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P Forterre

Publications and source records attributed to P Forterre.

At least 73 records · Page 4Linked to original sources
PubMed1995

Speculations on the origin of life and thermophily: review of available information on reverse gyrase suggests that hyperthermophilic procaryotes are not so primitive.

All present-day hyperthermophiles studied so far (either Bacteria or Archaea) contain a unique DNA topoisomerase, reverse gyrase, which probably helps to stabilize genomic DNA at high temperature. Herein the data relating this enzyme is reviewed and discussed from the perspective of the nature of the last detectable common ancestor and the origin of life. The sequence of the gene encoding reverse gyrase from an archaeon, Sulfolobus acidocaldarius, suggests that this enzyme contains both a helicase and a topoisomerase domains (Confalonieri et al., Proc. Natl. Acad. Sci., 1993, 90, 4735). Accordingly, it has been proposed that reversed gyrase originated by the fusion of DNA helicase and DNA topoisomerase genes. If reverse gyrase is essential for life at high temperature, its composite structure suggests that DNA helicases and topoisomerases appeared independently and first evolved in a mesophilic world. Such scenario contradicts the hypothesis that a direct link connects present day hyperthermophiles to a hot origin of life. We discuss different patterns for the early cellular evolution in which reverse gyrase appeared either before the emergence of the last common ancestor of Archaea, Bacteria and Eucarya, or in a lineage common to the two procaryotic domains. The later scenario could explain why all today hyperthermophiles are procaryotes.

Archaea↗
PubMed1995

Thermoreduction, a hypothesis for the origin of prokaryotes.

All thermophiles discovered so far are prokaryotes (Bacteria or Archaea). Furthermore, reconstructions of rRNA phylogenies suggest that the progenitor of all prokaryotes was a thermophile. These data are usually interpreted as supporting the hypothesis that all present day organisms, including eukaryotes, originated from hyperthermophiles. However, this scenario is difficult to reconcile with the RNA world theory, considering the instability of RNA at very high temperatures, and it is also contradicted by the finding of sophisticated devices for thermophilic adaptation in present day hyperthermophiles. Accordingly, I propose here 2 new hypotheses to explain the correlation between the procaryotic phenotype and thermophilic life without reference to a putative hot origin of life. Firstly, eukaryotes would be unable to live in thermophilic biotopes because of the susceptibility of their mRNA to degradation at high temperature. In prokaryotes, the absence of a nuclear membrane allows these organisms to bypass the problem of mRNA heat-induced hydrolysis by coupling transcription and translation. As a corollary of this first hypothesis, I also suggest that today prokaryotes might have originated from mesophilic ancestors via reductive evolution, in the process of adaptation to thermophily.

Biological Evolution↗
PubMed1994

Purification of a DNA topoisomerase II from the hyperthermophilic archaeon Sulfolobus shibatae. A thermostable enzyme with both bacterial and eucaryal features.

A type II DNA topoisomerase has been purified to homogeneity from the hyperthermophilic archaeon Sulfolobus shibatae. The enzyme is composed of two subunits of 60 and 47 kDa. It has a Stokes radius of 69 A and has a sedimentation coefficient of 7.8 S which gives a calculated native molecular mass of approximately 230 kDa, indicating a heterotetrameric structure. This enzyme is ATP and Mg2+ dependent and can relax both negatively and positively supercoiled DNA, but presents no supercoiling activity. The S. shibatae DNA topoisomerase II is more efficient in decatenation than in relaxation. The optimal temperature for the enzymatic activity is approximately 80 degrees C. This archaeal enzyme is not inhibited by the gyrase inhibitor novobiocin but is sensitive to several inhibitors of eucaryotic DNA topoisomerases of type II such as amsacrines, ellipticine, and the quinolone CP-115,953. Like all prokaryotic DNA topoisomerase II, the S. shibatae DNA topoisomerase II is a heterotetramer but the absence of supercoiling activity, the strong decatenase activity, and the pattern of antibiotic sensitivity of the S. shibatae DNA topoisomerase II is reminiscent of eucaryotic enzymes.

