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INSTITUT DE MICROBIOLOGIE DE LA MEDITERRANEE UNIVERSITE DE LA MEDITERRANEE
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Abergel Chantal


Directeur de Recherche CNRS

Tel : +33 4 91 82 54 22

E-mail:Chantal.Abergel@igs.cnrs-mrs.fr

Sujets:

The structural team is currently focusing on large DNA viruses such as Mimivirus and PBCV. A comprehensive structural and functional study of selected genes products was initiated, as they may hold important clues about the origin of DNA viruses and on the mecanisms used by viruses to highjack the host cell to its own benefit.

We first focused on genes seen for the first time in a virus such as enzymes involved in translation and DNA metabolism. We are now interested in genes conserved in large DNA viruses. Analyzing them is a great opportunity to discover new “entry” points (molecular switches) in the control of cell death (apoptosis), cell division (DNA replication), or bacterial infection (phagocytosis, cell trafficking). This in turn might lead to innovative therapeutic approaches.

We produce our protein targets using a standard protocol based on incomplete factorial design (Abergel et al., 2003, J Struct Funct Genomics ; 4:141-57). Activity measurement are performed using spectroscopique techniques every time possible or in collaboration with specialized laboratories. For each project we try to solve the structure of the protein of interest alone and in complex with predicted ligands or interactors.

The next step of our study is to produce these genes in vivo, study the physiological impact of their expression as well as their localization depending on the infectious stage of the host.



Publications:
  1. Legendre M, Audic S, Poirot O, Hingamp P, Seltzer V, Byrne D, Lartigue A, Lescot M, Bernadac A, Poulain J, Abergel C, Claverie JM (2010) mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus. Genome Res. ; :,2010 Apr 1 - PMID:20360389

  2. Parakkottil-Chothi M, Duncan GA, Armirotti A, Abergel C, Gurnon JR, Van Etten JL, Bernardi C, Damonte G, Tonetti M (2010) Identification of an L-rhamnose synthetic pathway in two nucleo-cytoplasmic large dna viruses. J Virol. ; :,2010 Jun 10 - PMID:20538863

  3. Claverie JM, Abergel C (2010) Mimivirus: the emerging paradox of quasi-autonomous viruses. Trends Genet. ; :,2010 Aug 7 - PMID:20696492

  4. Trapani S, Schoehn G, Navaza J, Abergel C (2010) Macromolecular crystal data phased by negative-stained electron-microscopy reconstructions. Acta Crystallogr D Biol Crystallogr.66 ;Pt 5:514-21,2010 May  - PMID:20445226

  5. Byrne D, Grzela R, Lartigue A, Audic S, Chenivesse S, Encinas S, Claverie JM, Abergel C (2009) The polyadenylation site of Mimivirus transcripts obeys a stringent "hairpin rule" Genome Res. ; :,2009 Apr 29 - PMID:19403753

  6. Claverie JM, Grzela R, Lartigue A, Bernadac A, Nitsche S, Vacelet J, Ogata H, Abergel C (2009) Mimivirus&Mimiviridae: giant viruses with an increasing number of potential hosts, including corals and sponges. J Invertebr Pathol. ; :,2009 May 17 - PMID:19457438

  7. Jeudy S, Lartigue A, Claverie JM, Abergel C (2009) Dissecting the unique nucleotide specificity of Mimivirus nucleoside diphosphate kinase. J Virol. ; :,2009 May 13 - PMID:19439473

  8. Claverie JM, Abergel C (2009) Mimivirus and its Virophage. Annu Rev Genet. ; :,2009 Aug 4 - PMID:19653859

  9. Claverie JM, Abergel C, Ogata H (2009) Mimivirus. Curr Top Microbiol Immunol.328 ;:89-121,2009  - PMID:19216436

  10. Vallenet D, Nordmann P, Barbe V, Poirel L, Mangenot S, Bataille E, Dossat C, Gas S, Kreimeyer A, Lenoble P, Oztas S, Poulain J, Segurens B, Robert C, Abergel C, Claverie JM, Raoult D, Médigue C, Weissenbach J, Cruveiller S (2008) Comparative analysis of Acinetobacters: three genomes for three lifestyles. PLoS ONE.3 ;3:e1805,2008  - PMID:18350144

