Unit: Molecular Biology of the Gene in Extremophiles
Director: Patrick FORTERRE
The living world is presently divided into three cellular lineages: the Bacteria, the Archaea and the Eucarya. We are interested in the events and mechanisms that lead to the establishment of these three lineages and in the role those viruses have played in that history. We focus our attention on viruses from hyperthermophilic archaea that exhibit an incredible morphological and genetic diversity. In the last year, we have obtained a robust phylogeny of the archaeal domain, and we have described several new virus families, including the first virus that exhibits extra cellular morphological development.
Viruses from hyperthermophilic Archaea.
(David Prangishvili, Monica Haëring, Alexandra Kessler, Soizick Lucas, Caroline Amsellem, Tamara Basta, Ariane Bize, Myriam Ztouti, Nicole Desnoues, Jean-Marie Clément, Guennadi Sezonov)
Viruses from hyperthermophilic Archaea exhibit an incredible morphological and genetic diversity, exceeding that of bacterial viruses. Their systematic study was initiated twenty years ago by Wolfram Zillig and Munich and followed up by Dr David Prangishvili, first in Regensburg (Germany) and now in our unit. In the last year, the collection of Dr Prangishvili has been successfully transferred at the Institut Pasteur. Culturing conditions have been set up for growing various DNA viruses of hyperthermophilic archaea, encompassing thirteen species assigned to six different viral families. These species, that infect archaea of the genera Sulfolobus and Acidianus, represent 75% of presently accessible hyperthermophilic archaeal viruses, and exist only in the collection of the Institut Pasteur.
Descriptions of four of these unique viruses have been prepared and published in four articles, one of them in Nature. The latter describes the virus ATV (Acidianus double-tailed virus) that exhibits a spectacular extra-cellular development stage observed for the first time in any virus (Figure 1). Several reviews on viruses of hyperthermophilic archaea have been prepared and published in such fundamental editions as "The Bacteriophages" (second edition), Methods in Microbiology, and Trends in Microbiology.
For studies on transcription of archaeal viruses, an in vitro transcription system has been established, in collaboration with Stephen Bell, MRC Research Centre, Cambridge. We have thus isolated and characterize a transcription regulator that specifically activates transcription of genes of viruses from the family Rudiviridae. The structure of this winged helix-turn-helix protein was studied in collaboration with Unité de RMN des Biomolécules, Institut Pasteur (Muriel Delepierre) (Figure 2). We continued our collaboration with the laboratory of Roger Garrett (University of Copenhagen) for the sequencing and analysis of viral genomes.
The project "Archaeal viruses: deciphering structure and function of proteins and enzymes from a new class of extremophiles" started in the frame of the ANR Program, in collaboration with Christian Cambillau, AFMB, CNRS, the University of Provence and the University of the Mediterranée, and Herman van Tilbeurgh (University Paris-Sud/CNRS) (coordinator D.Prangishvili).
Another of our objectives is to use some of our viruses to develop new genetic tools for hyperthermophilic Archaea. Finally, we also plan to search for further new viruses by collecting samples in future expeditions in various terrestrial hot springs. Screening for new hyperthermophilic archaeal viruses in geothermal environments of Kamchatka peninsula in the Far East of Russia was initiated in collaboration with the Institute of Microbiology, Russian Academy of Sciences (E. Boch-Osmolovskaya).
Genome evolution, molecular phylogeny and comparative genomics
(Simonetta Gribaldo, Guennadi Sezonov, Lars Jermiin, Patrick Forterre)
We use in silico approaches (molecular phylogeny, comparative genomics) to study the evolution of major molecular systems, the mechanisms of genome evolution and to reconstruct deep phylogenies with a focus on the evolutionary history of Archaea. One of our aims is also to identify new fundamental molecular mechanisms which are conserved between cellular lineages.
We have set up robust and convergent phylogenies of the domain Archaea based on both ribosomal proteins and RNA polymerases (collaboration with Céline Brochier, University of Aix-Marseille). This result shows the existence of a core of genes that have been vertically inherited and are therefore excellent molecular markers to reconstruct the history of Archaea. We have shown than Nanoarchaea, the smallest cells presently known, did not correspond to a new archaeal phylum, as widely assumed, but are probably distantly related to Therococcales (Euryarchaeota). In the course of this work, we have observed a correlation between the rapid evolutionary rate of the genome of the archaeon Methanopyrus kandleri and the lack of the transcription factor TFS. This suggests a link between the fidelity of transcription and the rate of genome evolution that could be conserved from Bacteria to Humans. We have started to test this hypothesis using mutants of the functional analogous proteins in Bacteria (GreA, GreB). In our preliminary work, we have identified a third bacterial protein that seem to function together with GreA and GreB for protection against UV irradiation. Interestingly, this protein has an orthologue of unknown function in human that could be a new transcription factor.
We are interested in the role that viruses could have play in the history of cellular life and especially in the origin of modern DNA genomes. We have published our hypotheses on the different stages of the RNA world, the origin of viruses and the viral invention of DNA in " Biochimie ". This publication has been discussed in a dedicated paper in Nature. We have also published a review paper on the last universal common ancestor (LUCA) in Médecine/ Sciences.
Epistemological and historical studies of the work of Carl Woese
The elaboration of the archaeal concept by Carl Woese has triggered a revolution in our understanding of the living world. One of our PhD students, Chloé Terras, has undertaken an historical study to better understand the origin of this revolution and its impact on the history of biology. This year, she was able to make a filmed interview of Carl Woese in the US.
Figure 1 : Extracellular morphological development of the virus ATV.
Figure 2 : Structural model of transcription activator Sta1 of the archeon Sulfolobus and its activating effect on gene transcription in Sulfolobus virus SIRV1.
Keywords: Archaea, Virus, Evolution, comparative genomics, Replication, Transcription, Molecular phylogeny