DNA Topoisomerases, Type II↗
PubMed1994

DNA intercalating drugs inhibit positive supercoiling induced by novobiocin in halophilic archaea.

The two DNA intercalators, actinomycin D and 2-methyl-9-hydroxy-ellipticine, and the DNA minor groove ligant DAPI inhibited the growth of the haloarchaeon Halobacterium sp. GRB and bind to its plasmid pGRB-1. In contrast to specific DNA topoisomerase II inhibitors, they produced neither double-stranded breaks nor relaxation of plasmidic DNA. The two DNA intercalators inhibited positive supercoiling induced by novobiocin, suggesting that positive supercoiling in haloarchaea is due to transcription, as in the domain Bacteria. Plasmids from haloarchaea could thus be used to prescreen for DNA intercalators and to discriminate between different drug families via their mode of action.

DNA-Binding Proteins↗
PubMed1994

DNA stability at temperatures typical for hyperthermophiles.

We have studied the fate of covalently-closed circular DNA in the temperature range from 95 to 107 degrees C. Supercoiled plasmid was not denatured up to the highest temperature tested. However, it was progressively transformed into open DNA by cleavage and then denatured. Thermodegradation was not dependent on the DNA supercoiling density. In particular, DNA made positively supercoiled by an archaeal reverse gyrase was not more resistant to depurination and thermodegradation than negatively supercoiled DNA. Thermodegradation was similar in aerobic or anaerobic conditions but strongly reduced in the presence of physiological concentrations of K+ or Mg2+. These results indicate that the major problem faced by covalently closed DNA in hyperthermophilic conditions is not thermodenaturation, but thermodegradation, and that intracellular salt concentration is important for stability of DNA primary structure. Our data suggest that reverse gyrase is not directly required to protect DNA against thermodegradation or thermodenaturation.

DNA Topoisomerases, Type I↗
PubMed1994

PCR-mediated cloning and sequencing of the gene encoding glutamate dehydrogenase from the archaeon Sulfolobus shibatae: identification of putative amino-acid signatures for extremophilic adaptation.

Highly degenerate oligodeoxyribonucleotides (oligos) were used to PCR amplify the most conserved region of the glutamate dehydrogenase (GDH)-encoding gene from the extreme thermophilic archaeon, Sulfolobus shibatae. The amplified fragment was cloned and sequenced, and then used as a homologous probe to clone a genomic restriction fragment containing the near-complete gdhA gene. The deduced amino acid (aa) sequence shows a very high degree of similarity with the aa sequence previously determined by direct sequencing of the purified enzyme from Sulfolobus solfataricus [Maras et al., Eur. J. Biochem. 203 (1992) 81-87]. The introduction of this new sequence into our GDH phylogenetic trees [Benachenhou-Lahfa et al., J. Mol. Evol. 35 (1993) 335-346] showed that it is a new member of hexameric GDH family II, and did not modify the topology of the trees. Comparison of the primary structures of extremophilic GDH enzymes (halophilic, thermophilic and hyperthermophilic) with those of their non-halophilic and mesophilic counterparts in this family II led us to identify a few aa changes which seem to be specific either to hyperthermophilic or halophilic adaptation.

Adaptation, Physiological↗
PubMed1994

Effects of salt and temperature on plasmid topology in the halophilic archaeon Haloferax volcanii.

We report here the effect of environmental parameters, salinity, temperature, and an intercalating drug on plasmid topology in the halophilic archaeon Haloferax volcanii. We first studied the topological state of the plasmid pHV11 in media of different salt compositions and concentrations. The superhelical density of plasmid PHV11 varies in a way that depends on the kind of salt and on the concentrations of individual salts. With respect to growth temperature, the plasmid linking number increased at higher temperature in a linear way, contrary to what has been reported for Escherichia coli, in which the plasmid linking number decreased at higher temperature. These results suggest that some of the mechanisms that control DNA supercoiling in halophilic Archaea may be different from those described for E. coli. However, homeostatic control of DNA supercoiling seems to occur in haloarchaea, as in Bacteria, since we found that relaxation of DNA by chloroquine triggers an increase in negative supercoiling.