  11. Santini S, Monchois V, Mouz N, Sigoillot C, Rousselle T, Claverie JM, Abergel C (2008) Structural characterization of CA1462, the Candida albicans thiamine pyrophosphokinase. BMC Struct Biol.8 ;:33,2008  - PMID:18652651

  12. Abergel C, Rudinger-Thirion J , Giegé R, Claverie JM (2007) Virus-Encoded Aminoacyl-tRNA Synthetases: Structural and Functional Characterization of Mimivirus TyrRS and MetRS. J Virol.81 ;22:12406-17,2007 Nov - PMID:17855524

  13. Abergel C, Monchois V, Byrne D, Chenivesse S, Lembo F, Lazzaroni JC, Claverie JM (2007) Structure and evolution of the Ivy protein family, unexpected lysozyme inhibitors in Gram-negative bacteria. Proc Natl Acad Sci U S A.104 ;15:6394-9,2007 Apr 10 - PMID:17405861

  14. Jeudy S, Claverie JM, Abergel C (2006) The nucleoside diphosphate kinase from mimivirus: a peculiar affinity for deoxypyrimidine nucleotides. J Bioenerg Biomembr.38 ;3-4:247-54,2006 Aug - PMID:16957983

  15. Trapani S, Abergel C, Gutsche I, Horcajada C, Fita I, Navaza J (2006) Combining experimental data for structure determination of flexible multimeric macromolecules by molecular replacement. Acta Crystallogr D Biol Crystallogr.62 ;Pt 5:467-75,2006 May - PMID:16627938

  16. Claverie JM, Ogata H, Audic S, Abergel C, Suhre K, Fournier PE (2006) Mimivirus and the emerging concept of "giant" virus. Virus Res.117 ;1:133-44,2006 Apr - PMID:16469402

  17. Fournier PE, Vallenet D, Barbe V, Audic S, Ogata H, Poirel L, Richet H, Robert C, Mangenot S, Abergel C, Nordmann P, Weissenbach J, Raoult D, Claverie JM (2006) Comparative genomics of multidrug resistance in Acinetobacter baumannii. PLoS Genet.2 ;1:e7,2006 Jan - PMID:16415984

  18. Jeudy S, Stelter M, Coutard B, Kahn R, Abergel C (2005) Preliminary crystallographic analysis of the Escherichia coli YeaZ protein using the anomalous signal of a gadolinium derivative. Acta Crystallogr Sect F Struct Biol Cryst Commun.61 ;Pt 9:848-51,2005 Sep 1 - PMID:16511176

  19. Ogata H, Abergel C, Raoult D, Claverie JM (2005) Response to Comment on The 1.2-Megabase Genome Sequence of Mimivirus Science, Vol 308, Issue 5725, 1114 Science, Vol 308, Issue 5725, 1114,2005 Jun

  20. Jeudy S, Coutard B, Lebrun R, Abergel C (2005) Acanthamoeba polyphaga mimivirus NDK: preliminary crystallographic analysis of the first viral nucleoside diphosphate kinase. Acta Crystallogr Sect F Struct Biol Cryst Commun.61 ;Pt 6:569-72,2005 Jun 1 - PMID:16511098

  21. Malarte G, Leroy G, Lojou E, Abergel C, Bruschi M, Giudici-Orticoni MT. (2005) Insight into Molecular Stability and Physiological Properties of the Diheme Cytochrome CYC(41) from the Acidophilic Bacterium Acidithiobacillus ferrooxidans. Biochemistry ;44(17):6471-81,2005 May 3 - PMID:15850381

