ICON LBMGE

 





   Genomes at IGM / LBMGE

 

 

 

 


 

Pyrococcus abyssi GE5 strain "Orsay"
sequence has been completed in 1998 by Genoscope (http://www.genoscope.cns.fr/), and deposited in GenBank/Embl under accession number AL096836.
Annotation of genomic sequence has been made by Genoscope, Evry France, LBS/IGBMC Illkirch-Graffenstaden France and LBMGE /IGM Orsay France

Genome description has been published in:
Cohen G., Barbe V., Flament D., Galperin M., Heilig R., Lecompte O., Poch O., Prieur D., Quérellou J., Ripp R., Thierry J., Van J. der Oost, Weissenbach J., Zivanovic Y. and Forterre P.
An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi
Mol Microbiol. 2003 47:1495-512
.


P.abyssi PDF version

 
 
 
 
 

 

Sulfolobus solfataricus P2
sequence and annotation has been completed in 2001, in a joint effort by IMB/NRC Halifax Canada, MGG/IMB Copenhagen Denmark, Wageningen University, Laboratory of Microbiology, The Netherlands and LBMGE /IGM Orsay France. Accession number in GenBank is AE006641 .

Genome description has been published in:
Proc. Natl. Acad. Sci. USA, Vol. 98, Issue 14, 7835-7840, July 3,2001.

Sulfolobus solfataricus P2 PDF version

 
 
 
 
  Bacteriophage T5 Bacteriophage T5
st0 deletion mutant + wt insertion
 
Bacteriophage T5
Sequence subcontracted to Integrated genomics
This a joint project by:
Transports Membranaires de Macromolécules, IBBMC Orsay France
LBMGE IGM, Orsay France
EAN IGM, Orsay France
labs

Unpublished

GenBank accession numbers: AY692264 (st0 deletion mutant) & AY734508 wild type insertion 
 
 
 
  Kluyveromyces lactis
(image from wikimedia.org)
Kluyveromyces lactis
Sequence completed by Genoscope (http://www.genoscope.cns.fr/)
Annotation of K. lactis is a joint project by IGM / Genolevures / Institut Pasteur
Published in :

Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuvéglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisramé A, Boyer J, Cattolico L, Confanioleri F, De Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wésolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic Y, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet JL.
Genome evolution in yeasts.
Nature. 2004 Jul 1;430(6995):35-44.

Zivanovic Y, Wincker P, Vacherie B, Bolotin-Fukuhara M, Fukuhara H.
Complete nucleotide sequence of the mitochondrial DNA from Kluyveromyces lactis.
FEMS Yeast Res. 2005 Feb;5(4-5):315-22.

 
       
  Thermococcus gammatolerans Thermococcus gammatolerans  Thermococcus gammatolerans Free access
Shotgun sequence by Genoscope
This a project by:
Laboratoire de Genomique des Archaea, IGM Orsay France

Accepted for publication in Genome Biology on 06/11/09:
Genome analysis and genome-scale proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea.
Y. Zivanovic, J. Armengaud, A. Lagorce, C. Leplat, P Guerin, M. Dutertre, V. Anthouard, P. Forterre, P. Winker, and F. Confalonieri

GenBank accession number: CP001398 
 
  Vampirococcus lugosii Vampirococcus lugosii  Vampirococcus lugosii Free access
Isolation / amplification / sequencing by
Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France.
Institut de Biologie Intégrative de la Cellule, CNRS, Université Paris-Saclay, Orsay, France

This a project by:
ESE, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France.
I2BC, CNRS, Université Paris-Saclay, Orsay, France

Publication NATURE COMMUNICATIONS | (2021)12:2454 | https://doi.org/10.1038/s41467-021-22762-4
Reductive evolution and unique predatory mode in the CPR bacterium Vampirococcus lugosii .
David Moreira, Yvan Zivanovic, Ana I. López-Archilla, Miguel Iniesto & Purificación López-García

GenBank accession number: PRJNA678638  
 
       