Archaea↗
PubMed1994

Comparison of plasmid DNA topology among mesophilic and thermophilic eubacteria and archaebacteria.

Several plasmid DNAs have been isolated from mesophilic and thermophilic archaebacteria. Their superhelical densities were estimated at their host strain's optimal growth temperature, and in some representative strains, the presence of reverse gyrase activity (positive DNA supercoiling) was investigated. We show here that these plasmids can be grouped in two clusters with respect to their topological state. The group I plasmids have a highly negatively supercoiled DNA and belong to the mesophilic archaebacteria and all types of eubacteria. The group II plasmids have DNA which is close to the relaxed state and belong exclusively to the thermophilic archaebacteria. All archaebacteria containing a relaxed plasmid, with the exception of the moderately thermophilic methanogen Methanobacterium thermoautotrophicum Marburg, also exhibit reverse gyrase activity. These findings show that extrachromosomal DNAs with very different topological states coexist in the archaebacterial domain.

Archaea↗
PubMed1993

ATP-independent DNA topoisomerase from Fervidobacterium islandicum.

Thermotogales are thermophilic eubacteria belonging to a very slowly evolving branch in the eubacterial tree. In this report, we describe the purification and characterization of an ATP-independent DNA topoisomerase from the Thermotogale, Fervidobacterium islandicum. The enzyme, a monomer of about 75 kDa, is a type I DNA topoisomerase sharing many properties with the other bacterial topoisomerases I: it absolutely requires Mg2+ for activity, relaxes negatively but not positively supercoiled DNA and is inhibited by single-stranded M13 DNA and spermidine. A feature of the F. islandicum ATP-independent DNA topoisomerase I is its thermophily. The optimal temperature for the enzymatic activity is 75 degrees C. 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.

DNA Topoisomerases, Type I↗
PubMed1993

Reverse gyrase: a helicase-like domain and a type I topoisomerase in the same polypeptide.

Reverse gyrase is a type I DNA topoisomerase able to positively supercoil DNA and is found in thermophilic archaebacteria and eubacteria. The gene coding for this protein was cloned from Sulfolobus acidocaldarius DSM 639. Analysis of the 1247-amino acid sequence and comparison of it with available sequence data suggest that reverse gyrase is constituted of two distinct domains: (i) a C-terminal domain of approximately 630 amino acids clearly related to eubacterial topoisomerase I (Escherichia coli topA and topB gene products) and to Saccharomyces cerevisiae top3; (ii) an N-terminal domain without any similarity to other known topoisomerases but containing several helicase motifs, including an ATP-binding site. These results are consistent with those from our previous mechanistic studies of reverse gyrase and suggest a model in which positive supercoiling is driven by the concerted action of helicase and topoisomerase in the same polypeptide: this constitutes an example of a composite gene formed by a helicase domain and a topoisomerase domain.

Amino Acid Sequence↗
PubMed1993

Evolution of glutamate dehydrogenase genes: evidence for two paralogous protein families and unusual branching patterns of the archaebacteria in the universal tree of life.

The existence of two families of genes coding for hexameric glutamate dehydrogenases has been deduced from the alignment of 21 primary sequences and the determination of the percentages of similarity between each pair of proteins. Each family could also be characterized by specific motifs. One family (Family I) was composed of gdh genes from six eubacteria and six lower eukaryotes (the primitive protozoan Giardia lamblia, the green alga Chlorella sorokiniana, and several fungi and yeasts). The other one (Family II) was composed of gdh genes from two eubacteria, two archaebacteria, and five higher eukaryotes (vertebrates). Reconstruction of phylogenetic trees using several parsimony and distance methods confirmed the existence of these two families. Therefore, these results reinforced our previously proposed hypothesis that two close but already different gdh genes were present in the last common ancestor to the three Ur-kingdoms (eubacteria, archaebacteria, and eukaryotes). The branching order of the different species of Family I was found to be the same whatever the method of tree reconstruction although it varied slightly according the region analyzed. Similarly, the topological positions of eubacteria and eukaryotes of Family II were independent of the method used. However, the branching of the two archaebacteria in Family II appeared to be unexpected: (1) the thermoacidophilic Sulfolobus solfataricus was found clustered with the two eubacteria of this family both in parsimony and distance trees, a situation not predicted by either one of the contradictory trees recently proposed; and (2) the branching of the halophilic Halobacterium salinarium varied according to the method of tree construction: it was closer to the eubacteria in the maximum parsimony tree and to eukaryotes in distance trees. Therefore, whatever the actual position of the halophilic species, archaebacteria did not appear to be monophyletic in these gdh gene trees. This result questions the firmness of the presently accepted interpretation of previous protein trees which were supposed to root unambiguously the universal tree of life and place the archaebacteria in this tree.

