Boosting research on extremophiles with next-generation proteomics and metaproteomics
Résumé
Next-generation proteomics allows quickly identifying and quantifying the whole set of proteins of any microorganism. Comparative studies after irradiation of radiotolerant microorganisms point at the key players involved in DNA repair. For carrying out this methodology, a high-quality genome annotation is a crucial starting point. Proteogenomics, the alliance of proteomics and genomics, became important as new genes and regulatory mechanisms can be fully uncovered. Metaproteomics characterizes complex microbial communities as a whole and is highly complementary to metagenomics. We applied next-generation proteomics on Deinococcus deserti VCD115, a bacterium from the Thermus-Deinococcus phylum that was isolated from surface sands from Sahara. This microorganism exhibits an astonishing ability to withstand desiccation and ionizing radiations. We sequenced and annotated its genome by proteogenomics. We investigated the existence of remaining unannotated genes, defined properly translational start sites, and listed post-translational modifications at the N-termini of proteins. We observed the unusual use of non-canonical codons in Deinococcaceae for the translation of specific transcripts and an unexpected large proportion of leaderless mRNAs. Furthermore, we discovered the prominent use of acetylation at the N-termini of proteins, as well as a specific pattern at most translational starts, a common trait for all the order Deinococcaceae which is not conserved in the Thermus order. We also developed an original metaproteomics strategy in order to characterize the microorganisms present in extreme environments consisting in biofilms and water samples from spent nuclear fuel pools. Identification of peptide sequences by high resolution tandem mass spectrometry is helpful for defining the taxa present in these samples and characterizing their main molecular processes. Moreover, this new concept is of prime interest for directing screening and isolation. Its perspectives will be drawn and illustrated with several examples. Références: Armengaud J (2016) Next-generation proteomics faces new challenges in environmental biotechnology. Curr Opin Biotechnol. 38:174-82. Pible O, Armengaud J (2015) Improving the quality of genome, protein sequence, and taxonomy databases: a prerequisite for microbiome meta-omics 2.0. Proteomics. 15:3418-23. de Groot A, Roche D, Fernandez B, Ludanyi M, Cruveiller S, Pignol D, Vallenet D, Armengaud J, Blanchard L (2014) RNA sequencing and proteogenomics reveal the importance of leaderless mRNAs in the radiation-tolerant bacterium Deinococcus deserti. Genome Biol Evol. 6:932-48. Baudet M, Ortet P, Gaillard JC, Fernandez B, Guérin P, Enjalbal C, Subra G, de Groot A, Barakat M, Dedieu A, Armengaud J (2010) Proteomics-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons. Mol Cell Proteomics. 9:4
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