Pyrococcus abyssi is an hyperthermophilic euryarcheaon thriving in deep-sea hydrothermal vents , growing optimally at 96°C in strict anaerobic conditions and metabolizing sulfur. It has been sampled in the North Fiji basin (SW Pacific) at 2000 mt depth in 1989.
Sulfolobus solfatricus is an aerobic crenarchaeon that grows optimally at 80°C and pH 2-4 metabolizing sulfur which growths in volcanic solfataras. It is the most widely studied organism of the crenarchaeal branch of the Archaea
Bacteriophage T5 is a lytic, linear, double stranded "nicked" DNA phage belonging to Siphoviridae family. The phagic infection is a two step mechanism, in which the first-step transfer segment allows expression of pre-early genes necessary for complete DNA transfer and initiation of the lytic cycle. We have sequenced the deletion mutant st0, a widely used laboratory strain for primary sequence determination. Subsequently, full wild type genome has been reconstructed by incorporating the sequence of the wild type insertion from HER28 strain (obtained from Reference Center For Bacterial Viruses, Laval University, Quebec, Canada)
Kluyveromyces lactis, a yeast commonly used in genetic studies, cheese and yogurt production, and could potentially be used to produce drug compounds.
A large scale comparative genomic study as been undertaken, leading to sequencing and comparison of 3 other hemiascomycetous yeasts (Candida glabrata, Debaryomyces hansenii, and Yarrowia lipolytica.)
Thermococcus gammatolerans, was isolated from samples collected from hydrothermal chimnneys. This organism withstands 5 kGy irradiation without any detectable lethality and thus it is one of the most radioresistant organisms known amongst the Archaea. Complete sequencing, assembly and annotation was performed at LGA, Orsay. Complete proteome analysis performed in collaboration with CEA, DSV, IBEB Laboratoire de Biochimie des Systèmes Perturbés, Bagnols-sur-Cèze, F-30207, France. Transcriptonal response to Cadmium and gamma-irradiation analysis performed at LGA.


LBMGE has been directly involved in genome sequencing of these two hyperthermophilic archeons during the past years.
Both strains are widely studied model microorganisms in various fields of investigation such as studies on adaptation to extreme temperatures and pH growth conditions, aerobic and anaerobic sulfur metabolism analysis, molecular deciphering of DNA replication mecanism in archaea, phylogeny and rooting of the tree of life, comparative genomics of closely related strains and many others.

This page provides direct links to genomic annotation databases for P. abyssi and S. solfataricus, bacteriophage T5 and T gammatolerans
All databases on this site are maintained by Y. Zivanovic.

 



Some references related to these projects:

 P. abyssi:
  • Lopez, P., Philippe, H, Myllykallio, H. and Forterre, P.
    Identification Of Putative Chromosomal Origins Of Replication In Archaea.
    Mol. Microbiol. 32, 883-886 (1999)
  • H. Myllykallio, P. Lopez, P. López-García, R. Heilig, W. Saurin, Y. Zivanovic, H. Philippe, and P. Forterre
    Bacterial Mode Of Replication With An Eukaryotic-Like Machinery In A Hyperthermophilic Archaeon
    Science, 288, 2212-2215 (2000)
  • O. Matte-Tailliez, Y. Zivanovic and P. Forterre
    Mining archaeal proteomes for eukaryotic proteins with novel functions: the PACE case
    Trends Genet. 16, 533,536 (2000) link on this site : PACE Proteins
  • Zivanovic, Y., Myllykallio, H. and Forterre, P.
    Bacterial genomic reorganization upon DNA replication.
    Science 292, 803a (2001)
  • Zivanovic Y., Lopez P, Philippe P and Forterre P
    Pyrococcus genome comparison evidences chromosome shuffling-driven evolution.
    Nucleic Acids Research, 30, 2656-62 (2002)
  • Cohen G., Barbe V., Flament D., Galperin M., Heilig R., Lecompte O., Poch O., Prieur D., QuŽrellou J., Ripp R., Thierry J., Van J. der Oost, Weissenbach J., Zivanovic Y. and Forterre P.
    An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi
    Mol. Microbiol. in Press (2002)

