Patrick Forterre

..Reconstruction of phylogenetic trees showed that the archaeal gene is equally distantly related to both eukaryotes and bacteria, independently of the numerous substitutions observed at critical positions...

..The later scenario could explain why all today hyperthermophiles are procaryotes...

..This result emphasizes the importance of reverse gyrase in the adaptation of life to very high temperatures, and strengthens the idea that evolution of this enzyme was crucial in the origin of hyperthermophiles...

..The phenotypic and genotypic characterization of these new groups is now a top priority for further studies on archaeal evolution...

..A hyperthermophilic LUCA would have suggested a circular, double-stranded DNA genome; however, recent data favor a mesophilic or moderately thermophilic LUCA...

..As viral and plasmid-encoded proteins are usually very divergent from their cellular counterparts, this would explain the puzzling phylogenies and distribution of many DNA informational proteins between the three domains of life...

..I suggest here that DNA and DNA replication mechanisms appeared first in the virus world before being transferred into cellular organisms...

..Nevertheless, the phylogeny of Archaea and the nature of the last universal common ancestor are still matters for debate...

..Since genetic tools for hyperthermophilic archaea are just emerging, we utilized immuno-detection approaches to get the first in vivo data on the role(s) of these proteins in the hyperthermophilic crenarchaeon Sulfolobus acidocaldarius...

..This strengthens the idea that plasmids and viruses are a reservoir of novel protein families involved in DNA replication...

..Understanding the precise biochemical function and biological role of these two proteins (which are probably essential for genome maintenance) remains a major challenge...

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..Kae1 is thus a novel and atypical universal DNA interacting protein whose importance could rival those of RecA (RadA/Rad51) in the maintenance of genome integrity in all living cells...

..This structure, combined with a wealth of experimental data gathered on these enzymes, allows us to propose a structural model for the two-gate DNA transfer mechanism...

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..Direct interaction between Kae1p and Bud32p in yeast is required both for the transcription and the telomere homeostasis function of EKC/KEOPS...

..It is one of the most radioresistant organisms known amongst the Archaea. We report the determination and annotation of its complete genome sequence, its comparison with other Thermococcales genomes, and a proteomic analysis...

..Some membrane vesicles of Thermococcus nautilus harbour the plasmid pTN1, suggesting that vesicles can be involved in plasmid transfer between species...

..Our results indicate that C. symbiosum and its relatives are not Crenarchaeota, but should be considered as a third archaeal phylum, which we propose to name Thaumarchaeota (from the Greek 'thaumas', meaning wonder)...

..We believe that this gene organization is biologically relevant and, moreover, that it suggests the existence of a mechanism coupling DNA replication and translation in Archaea and Eukarya...

..Here, we have systematically analyzed the genomic environment of all known DNA replication genes in 27 archaeal genomes to infer new connections for DNA replication proteins from conserved genomic associations...

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..By analogy with the mechanism of action of known type II topoisomerases, we suggest that Spo11 catalyses the formation of double-strand breaks that initiate meiotic recombination in S. cerevisiae...

..Short Okazaki fragments and a high replication speed imply a very efficient turnover of Okazaki fragments in Archaea. Archaea therefore have a unique replication system showing mechanistic similarities to both Bacteria and Eukarya...

..We suggest to name members of the Kae1(OSGEP)/YgjD family UGMP, for Universal Genome Maintenance Proteins...

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..coli Mrp protein and contains representants of the three domains of life. The conservation of MinD-like proteins in the three domains of life suggests that these proteins play a central role in cellular metabolism...

..We also proposed that topoisomerases have played a critical role in the origin of modern genomes and in the emergence of the three cellular domains...

..Our ChIP-chip analysis also revealed that Mcm alters the binding specificity to the oriC region according to the growth phase, consistent with its role as a licensing factor...

..Moreover, although pGT5 is known to be relaxed in vivo, Rep75 was not able to act on a relaxed plasmid in vitro, whether or not it contained the dso...

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..Finally, we show that NC is inhibited by ATP or dATP at concentrations that promote NTT. We propose a model in which the NTT activity of Rep75 plays a role in the regulation of pGT5 replication in vivo...

..furiosus. We discuss the implications of genomic rearrangements on gene orientation and composition biases, and their consequences on sequence evolution...

..Our findings reveal complexity in the evolution of thymidine in present-day DNA. Because ThyX proteins are found in many pathogenic microbes, they present a previously uncharacterized target for antimicrobial compounds...

..The finding that radicicol can inhibit at least two different antitumoral drug targets in human, and interferes with drugs currently used in cancer treatment, could have implications in cancer therapy...

..Although several hypotheses have been recently proposed to explain the origin of viruses, the emergence of virions, as a specific mechanism for gene dissemination, remains unexplained...

