Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets

Chantal Abergel, Bruno Coutard, Deborah Byrne, Sabine Chenivesse, Jean Baptiste Claude, Céline Deregnaucourt, Thierry Fricaux, Celine Gianesini-Boutreux, Sandra Jeudy, Régine Lebrun, Caroline Maza, Cédric Notredame, Olivier Poirot, Karsten Suhre, Majorie Varagnol, Jean Michel Claverie

Research output: Contribution to journalArticle

56 Citations (Scopus)

Abstract

With more than 100 antibacterial drugs at our disposal in the 1980's, the problem of bacterial infection was considered solved. Today, however, most hospital infections are insensitive to several classes of antibacterial drugs, and deadly strains of Staphylococcus aureus resistant to vancomycin - the last resort antibiotic - have recently begin to appear. Other life-threatening microbes, such as Enterococcus faecalis and Mycobacterium tuberculosis are already able to resist every available antibiotic. There is thus an urgent, and continuous need for new, preferably large-spectrum, antibacterial molecules, ideally targeting new biochemical pathways. Here we report on the progress of our structural genomics program aiming at the discovery of new antibacterial gene targets among evolutionary conserved genes of uncharacterized function. A series of bioinformatic and comparative genomics analyses were used to identify a set of 221 candidate genes common to Gram-positive and Gram-negative bacteria. These genes were split between two laboratories. They are now submitted to a systematic 3-D structure determination protocol including cloning, protein expression and purification, crystallization, X-ray diffraction, structure interpretation, and function prediction. We describe here our strategies for the 111 genes processed in our laboratory. Bioinformatics is used at most stages of the production process and out of 111 genes processed - and 17 months into the project - 108 have been successfully cloned, 103 have exhibited detectable expression, 84 have led to the production of soluble protein, 46 have been purified, 12 have led to usable crystals, and 7 structures have been determined.

Original languageEnglish
Pages (from-to)141-157
Number of pages17
JournalJournal of Structural and Functional Genomics
Volume4
Issue number2-3
DOIs
Publication statusPublished - 2003
Externally publishedYes

Fingerprint

Microbial Genes
Genomics
Genes
Pseudogenes
Computational Biology
Bioinformatics
Anti-Bacterial Agents
Enterococcus faecalis
Vancomycin
Cross Infection
Crystallization
Gram-Negative Bacteria
Mycobacterium tuberculosis
Bacterial Infections
X-Ray Diffraction
Pharmaceutical Preparations
Staphylococcus aureus
Organism Cloning
Proteins
Cloning

Keywords

  • Anti-bacterial
  • Bioinformatics
  • Comparative Genomics
  • Escherichia coli
  • Structural Genomics

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Genetics

Cite this

Abergel, C., Coutard, B., Byrne, D., Chenivesse, S., Claude, J. B., Deregnaucourt, C., ... Claverie, J. M. (2003). Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets. Journal of Structural and Functional Genomics, 4(2-3), 141-157. https://doi.org/10.1023/A:1026177202925

Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets. / Abergel, Chantal; Coutard, Bruno; Byrne, Deborah; Chenivesse, Sabine; Claude, Jean Baptiste; Deregnaucourt, Céline; Fricaux, Thierry; Gianesini-Boutreux, Celine; Jeudy, Sandra; Lebrun, Régine; Maza, Caroline; Notredame, Cédric; Poirot, Olivier; Suhre, Karsten; Varagnol, Majorie; Claverie, Jean Michel.

In: Journal of Structural and Functional Genomics, Vol. 4, No. 2-3, 2003, p. 141-157.

Research output: Contribution to journalArticle

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', Journal of Structural and Functional Genomics, vol. 4, no. 2-3, pp. 141-157. https://doi.org/10.1023/A:1026177202925
Abergel, Chantal ; Coutard, Bruno ; Byrne, Deborah ; Chenivesse, Sabine ; Claude, Jean Baptiste ; Deregnaucourt, Céline ; Fricaux, Thierry ; Gianesini-Boutreux, Celine ; Jeudy, Sandra ; Lebrun, Régine ; Maza, Caroline ; Notredame, Cédric ; Poirot, Olivier ; Suhre, Karsten ; Varagnol, Majorie ; Claverie, Jean Michel. / Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets. In: Journal of Structural and Functional Genomics. 2003 ; Vol. 4, No. 2-3. pp. 141-157.
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