High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.

Détails

Ressource 1Télécharger: BIB_23EB15A4F7BE.P001.pdf (1609.72 [Ko])
Etat: Public
Version: de l'auteur
ID Serval
serval:BIB_23EB15A4F7BE
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Institution
Titre
High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.
Périodique
PloS one
Auteur(s)
Greub G., Kebbi-Beghdadi C., Bertelli C., Collyn F., Riederer B.M., Yersin C., Croxatto A., Raoult D.
ISSN
1932-6203 (Electronic)
ISSN-L
1932-6203
Statut éditorial
Publié
Date de publication
23/12/2009
Peer-reviewed
Oui
Volume
4
Numéro
12
Pages
e8423
Langue
anglais
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: epublish
Résumé
With the availability of new generation sequencing technologies, bacterial genome projects have undergone a major boost. Still, chromosome completion needs a costly and time-consuming gap closure, especially when containing highly repetitive elements. However, incomplete genome data may be sufficiently informative to derive the pursued information. For emerging pathogens, i.e. newly identified pathogens, lack of release of genome data during gap closure stage is clearly medically counterproductive.
We thus investigated the feasibility of a dirty genome approach, i.e. the release of unfinished genome sequences to develop serological diagnostic tools. We showed that almost the whole genome sequence of the emerging pathogen Parachlamydia acanthamoebae was retrieved even with relatively short reads from Genome Sequencer 20 and Solexa. The bacterial proteome was analyzed to select immunogenic proteins, which were then expressed and used to elaborate the first steps of an ELISA.
This work constitutes the proof of principle for a dirty genome approach, i.e. the use of unfinished genome sequences of pathogenic bacteria, coupled with proteomics to rapidly identify new immunogenic proteins useful to develop in the future specific diagnostic tests such as ELISA, immunohistochemistry and direct antigen detection. Although applied here to an emerging pathogen, this combined dirty genome sequencing/proteomic approach may be used for any pathogen for which better diagnostics are needed. These genome sequences may also be very useful to develop DNA based diagnostic tests. All these diagnostic tools will allow further evaluations of the pathogenic potential of this obligate intracellular bacterium.

Mots-clé
Bacterial Proteins/genetics, Bacterial Proteins/immunology, Blotting, Western, Chlamydiales/genetics, Chlamydiales/pathogenicity, Electrophoresis, Gel, Two-Dimensional, Enzyme-Linked Immunosorbent Assay, Gene Expression Regulation, Bacterial, Genome, Bacterial/genetics, High-Throughput Screening Assays/methods, Humans, Proteomics/methods, Recombinant Proteins/metabolism, Sequence Analysis, DNA/methods, Time Factors, Virulence/genetics
Pubmed
Web of science
Open Access
Oui
Création de la notice
12/01/2010 17:56
Dernière modification de la notice
20/08/2019 14:01
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