata are stained with 4-6-diamidino-2-phenylindole (DAPI), the nucleomorph exhibits a blue fluorescence characteristic of DNA-DAPI complexes. This fluorescence is removed by DNase digestion, but not by RNase. When cells are prepared for electron microscopy by the method of Ryter and Kellenberger (Schreil 1964), a network of fine DNA-like fibrils is observed in the nucleomorph matrix. It is estimated that the nucleomorph contains between 10⁸ and 10⁹ daltons of DNA. The presence of DNA in nucleomorphs strongly supports the hypothesis that the nucleomorph is the vestigial nucleus of a eukaryotic endosymbiont. It is postulated that this eukaryotic symbiont was an ancestral red alga or an organism closely related to red algae. The cryptomonad host cell, on the other hand, is not evolutionarily close to any other group of algae.     

Chemotaxonomic evidence suggests that Eriocephalus tenuifolius is the source of Cape chamomile oil and not Eriocephalus punctulatus

The distinct blue essential oil obtained from Eriocephalus sp. (Asteraceae) is known in commerce as Cape chamomile and has become an important ingredient in flavour and fragrance formulations. To date, it is commonly accepted that Cape chamomile oil is obtained from Eriocephalus punctulatus. Samples of E. tenuifolius DC (n = 35) and E. punctulatus DC (n = 17) were collected from different localities in South Africa and Lesotho. The hydrodistilled essential oil was analysed by gas chromatography coupled to mass selective detector and flame ionisation detector (GC–MS-FID). The GC–MS data was exported to MetAlign? for spectral alignment and differentiation. The mid-infrared red (MIR) spectral data was processed using principal component analysis (PCA), partial least squares (PLS) and orthogonal projections to latent structures discriminant analysis (OPLS-DA) algorithms. The oil from E. punctulatus showed a different profile from the commercial sample which mostly contained 1,8-cineole, piperitone, yomogi alcohol and pogostol. MetAlign? successfully discriminated between the oil obtained from the two species and this data together with multivariate analysis showed that the commercial oil was similar to E. tenuifolius oil. Using the MIR data, a three component OPLS-DA model was constructed which convincingly discriminated between E. tenuifolius and E. punctulatus oil. The developed model further predicted the botanical origin of the commercial oils to be E. tenuifolius. The statistical performance of the model was excellent with an R²X (cum) = 0.897; R²Y (cum) = 0.991 and Q²Y (cum) = 0.987.     

Evidence suggests plagiotropic clonal species have evolved a branching physiology emphasizing regulation by nodal roots

In the plagiotropic nodally rooting clonal herb, Trifolium repens,the development of branches on stems is primarily controlled by the presence of nodal roots, and apical dominance is of secondary importance; only six to ten branches form distal to the youngest nodal root on a horizontal stem. We assessed the hypothesis that this phenomenon is general for clonal herbs with prostrate nodally rooting stems, and that they all have the same physiological system regulating branching, by testing a selection of species from diverse angiosperm families that exhibit either phalanx (Leptinella (Asteraceae), Hydrocotyle (Apiaceae), Acaena (Rosaceae)) or guerilla (Vinca (Apocynaceae), Glechoma and Lamiastrum (Lamiaceae)) growth strategies. In all these species the establishment of a single nodal root on a prostrate stem, otherwise prevented from nodally rooting, induced the outgrowth of a limited number of axillary buds (the number of which was species specific) at the nodes immediately distal to the newly established root, thereby indicating a phenotypic response similar to that in T. repens. Furthermore, their branching responses to manipulative treatments were also similar to those of T. repens, indicating that their regulatory physiology of axillary bud outgrowth from their prostrate stems is similar. We conclude that, for the group of prostrate nodally rooting clonal herbs as a whole, the apical dominance phenotype arises predominantly from variation in the supply of resources from nodal roots rather than from repression of axillary buds by apical tissues (apical dominance). We suggest that evolution of such a physiological mechanism enhances the exploration for patchily distributed favourable nodal rooting sites by regulating shoot development so as to efficiently utilise the diminishing intra-plant availability of root-supplied resources. For the species examined, inter-specific variation in intensity of branching response to a nodal root is shown to be linked to a trade off in foraging strategy, with the allocation of resources primarily to explorative growth (long internodes, few branches) in guerilla species or to exploitive growth (short internodes, many branches) in phalanx species.Co-ordinating editor: J. Tuomi     

Preliminary evidence suggests that beech scale insect honeydew has a negative effect on terrestrial litter decomposition rates in

Honeydew production by New Zealand beech scale insects (Ultracoelostoma spp., Hemiptera: Margarodidae) is widely considered to have a positive influence on native animal abundance and ecosystem functioning. As a first assessment of whether there is a positive relationship between honeydew throughfall and litter decomposition rates, we placed experimental litter bags in each of 10 high and 10 low honeydew plots in mixed southern beech (Nothofagus) forest at each of two sites, Lakehead and Rotoiti, in the Nelson Lakes National Park. High and low honeydew plots were selected using sooty mould biomass on the forest floor as a surrogate for honeydew throughfall, as sooty mould biomass was shown to be strongly correlated (r = 0.906) with scale insect population size at the Rotoiti site. Contrary to our expectation, terrestrial litter decomposition was significantly lower in high honeydew plots than in low honeydew plots, at both Lakehead and Rotoiti. The presence of introduced wasps (Vespula spp., Hymenoptera: Vespidae) at the Lakehead site did not appear to have any significant effect on litter decomposition rates, despite the fact that wasps are thought to intercept much of the honeydew produced in this forest. Variance in litter decomposition rates between high and low honeydew treatments was predominantly determined by a direct relationship between sooty mould biomass and litter decomposition rate at the scale of individual litter bags. However, the mechanistic explanation for the observed relationship is unclear. Future studies should be directed towards quantifying the functional relationship between honeydew throughfall and growth rates of sooty mould, and their subsequent effects on abiotic conditions, microarthropod community dynamics and microbial activity rates in litter.