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..The presence of such protein in Archaea, Bacteria, and Eucarya suggests an early origin of DNA-motor proteins that could have emerged and diversified by domain shuffling...

..No gyrA-like gene has been found near top2B. A gene coding for a transaminase B-like protein was found in the upstream region of top2B...

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..furiosus cells that had or had not been exposed to gamma rays. We did not detect any significant protein induction following DNA damage in either species...

..The findings concerning DNA gyrase and negative supercoiling in Thermotogales put into question the role of reverse gyrase in hyperthermophiles...

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..DNA in vesicle preparations is remarkably resistant to DNase treatment and thermodenaturation, indicating that association with vesicles could be an important factor determining DNA stability in natural environments...

..Vector pYS2 proved to be very stable and was maintained at high copy number under selective conditions in both Escherichia coli and P. abyssi...

..The origin of life on our planet would correspond to the establishment of the first organism corresponding to this definition...

..Phylogenetic analysis of Rep proteins from rolling-circle replicons suggest that diverse families diverged before the separation of the domains Archaea, Bacteria, and Eucarya...

..These results indicate that DNA topology can change with physiological states and environmental modifications in hyperthermophilic archaea...

..Our data suggest that archaeal and eukaryotic Cdc6 and MCM proteins function similarly in replication initiation and imply that an oriC association of MCM could be regulated by an unknown mechanism in Archaea...

..The major difference involves organisms living in similar environments, suggesting that LGTs are mainly directed by the physical proximity of the organisms rather than by their phylogenetic proximity...

..To our knowledge, this is the first report of a 5'-3' nuclease potentially associated with Rad50 and Mre11-like proteins that may lead to the processing of double-stranded breaks in 3' single-stranded tails...

..This result supports the idea that proteins encoded by plasmid and viruses that have no cellular homologues could be a reservoir of new folds for structural genomic studies...

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..fulgidus, and suggests that gyrase activity predominates over reverse gyrase whenever the two topoisomerases coexist in cells...

..Fluorescence quenching titrations also showed that AFV3-109 interacts with dsDNA. Genomic sequence analysis revealed bacterial homologs of AFV3-109 as a part of a putative previously unidentified prophage sequences in some Firmicutes...

..Studies about thermostability show that the enzyme is more stable when incubated undiluted in the storage buffer. In these conditions, 60% activity was retained after a 30 min preincubation at 75 degrees C...

..In contrast, the bacteria E.coli was resistant to this drug. Radicicol thus appears to be a very promising compound to study the mechanism of Topo IIB in vitro, as well as the biological roles of these enzymes in vivo...

..Our cell fractionation assays further suggest that "P. abyssi" contains a highly efficient DNA repair system which is continuously ready to repair the DNA damage caused by high temperature and/or ionizing radiation...

..nov. The type strain is EJ3(T) (= DSM 15229(T) = JCM 11827(T))...

..Here, we provide a unifying view on archaeal viruses, and present them as a particular assemblage that is fundamentally different in morphotype and genome from the DNA viruses of the other two domains of life, the Bacteria and Eukarya...

..So, where did it come from? It is my contention that Topo V, and many other orphan proteins, could have a viral origin...

..The existence of operational proteins highly conserved between Archaea and Eukarya involved in a central metabolic pathway challenge evolutionary scenarios in which eukaryal operational proteins are strictly of bacterial origin...

..However, proteins probably from bacterial origin, including some from mesophilic bacteria, are also present in the P. abyssi genome...

..The proposed biological relevance of these observations is that these proteins might model the behaviour of DNA in constrained chromatin environments...

..marinus sp. nov. and T. radiotolerans sp. nov. The type strain of T. marinus is strain EJ1T (= DSM 15227T = JCM 11825T) and the type strain of T. radiotolerans is strain EJ2T (= DSM 15228T = JCM 11826T)...

..Considering its functional analogy with bacteriophages, we classify this virus as a virophage. The virophage could be a vehicle mediating lateral gene transfer between giant viruses...

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..However, it also questions the role of this enzyme in thermophilic bacteria and the selective advantage its presence could provide...

..However, some incongruence remained between the two phylogenies. This may be due either to undetected LGT and/or to a lack of sufficient phylogenetic signal in the datasets...

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..Confirming the phylogenetic position of N. equitans is thus crucial for deciphering the history of the archaeal domain...

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..We analyzed archaeal phylogeny using two concatenated datasets consisting of 14 proteins involved in transcription and 53 ribosomal proteins (3,275 and 6,377 positions, respectively)...

..Owing to this unique functional feature, we propose to call this family as GPN-loop GTPase...

..Another T3/T7 viral-like RNA polymerase is functional in the chloroplast, indicating that a strong selection pressure has favored replacement of some cellular proteins by viral proteins in organelle evolution...

..One of the viruses, Acidianus filamentous virus 9, AFV9, was isolated and its structure and genome were studied in detail...