Evidence for an evolutionary antagonism between Mrr and Type III modification systems

The Mrr protein of Escherichia coli is a laterally acquired Type IV restriction endonuclease with specificity for methylated DNA. While Mrr nuclease activity can be elicited by high-pressure stress in E. coli MG1655, its (over)expression per se does not confer any obvious toxicity. In this study, however, we discovered that Mrr of E. coli MG1655 causes distinct genotoxicity when expressed in Salmonella typhimurium LT2. Genetic screening enabled us to contribute this toxicity entirely to the presence of the endogenous Type III restriction modification system (StyLTI) of S. typhimurium LT2. The StyLTI system consists of the Mod DNA methyltransferase and the Res restriction endonuclease, and we revealed that expression of the LT2 mod gene was sufficient to trigger Mrr activity in E. coli MG1655. Moreover, we could demonstrate that horizontal acquisition of the MG1655 mrr locus can drive the loss of endogenous Mod functionality present in S. typhimurium LT2 and E. coli ED1a, and observed a strong anti-correlation between close homologues of MG1655 mrr and LT2 mod in the genome database. This apparent evolutionary antagonism is further discussed in the light of a possible role for Mrr as defense mechanism against the establishment of epigenetic regulation by foreign DNA methyltransferases

The naked truth: a comprehensive clarification and classification of current 'myths' in naked mole-rat biology.

The naked mole-rat (Heterocephalus glaber) has fascinated zoologists for at least half a century. It has also generated considerable biomedical interest not only because of its extraordinary longevity, but also because of unusual protective features (e.g. its tolerance of variable oxygen availability), which may be pertinent to several human disease states, including ischemia/reperfusion injury and neurodegeneration. A recent article entitled 'Surprisingly long survival of premature conclusions about naked mole-rat biology' described 28 'myths' which, those authors claimed, are a 'perpetuation of beautiful, but falsified, hypotheses' and impede our understanding of this enigmatic mammal. Here, we re-examine each of these 'myths' based on evidence published in the scientific literature. Following Braude et al., we argue that these 'myths' fall into four main categories: (i) 'myths' that would be better described as oversimplifications, some of which persist solely in the popular press; (ii) 'myths' that are based on incomplete understanding, where more evidence is clearly needed; (iii) 'myths' where the accumulation of evidence over the years has led to a revision in interpretation, but where there is no significant disagreement among scientists currently working in the field; (iv) 'myths' where there is a genuine difference in opinion among active researchers, based on alternative interpretations of the available evidence. The term 'myth' is particularly inappropriate when applied to competing, evidence-based hypotheses, which form part of the normal evolution of scientific knowledge. Here, we provide a comprehensive critical review of naked mole-rat biology and attempt to clarify some of these misconceptions

Identification and structural characterization of FYVE domain-containing proteins of Arabidopsis thaliana

<p>Abstract</p> <p>Background</p> <p>FYVE domains have emerged as membrane-targeting domains highly specific for phosphatidylinositol 3-phosphate (PtdIns(3)<it>P</it>). They are predominantly found in proteins involved in various trafficking pathways. Although FYVE domains may function as individual modules, dimers or in partnership with other proteins, structurally, all FYVE domains share a fold comprising two small characteristic double-stranded β-sheets, and a C-terminal α-helix, which houses eight conserved Zn²⁺ion-binding cysteines. To date, the structural, biochemical, and biophysical mechanisms for subcellular targeting of FYVE domains for proteins from various model organisms have been worked out but plant FYVE domains remain noticeably under-investigated.</p> <p>Results</p> <p>We carried out an extensive examination of all <it>Arabidopsis </it>FYVE domains, including their identification, classification, molecular modeling and biophysical characterization using computational approaches. Our classification of fifteen <it>Arabidopsis </it>FYVE proteins at the outset reveals unique domain architectures for FYVE containing proteins, which are not paralleled in other organisms. Detailed sequence analysis and biophysical characterization of the structural models are used to predict membrane interaction mechanisms previously described for other FYVE domains and their subtle variations as well as novel mechanisms that seem to be specific to plants.</p> <p>Conclusions</p> <p>Our study contributes to the understanding of the molecular basis of FYVE-based membrane targeting in plants on a genomic scale. The results show that FYVE domain containing proteins in plants have evolved to incorporate significant differences from those in other organisms implying that they play a unique role in plant signaling pathways and/or play similar/parallel roles in signaling to other organisms but use different protein players/signaling mechanisms.</p

Genome Stability of Lyme Disease Spirochetes: Comparative Genomics of Borrelia burgdorferi Plasmids

Lyme disease is the most common tick-borne human illness in North America. In order to understand the molecular pathogenesis, natural diversity, population structure and epizootic spread of the North American Lyme agent, Borrelia burgdorferi sensu stricto, a much better understanding of the natural diversity of its genome will be required. Towards this end we present a comparative analysis of the nucleotide sequences of the numerous plasmids of B. burgdorferi isolates B31, N40, JD1 and 297. These strains were chosen because they include the three most commonly studied laboratory strains, and because they represent different major genetic lineages and so are informative regarding the genetic diversity and evolution of this organism. A unique feature of Borrelia genomes is that they carry a large number of linear and circular plasmids, and this work shows that strains N40, JD1, 297 and B31 carry related but non-identical sets of 16, 20, 19 and 21 plasmids, respectively, that comprise 33–40% of their genomes. We deduce that there are at least 28 plasmid compatibility types among the four strains. The B. burgdorferi ∼900 Kbp linear chromosomes are evolutionarily exceptionally stable, except for a short ≤20 Kbp plasmid-like section at the right end. A few of the plasmids, including the linear lp54 and circular cp26, are also very stable. We show here that the other plasmids, especially the linear ones, are considerably more variable. Nearly all of the linear plasmids have undergone one or more substantial inter-plasmid rearrangements since their last common ancestor. In spite of these rearrangements and differences in plasmid contents, the overall gene complement of the different isolates has remained relatively constant