 

S. solfataricus:

  • She, Q., Singh, R.K., Confalonieri, F., Zivanovic, Y., Gordon, P., Allard, G., Awayez, M.J., Chan-Weiher, C-Y., Clausen, I.G., Curtis, B., De Moors, A., Erauso, G., Gordon, P.M.K., Heikamp de Jong, I., Jeffries, A., Kozera, C.J., Medina, N., Peng, X., Phan, H., Redder, P., Schenk, M.E., Theriault, C., Tolstrup, N., Charlebois, R.L.M., Doolittle, W.F., Duguet, M., Gaasterland, T., Garrett, R.A., Ragan, M., Sensen, C.W. and Van der Oost, J.
    The genome sequence of the crenarchaeon Sulfolobus solfataricus P2.
    Proc. Natl. Acad. Sci. USA 98, 7835-7840. (2001)
  • Forterre, P., Confalonieri, F. and Knapp, S.
    Identification Of The Gene Encoding Archaeal-Specific Dna Binding Proteins Of The Sac10b Family
    Mol. Microbiol. 32, 669-670 (1999)
  • R. Charlebois, R. Singh, C.C.-Y. Chan-Weilher, G. Allard, C. Chow, F.,Confalonieri, B. Curtis, M. Duguet, D. Faguy, T. Gaasterland, R. Garrett, A.,Jeffries, C. Kozera, N. Kushwala, E. Lafleur, N. Medina, X. Peng, S.,Penny,Q. She,A. Stjohn, J. Van Der Oost, F. Young, Y. Zivanovic, W.,Doolittle, M. Ragan & C. Sensen.
    Gene Content and Organization Of A 281 Kbp Contig From The Genome Of The Extremely Thermophilic Archaeon Sulfolobus Solfataricus P2.
    Genome 43, 116-36 (1999)
  • Q She, F Confalonieri, Y Zivanovic, N Medina, A Billault, M J. Awayez, H P, Thi-Hgoc, B-T T Pham, J Van Der Oost, M Duguet, and R Garrett
    A Bac Library and Paired-PCR Approach To Mapping and Completing The Genome Sequence Of Sulfolobus Solfataricus P2: An EC Perspective
    DNA Seq., 11(3-4),183-92. (2000)
  • Brügger K., Redder P., She Q., Confalonieri F., Zivanovic Y. and Garrett R. A.
    Mobile elements in archaeal genomes
    FEMS Microb. Lett., 206, 131-141 (2002)

Kluyveromyces lactis:

  • Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuvéglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisramé A, Boyer J, Cattolico L, Confanioleri F, De Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wésolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic Y, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet JL.
    Genome evolution in yeasts.
    Nature. 2004 Jul 1;430(6995):35-44.
  • Zivanovic Y, Wincker P, Vacherie B, Bolotin-Fukuhara M, Fukuhara H.
    Complete nucleotide sequence of the mitochondrial DNA from Kluyveromyces lactis.
    FEMS Yeast Res. 2005 Feb;5(4-5):315-22.
Thermococcus gammatolerans:
  • Recovery of ionizing-radiation damage after high doses of gamma ray in the hyperthermophilic archaeon Thermococcus gammatolerans.
    Tapias A, Leplat C, Confalonieri F.
    Extremophiles. 2009
  • Genome-wide transcriptional response of the archaeon Thermococcus gammatolerans to Cadmium
    A Lagorce, A Fourcans, M Dutertre, B Bouissiere, P Forterre, X Gidrol, Y Zivanovic And F Confalonieri
    Submitted to publication
  • Genome analysis and genome-scale proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea.
    Y. Zivanovic, J. Armengaud, A. Lagorce, C. Leplat, P Guerin, M. Dutertre, V. Anthouard, P. Forterre, P. Winker, and F. Confalonieri
    Submitted to publication