Algorithms↗
PubMed1992

The nature of the last universal ancestor and the root of the tree of life, still open questions.

The nature of the last universal ancestor to all extent cellular organisms and the rooting of the universal tree of life are fundamental questions which can now be addressed by molecular evolutionists. Several scenarios have been proposed during the last years, based on the phylogenies of ribosomal RNA and of duplicated proteins, which suggest that the last universal ancestor was either an RNA progenote or an hyperthermophilic prokaryote. We discuss these hypotheses in the light of new data on the evolution of DNA metabolizing enzymes and of contradictions between different protein phylogenies. We conclude that the last universal ancestor was a member of the DNA world already containing several DNA polymerases and DNA topoisomerases. Furthermore, we criticize current data which suggest that the rooting of the universal tree of life is located in the eubacterial branch and we conclude that both rooting the universal tree and the nature of the last universal ancestor are still open questions.

Archaea↗
PubMed1992

Evidence that a plasmid from a hyperthermophilic archaebacterium is relaxed at physiological temperatures.

A plasmid of 3.45 kb (pGT5) was recently discovered in a strain of hyperthermophilic archaebacterium which was isolated from samples collected in a deep-sea hydrothermal vent. This strain (GE5) grows within a temperature range of 68 to 101.5 degrees C, and we show here that it contains a strong ATP-dependent reverse gyrase activity (positive DNA supercoiling). By comparison with eubacterial plasmids of known superhelical densities, we estimated the superhelical density of the archaebacterial plasmid pGT5 to be -0.026 at 25 degrees C. The equation which relates the change of the rotation angle of the DNA double helix with temperature was validated at 95 degrees C, the optimal growth temperature of the GE5 strain. Considering these new data, the superhelical density of plasmid pGT5 was calculated to be -0.006 at the physiological temperature of 95 degrees C, which is close to the relaxed state. This finding shows that the DNA topology of a plasmid isolated from a hyperthermophilic archaebacterium containing reverse gyrase activity is strikingly different from that of typical eubacterial plasmids.

Archaea↗
PubMed1991

Reverse gyrase in thermophilic eubacteria.

The presence of reverse gyrase, an unusual ATP-dependent type I topoisomerase first isolated from thermophilic archaebacteria, has been detected in four strains of Thermotogales, an order of extremely thermophilic eubacteria. This result suggests that reverse gyrase plays a key role in high-temperature-living organisms, independently of the evolutionary kingdom to which they belong.

Archaea↗
PubMed1990

Purification and characterization of a DNA polymerase from the archaebacterium Thermoplasma acidophilum.

A thermophilic DNA polymerase has been purified to near homogeneity from the archaebacterium Thermoplasma acidophilum. Analysis of the purified enzyme by sodium dodecyl sulfate gel electrophoresis revealed a single polypeptide of 88 kDa which co-sediments with the DNA polymerase activity on sucrose gradients. Combination of sedimentation and gel filtration analyses indicates that this DNA polymerase is an 88-kDa monomeric enzyme in its native form. The DNA polymerase is resistant to aphidicolin, slightly sensitive to 2',3'-dideoxyribosylthymine triphosphate and inhibited by N-ethylmaleimide when preincubation with this reagent is performed at 65 degrees C. We find that a 3'----5' exonuclease activity is associated with the purified DNA polymerase; the two activities of the enzyme are optimal at 65 degrees C but the exonuclease activity is active in a broader range of lower temperatures and is more thermostable than the DNA polymerase activity.

Archaea↗