  22. Abergel C, Chenivesse S, Byrne D, Suhre K, Arondel V, Claverie JM (2005) Mimivirus TyrRS: preliminary structural and functional characterization of the first amino-acyl tRNA synthetase found in a virus. Acta Crystallogr Sect F Struct Biol Cryst Commun.61 ;Pt 2:212-5,2005 Feb 1 - PMID:16510997

  23. Raoult D, Audic S, Robert C, Abergel C, Renesto P, Ogata H, La Scola B, Suzan M, Claverie JM. (2004) The 1.2-Mb Genome Sequence of Mimivirus. Science. 2004 Nov 19 ;306(5700):1344-50. Epub 2004 Oct 14. - PMID:15486256

  24. Abergel C. (2004) Spectacular improvement of X-ray diffraction through fast desiccation of protein crystals. Acta Crystallogr D Biol Crystallogr. 2004 Aug ;60(Pt 8):1413-6. - PMID:15272164

  25. Poirot O, Suhre K, Abergel C, O'Toole E, Notredame C (2004) 3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment. Nucleic Acids Res. 2004 Jul 1 ;32(Web Server issue):W37-40. - PMID:15215345

  26. Claude JB, Suhre K, Notredame C, Claverie JM, Abergel C (2004) CaspR: a web-server for automated molecular replacement using homology modelling. Nucleic Acids Res. 2004 Jul 1 ;32(Web Server issue):W606-9. - PMID:15215460

  27. Enault F, Suhre K, Poirot O, Abergel C, Claverie JM (2004) Phydbac2: improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis Nucleic Acids Res. 2004 Jul 1 ;32(Web Server issue):W336-9. - PMID:15215406

  28. O'Sullivan O, Suhre K, Abergel C, Higgins DG, Notredame C. (2004) 3DCoffee: combining protein sequences and structures within multiple sequence alignments. J Mol Biol. 2004 Jul 2 ;340(2):385-95. - PMID:15201059

  29. Enault F, Suhre K, Poirot O, Abergel C, Claverie JM (2003) Phydbac (phylogenomic display of bacterial genes): An interactive resource for the annotation of bacterial genomes. Nucleic Acids Res 2003 Jul 1 ;31(13):3720-2. - PMID:12824402

  30. Abergel C, Nitschke W, Malarte G, Bruschi M, Claverie JM, Giudici-Orticoni MT (2003) The structure of Acidithiobacillus ferrooxidans c(4)-cytochrome: a model for complex-induced electron transfer tuning. Structure (Camb) 2003 May ;11(5):547-55. - PMID:12737820

  31. Abergel C, Coutard B, Byrne D, Chenivesse S, Claude JB, Deregnaucourt C, Fricaux T, Gianesini-Boutreux C, Jeudy S, Lebrun R, Maza C, Notredame C, Poirot O, Suhre K, Varagnol M, Claverie JM. (2003) Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets. J Struct Funct Genomics. 2003 ;4(2-3):141-57. - PMID:14649299

  32. Notredame C. and Abergel C. (2003) Using T-Coffee to assess the reliability of multiple sequence alignments. Bioinformatics and Genomes (M.A. Andrade, ed.) Horizon Scientific Press, Wymondham,UK, pp 27-49

  33. Claverie JM, Monchois V, Audic S, Poirot O, Abergel C (2002) In Search of new anti-bacterial target genes: a comparative/structural genomics approach. Comb Chem High Throughput Screen 2002 Nov ;5(7):511-22. - PMID:12470264

  34. Ogata H, Audic S, Abergel C, Fournier PE, Claverie JM (2002) Protein coding palindromes are a unique but recurrent feature in Rickettsia. Genome Res 2002 May ;12(5):808-16. - PMID:11997347

  35. Monchois V., Vincentelli R., Abergel C., Deregnaucourt C., Claverie J.-M. and Monchois V. (2002) Proficient target selection in structural genomic by In vitro protein expression on Gateway recombination plasmids. Cell-Free Translation Systems (Spirin Ed.) Springer Verlag : () 197- 202.

