Bacterial toxin-antitoxin systems: Translation inhibitors everywhere

Toxin-antitoxin (TA) systems are composed of two elements: a toxic protein and an antitoxin which is either an RNA (type I and III) or a protein (type II). Type II systems are abundant in bacterial genomes in which they move via horizontal gene transfer. They are generally composed of two genes organized in an operon, encoding a toxin and a labile antitoxin. When carried by mobile genetic elements, these small modules contribute to their stability by a phenomenon denoted as addiction. Recently, we developed a bioinformatics procedure that, along with experimental validation, allowed the identification of nine novel toxin super-families. Here, considering that some toxin super-families exhibit dramatic sequence diversity but similar structure, bioinformatics tools were used to predict tertiary structures of novel toxins. Seven of the nine novel super-families did not show any structural homology with known toxins, indicating that combination of sequence similarity and three-dimensional structure prediction allows a consistent classification. Interestingly, the novel super-families are translation inhibitors similar to the majority of known toxins indicating that this activity might have been selected rather than more detrimental traits such as DNA-gyrase inhibitors, which are very toxic for cells

Generalizations of the thermal Bogoliubov transformation

The thermal Bogoliubov transformation in thermo field dynamics is generalized in two respects. First, a generalization of the $\alpha$--degree of freedom to tilde non--conserving representations is considered. Secondly, the usual $2\times2$ Bogoliubov matrix is extended to a $4\times4$ matrix including mixing of modes with non--trivial multiparticle correlations. The analysis is carried out for both bosons and fermions.Comment: 20 pages, Latex, Nordita 93/33

Diversity of bacterial type II toxin–antitoxin systems: a comprehensive search and functional analysis of novel families

Type II toxin–antitoxin (TA) systems are generally composed of two genes organized in an operon, encoding a labile antitoxin and a stable toxin. They were first discovered on plasmids where they contribute to plasmid stability by a phenomenon denoted as ‘addiction’, and subsequently in bacterial chromosomes. To discover novel families of antitoxins and toxins, we developed a bioinformatics approach based on the ‘guilt by association’ principle. Extensive experimental validation in Escherichia coli of predicted antitoxins and toxins increased significantly the number of validated systems and defined novel toxin and antitoxin families. Our data suggest that toxin families as well as antitoxin families originate from distinct ancestors that were assembled multiple times during evolution. Toxin and antitoxin families found on plasmids tend to be promiscuous and widespread, indicating that TA systems move through horizontal gene transfer. We propose that due to their addictive properties, TA systems are likely to be maintained in chromosomes even though they do not necessarily confer an advantage to their bacterial hosts. Therefore, addiction might play a major role in the evolutionary success of TA systems both on mobile genetic elements and in bacterial chromosomes

ISbrowser: an extension of ISfinder for visualizing insertion sequences in prokaryotic genomes

Insertion sequences (ISs) are among the smallest and simplest autonomous transposable elements. ISfinder (http://www-is.biotoul.fr/) is a dedicated IS database which assigns names to individual ISs to maintain a coherent nomenclature, an IS repository including >3000 individual ISs from both bacteria and archaea and provides a basis for IS classification. Each IS is indexed in ISfinder with various associated pieces of information (the complete nucleotide sequence, the sequence of the ends and target sites, potential open reading frames, strain of origin, distribution in other strains and available bibliography) and classified into a group or family to provide some insight into its phylogeny. ISfinder also includes extensive background information on ISs and transposons in general. Online tools are gradually being added. At present, it is difficult to visualize the global distribution of ISs in a given bacterial genome. Such information would facilitate understanding of the impact of these small transposable elements on shaping their host genome. Here we describe ISbrowser (http://www-genome.biotoul.fr/ISbrowser.php), an extension to the ISfinder platform and a tool which permits visualization of the position, orientation and distribution of complete and partial ISs in individual prokaryotic genomes

The Imaginary Part of Nucleon Self-energy in hot nuclear matter

A semiphenomenological approach to the nucleon self-energy in nuclear matter at finite temperatures is followed. It combines elements of Thermo Field Dynamics for the treatment of finite temperature with a model for the self-energy, which evaluates the second order diagrams taking the needed dynamics of the NN interaction from experiment. The approach proved to be accurate at zero temperature to reproduce Im(Sigma) and other properties of nucleons in matter. In the present case we apply it to determine Im(Sigma) at finite temperatures. An effective NN cross section is deduced which can be easily used in analyses of heavy ion reactions.Comment: 15 pages, 6 postscripts figures, to be published in Nucl. Phys.

ACLAME: A CLAssification of Mobile genetic Elements, update 2010

The ACLAME database is dedicated to the collection, analysis and classification of sequenced mobile genetic elements (MGEs, in particular phages and plasmids). In addition to providing information on the MGEs content, classifications are available at various levels of organization. At the gene/protein level, families group similar sequences that are expected to share the same function. Families of four or more proteins are manually assigned with a functional annotation using the GeneOntology and the locally developed ontology MeGO dedicated to MGEs. At the genome level, evolutionary cohesive modules group sets of protein families shared among MGEs. At the population level, networks display the reticulate evolutionary relationships among MGEs. To increase the coverage of the phage sequence space, ACLAME version 0.4 incorporates 760 high-quality predicted prophages selected from the Prophinder database. Most of the data can be downloaded from the freely accessible ACLAME web site (http://aclame.ulb.ac.be). The BLAST interface for querying the database has been extended and numerous tools for in-depth analysis of the results have been added

Two-Dimensional Thermofield Bosonization II: Massive Fermions

We consider the perturbative computation of the N-point function of chiral densities of massive free fermions at finite temperature within the thermofield dynamics approach. The infinite series in the mass parameter for the N-point functions are computed in the fermionic formulation and compared with the corresponding perturbative series in the interaction parameter in the bosonized thermofield formulation. Thereby we establish in thermofield dynamics the formal equivalence of the massive free fermion theory with the sine-Gordon thermofield model for a particular value of the sine-Gordon parameter. We extend the thermofield bosonization to include the massive Thirring model.Comment: 21 pages, to be published in Annals of Physic