Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes

Prokaryotic Mobile Genetic Elements (MGEs) such as transposons, integrons, phages and plasmids, play important roles in prokaryotic evolution and in the dispersal of cargo functions like antibiotic resistance. However, each of these MGE types is usually annotated and analysed individually, hampering a global understanding of phylogenetic and environmental patterns of MGE dispersal. We thus developed a computational framework that captures diverse MGE types, their cargos and MGE-mediated horizontal transfer events, using recombinases as ubiquitous MGE marker genes and pangenome information for MGE boundary estimation. Applied to ∼84k genomes with habitat annotation, we mapped 2.8 million MGE-specific recombinases to six operational MGE types, which together contain on average 13% of all the genes in a genome. Transposable elements (TEs) dominated across all taxa (∼1.7 million occurrences), outnumbering phages and phage-like elements (<0.4 million). We recorded numerous MGE-mediated horizontal transfer events across diverse phyla and habitats involving all MGE types, disentangled and quantified the extent of hitchhiking of TEs (17%) and integrons (63%) with other MGE categories, and established TEs as dominant carriers of antibiotic resistance genes. We integrated all these findings into a resource (proMGE.embl.de), which should facilitate future studies on the large mobile part of genomes and its horizontal dispersal.     

Expression of fluorescently tagged connexins: a novel approach to rescue function of oligomeric DsRed-tagged proteins

A novel, brilliantly red fluorescent protein, DsRed has become available recently opening up a wide variety of experimental opportunities for double labeling and fluorescence resonance electron transfer experiments in combination with green fluorescent protein (GFP). Unlike in the case of GFP, proteins tagged with DsRed were often found to aggregate within the cell. Here we report a simple method that allows rescuing the function of an oligomeric protein tagged with DsRed. We demonstrate the feasibility of this approach on the subunit proteins of an oligomeric membrane channel, gap junction connexins. Additionally, DsRed fluorescence was easily detected 12-16 h post transfection, much earlier than previously reported, and could readily be differentiated from co-expressed GFP. Thus, this approach can eliminate the major drawbacks of this highly attractive autofluorescent protein.     

Genetic variation of Citrus tristeza virus isolates from California and Spain: evidence for mixed infections and recombination

We examined the population structure and genetic variation of four genomic regions within and between 30 Citrus tristeza virus (CTV) isolates from Spain and California. Our analyses showed that most isolates contained a population of sequence variants, with one being predominant. Four isolates showed two major sequence variants in some genomic regions. The two major variants of three of these isolates showed very low nucleotide identity to each other but were very similar to those of other isolates, suggesting the possibility of mixed infections with two divergent isolates. Incongruencies of phylogenetic relationships in the different genomic regions and statistical analyses suggested that the genomes of some CTV sequence variants originated by recombination events between diverged sequence variants. No correlation was observed between geographic origin and nucleotide distance, and thus from a genetic view, the Spanish and Californian isolates analyzed here could be considered members of the same population.     

M-DNA: A complex between divalent metal ions and DNA which behaves as a molecular wire

M-DNA is a complex of DNA with divalent metal ions (Zn(2+), Co(2+), or Ni(2+)) which forms at pH conditions above 8. Upon addition of these metal ions to B-DNA at pH 8.5, the pH decreases such that one proton is released per base-pair per metal ion. Together with previous NMR data, this result demonstrated that the imino proton in each base-pair of the duplex was substituted by a metal ion and that M-DNA might possess unusual conductive properties. Duplexes of 20 base-pairs were constructed with fluorescein (donor) at one end and rhodamine (acceptor) at the other. Upon formation of M-DNA (with Zn(2+)) the fluorescence of the donor was 95 % quenched. Fluorescence lifetime measurements showed the presence of a very fast component in the decay kinetics with tau相似文献   

The morphological transition of Helicobacter pylori cells from spiral to coccoid is preceded by a substantial modification of the cell wall.

The peptidoglycan (murein) of Helicobacter pylori has been investigated by high-performance liquid chromatography and mass spectrometric techniques. Murein from H. pylori corresponded to the A1gamma chemotype, but the muropeptide elution patterns were substantially different from the one for Escherichia coli in that the former produced high proportions of muropeptides with a pentapeptide side chain (about 60 mol%), with Gly residues as the C-terminal amino acid (5 to 10 mol%), and with (1-->6)anhydro-N-acetylmuramic acid (13 to 18 mol%). H. pylori murein also lacks murein-bound lipoprotein, trimeric muropeptides, and (L-D) cross-linked muropeptides. Cessation of growth and transition to coccoid shape triggered an increase in N-acetylglucosaminyl-N-acetylmuramyl-L-Ala-D-Glu (approximately 20 mol%), apparently at the expense of monomeric muropeptides with tri- and tetrapeptide side chains. Muropeptides with (1-->6)anhydro-muramic acid and with Gly were also more abundant in resting cells.     

A quantitative and qualitative reanalysis of the endocast from the juvenile Paranthropus specimen l338y-6 from Omo, Ethiopia

Based on an analysis of its endocast, Holloway (1981 Am J Phys Anthropol 53:109-118) attributed the juvenile Omo L338y-6 specimen to Australopithecus africanus (i.e., gracile australopithecines) rather than to Paranthropus (Australopithecus) boisei (robust australopithecines) favored by other workers (Rak and Howell [1978] Am J Phys Anthropol 48:345-366). Holloway's attribution was based on the specimen's (1) low cranial capacity, (2) gracile-like meningeal vessels, (3) gracile-like cerebellar hemispheres, and (4) absence of an enlarged occipital/marginal (O/M) sinus system. Recent work, however, has shown that criteria 1 and 2 are not useful for sorting gracile from robust australopithecines (Culotta [1999] Science 284:1109-1111; Falk [1993] Am J Phys Anthropol 92:81-98). In this paper, we test criterion 3 by quantifying the endocranial cerebellar and occipital morphology reproduced on the Omo L338y-6 endocast, and comparing it to seven endocasts from South and East African early hominids. Our preliminary results show that metric analysis of this specimen cannot be used to sort it preferentially with either robust or gracile australopithecines. Finally, we demonstrate that, contrary to previous reports, the Omo L338y-6 endocast reproduces an enlarged left occipital sinus (criterion 4). This observation is consistent with the original attribution of the Omo specimen to robust australopithecines (Rak and Howell [1978] Am J Phys Anthropol 48:345-366). Furthermore, if Omo L338y-6 was a robust australopithecine, this discovery extends the occurrence of an enlarged O/M sinus system to one of the earliest known paranthropines. Am J Phys Anthropol 110:399-406, 1999.