  36. Claverie JM, Abergel C, Audic S, Ogata H (2001) Recent advances in computational genomics. Pharmacogenomics 2001 Nov ;2(4):361-72. - PMID:11722286

  37. Maurin M, Abergel C, Raoult D (2001) DNA gyrase-mediated natural resistance to fluoroquinolones in Ehrlichia spp. Antimicrob Agents Chemother 2001 Jul ;45(7):2098-105. - PMID:11408229

  38. Monchois V, Abergel C, Sturgis J, Jeudy S, Claverie JM (2001) Escherichia coli ykfE ORFan gene encodes a potent inhibitor of C-type lysozyme. J Biol Chem 2001 May 25 ;276(21):18437-41. - PMID:11278658

  39. Abergel C, Walburger A, Chenivesse S, Lazdunski C (2001) Crystallization and preliminary crystallographic study of the peptidoglycan-associated lipoprotein from Escherichia coli. Acta Crystallogr D Biol Crystallogr 2001 Feb ;57(Pt 2):317-9. - PMID:11173492

  40. Abergel C, Abousalham A, Chenivesse S, Riviere M, Moustacas-Gardies AM, Verger R (2001) Crystallization and preliminary crystallographic study of a recombinant phospholipase D from cowpea (Vigna unguiculata L. Walp). Acta Crystallogr D Biol Crystallogr 2001 Feb ;57(Pt 2):320-2. - PMID:11173493

  41. Abergel C, Journet L, Chenivesse S, Gavioli M, Lloubes R (2001) Crystallization and preliminary crystallographic study of the periplasmic domain of the Escherichia coli TolR protein. Acta Crystallogr D Biol Crystallogr 2001 Feb ;57(Pt 2):323-5. - PMID:11173494

  42. Abergel C, Monchois V, Chenivesse S, Jeudy S, Claverie JM (2000) Crystallization and preliminary crystallographic study of b0220, an 'ORFan' protein of unknown function from Escherichia coli. Acta Crystallogr D Biol Crystallogr 2000 Dec ;56 Pt 12:1694-5. - PMID:11092949

  43. Abergel C, Bruschi M, Chenivesse S, Guasco S, Leroy G, Guidici-Orticoni MT (2000) Crystallization and preliminary crystallographic study of an extremophile cytochrome c4 from Thiobacillus ferrooxidans. Acta Crystallogr D Biol Crystallogr 2000 Nov ;56 ( Pt 11):1432-3. - PMID:11053842

  44. Abergel C, Bouveret E, Claverie JM, Brown K, Rigal A, Lazdunski C, Benedetti H (1999) Structure of the Escherichia coli TolB protein determined by MAD methods at 1.95 A resolution. Structure Fold Des 1999 Oct 15 ;7(10):1291-300. - PMID:10545334

  45. Abergel C, Robertson DL, Claverie JM (1999) Hidden dUTPase sequence in human immunodeficiency virus type 1 gp120. J Virol 1999 Jan ;73(1):751-3. - PMID:9847382

  46. Claverie J.-M., Lopez F. and Abergel C (1999) A New Strategy and Software System for the Design of Functional Signatures in Protein Sequences, in Perspective in Structural Biology. Indian Acad. Sciences and the Universities Press,Hyderabad, India.(M. Vijayan, ed.). Chap. 51 : () 680- 700.