Allelic Variation of the Lyme Disease Spirochete Adhesin DbpA Influences Spirochetal Binding to Decorin, Dermatan Sulfate, and Mammalian Cells▿

After transmission by an infected tick, the Lyme disease spirochete, Borrelia burgdorferi sensu lato, colonizes the mammalian skin and may disseminate systemically. The three major species of Lyme disease spirochete—B. burgdorferi sensu stricto, B. garinii, and B. afzelii—are associated with different chronic disease manifestations. Colonization is likely promoted by the ability to bind to target tissues, and Lyme disease spirochetes utilize multiple adhesive molecules to interact with diverse mammalian components. The allelic variable surface lipoprotein decorin binding protein A (DbpA) promotes bacterial binding to the proteoglycan decorin and to the glycosaminoglycan (GAG) dermatan sulfate. To assess allelic variation of DbpA in GAG-, decorin-, and cell-binding activities, we expressed dbpA alleles derived from diverse Lyme disease spirochetes in B. burgdorferi strain B314, a noninfectious and nonadherent strain that lacks dbpA. Each DbpA allele conferred upon B. burgdorferi strain B314 the ability to bind to cultured kidney epithelial (but not glial or endothelial) cells, as well as to purified decorin and dermatan sulfate. Nevertheless, allelic variation of DbpA was associated with dramatic differences in substrate binding activity. In most cases, decorin and dermatan sulfate binding correlated well, but DbpA of B. afzelii strain VS461 promoted differential binding to decorin and dermatan sulfate, indicating that the two activities are separable. DbpA from a clone of B. burgdorferi strain N40 that can cause disseminated infection in mice displayed relatively low adhesive activity, indicating that robust DbpA-mediated adhesive activity is not required for spread in the mammalian host

The migration of beech ( Fagus sylvatica L.) up the Rhone: the Mediterranean history of a “mountain” species

http://dx.doi.org/10.1007/s00334-005-0068-9International audienceNew anthracological data on the beech (Fagus sylvatica L.), obtained through rescue excavations, allows the proposal of a new pattern of population by beech of the South of France since the Lateglacial. Due to itscurrent ecology and distribution it is considered to be a mountain species in the Mediterranean area despite the presence of beech forests, usually described as glacial relicts, at low altitudes in the South of France and in the Rhone valley (Sainte-Baume, Valbonne and Grand Fays). Our results, combined with previous pollen and charcoal data, show both an early spread from glacial refuges and a late disappearance of the species. During the glacial period, the beech remained in the southernmost zones. From there, it first spread during the Preboreal towards outposts in the Rhone delta, and during the Atlantic along the rhodanian corridor. During the Subboreal, a retreat of beech towards the Pre-Alps and the Rhone delta can be traced. The Iron Age and the Classical period experienced the maximal concentration of beech along the Rhone river, while it became more rare in the North and in the South. During the Middle Ages, it first disappeared from these distal areas, and later also in the valley (around A.D.1000), finally settling in its present mountainous distribution area (probably around the 14th century A.D.). Some crucial points of the proposed dynamics are further analysed: the paradoxical regression of beech in the valley during the Subboreal, the factors determining the expansion of beech from refuge areas during the Subatlantic and finally, the disappearance of the beech in the middle Rhone valley in rather recent times, a disappearance attributed to the strong human impact on the landscape.Les nouvelles données anthracologiques concernant le hêtre (Fagus sylvatica L.), obtenues grâce au développement de l'archéologie préventive, permettent de proposer un nouveau modèle de diffusion de cette espèce depuis le Tardiglaciaire. D'après son écologie et sa distribution actuelles, elle est considérée comme une espèce montagnarde dans la région méditerranéenne, en dépit de la présence de hêtraies, souvent envisagées comme des reliques glaciaires, à basse altitude dans le sud de la France et dans la vallée du Rhône (Sainte-Baume, Valbonne et le Grand Fays). Nos résultats, combinées aux données polliniques et anthracologiques préexistantes, montrent une diffusion précoce à partir des refuges glaciaires, et une disparition tardive de cette espèce. Au cours de la période glaciaire, le hêtre s'est maintenu dans les zones les plus méridionales, puis s'est diffusé au cours du Préboréal, à partir d'avant-postes localisés dans le delta du Rhône, et au cours de l'Atlantique le long du couloir rhodanien avant de se replier vers les Préalpes et le delta du Rhône au Subboréal. L'Âge du Fer et l'Antiquité connaissent la concentration maximale du hêtre le long du Rhône, alors qu'il se raréfie au nord et au sud de la zone. Au Moyen Âge, il disparaît tout d'abord de ces zones distales, et ensuite de la vallée (vers 1000 A.D.), pour s'installer définitivement dans sa zone de répartition actuelle (probablement autour du 14eme siècle). Quelques points cruciaux de la dynamique de peuplement sont analysés : la régression paradoxale du hêtre dans la vallée au Subboréal, le déterminisme de son expansion à partir des zones refuges au cours du Subatlantique et, finalement, sa disparition de la moyenne vallée du Rhône à une période récente, disparition attribuée à la forte emprise humaine sur le paysage