  47. Abergel C, Chavrier P, Claverie JM (1998) Triple association of CDC25-, Dbl- and Sec7-related domains in mammalian guanine-nucleotide-exchange factors. Trends Biochem Sci 1998 Dec ;23(12):472-3. - PMID:9868368

  48. Abergel C, Rigal A, Chenivesse S, Lazdunski C, Claverie JM, Bouveret E, Benedetti H (1998) Crystallization and preliminary crystallographic study of a component of the Escherichia coli tol system: TolB. Acta Crystallogr D Biol Crystallogr 1998 Jan 1 ;54 ( Pt 1):102-4. - PMID:9761825

  49. Audic S, Lopez F, Claverie JM, Poirot O, Abergel C (1997) SAmBA: an interactive software for optimizing the design of biological macromolecules crystallization experiments. Proteins 1997 Oct ;29(2):252-7. - PMID:9329089

  50. Bruschi M, Woudstra M, Guigliarelli B, Asso M, Lojou E, Petillot Y, Abergel C (1997) Biochemical and spectroscopic characterization of two new cytochromes isolated from Desulfuromonas acetoxidans. Biochemistry 1997 Sep 2 ;36(35):10601-8. - PMID:9271490

  51. Padlan EA, Abergel C, Tipper JP (1995) Identification of specificity-determining residues in antibodies. FASEB J 1995 Jan ;9(1):133-9. - PMID:7821752

  52. Abergel C, Tipper JP, Padlan EA (1994) Structural significance of sequence variability in antibody complementarity-determining regions. Res Immunol 1994 Jan ;145(1):49-53. - PMID:8008969

  53. Abergel C, Padlan EA, Kashmiri SV, Milenic D, Calvo B, Schlom J (1993) Crystallographic studies and primary structure of the antitumor monoclonal CC49 Fab'. Proteins 1993 Dec ;17(4):438-43. - PMID:8108385

  54. Moreau H, Abergel C, Carriere F, Ferrato F, Fontecilla-Camps JC, Cambillau C, Verger R (1992) Isoform purification of gastric lipases. Towards crystallization. J Mol Biol 1992 May 5 ;225(1):147-53. - PMID:1583687

  55. Abergel C, Claverie JM (1991) A strong propensity toward loop formation characterizes the expressed reading frames of the D segments at the Ig H and T cell receptor loci. Eur J Immunol 1991 Dec ;21(12):3021-5. - PMID:1660812

  56. Abergel C, Moulard M, Moreau H, Loret E, Cambillau C, Fontecilla-Camps JC (1991) Systematic use of the incomplete factorial approach in the design of protein crystallization experiments. J Biol Chem 1991 Oct 25 ;266(30):20131-8. - PMID:1939074

  57. Devaux C, Defendini ML, Alzari PM, Abergel C, Granier C, Fontecilla-Camps JC, Alzar PM (1991) Crystallization and preliminary X-ray diffraction data of the Fab fragment of a monoclonal antibody against apamin, a bee venom neurotoxin. FEBS Lett 1991 Jul 29 ;286(1-2):64-6. - PMID:1747157

  58. Abergel C, Martinez C, Fontecilla-Camps J, Cambillau C, de Geus P, Lauwereys M (1990) Crystallization and preliminary X-ray study of a recombinant cutinase from Fusarium solani pisi. J Mol Biol 1990 Sep 20 ;215(2):215-6. - PMID:2213880

  59. Abergel C, Loret E, Rochat H, Fontecilla-Camps JC (1990) Crystallization and preliminary X-ray study of AaH IT2, and insect-specific toxin from the scorpion Androctonus australis Hector. J Mol Biol 1990 Aug 5 ;214(3):637-8. - PMID:2388262

  60. Bourne Y, Abergel C, Cambillau C, Frey M, Rouge P, Fontecilla-Camps JC (1990) X-ray crystal structure determination and refinement at 1.9 A resolution of isolectin I from the seeds of Lathyrus ochrus. J Mol Biol 1990 Jul 20 ;214(2):571-84. - PMID:2380988

  61. Abergel C, Loret E, Claverie JM (1989) Conformational analysis of T immunogenic peptides by circular dichroism spectroscopy. Eur J Immunol 1989 Oct ;19(10):1969-72. - PMID:2511030