Life Sciences Division

 

 

 

 

Major research topics

 

 

I. Cellular response to oxidative stress and toxic metals

 

Any disturbance in the environment of one cell results in profound modifications of its physiology. The 'omics' approaches (proteomics, transcriptomics, metabolomics) are perfectly suited to the global study of these responses and to the understanding of their dynamics. We rely on these techniques to characterize the cellular response to oxidative stress and exposure to various toxic metals in the yeast Saccharomyces cerevisiae (Vido et al., 2001; Fauchon et al., 2002; Lafaye et al., 2005; Molin et al., 2007; Pereira et al., 2008). In addition, we combine biochemistry and cell biology approaches to study signal transduction events leading to the activation of transcription factors, such as Msn2 and Maf1 (Boisnard et al., 2009).

 

 

Figure 1 : Using 2D-gels, we compare the proteomes of yeast cells grown in different conditions. Here, comparison between growth in absence (above) or presence (below) of chromate.

 

 

 

 

II. Origins and consequences of protein carbonylations

 

In proteins, oxidation of side chain residues leads to the formation of oxidized methionines, non-physiological disulfide bonds and to the appearance of carbonyl groups. This last modification is irreversible and can solely be suppressed through proteolysis. Relying on the expertise of the laboratory in both biochemistry and protein identification by 2D-page, we are initiating a project that aims at understanding the phenomena responsible for the accumulation of carbonylated proteins during cellular aging.

 

 

 

 

 

Figure 2 : After a derivatization step, carbonylated proteins from whole-cell extracts are detected by Western-blot. H2O2 addition in growth medium results in increased carbonylation of proteins.

 

 

 

III. Study and mathematical modeling of the yeast sulfur metabolism

 

We have shown that cadmium causes a strong redirection of sulfur metabolites toward the synthesis of glutathione, which traps the metal, thus leading to cell detoxification (Fauchon et al., 2002 ; Lafaye et al., 2005); whereas chromate triggers a cellular response similar to sulfur starvation (Pereira et al., 2008). To grasp the complexity of these metabolic responses, our approach is based on the construction and utilization of mathematical models of this metabolic pathway. These models are nurtured by the experiments performed in the lab, especially metabolomic, proteomic and transcriptomic experiments (Baudouin-Cornu et al., 2009).

 

 

 

Figure 3 : Schematic representation of Saccharomyces cerevisiae sulfur metabolism.

 

 

IV. Computational biology for integration of post-genomic data

 

Upon exposure to oxidative stress or toxic metals, cell survival requires the engagement of key biological networks (regulatory networks, signal transduction pathways, protein-protein interactions, metabolic pathways). To fully exploit the results of high-throughput experiments, we develop a formal framework for describing and studying the dynamics of these networks and their interconnections. We also develop dedicated inference algorithms (Michaut et al., 2008), especially for less annotated organisms such as the cyanobacteria Synechocystis (in collaboration with the F. Chauvat, LBI).

 

 

 

Figure 4 : Bioinformatics sheds a new light on biological networks and their relationships.

 

 

 

 

Baudouin-Cornu P, Thomas D.  (2007). Evolutionary biology: oxygen at life's boundaries. Nature. 445, 35-36.

Baudouin-Cornu P, Thomas D.  (2007). On the role played by oxygen in evolution. Med Sci (Paris). 23, 255-257.

Houot L, Floutier M, Marteyn B, Michaut M, Picciocchi A, Legrain P, Aude JC, Cassier-Chauvat C, Chauvat F. (2007).Cadmium triggers an integrated reprogramming of the metabolism of Synechocystis PCC6803, under the control of the Slr1738 regulator. BMC Genomics. 8: 350.

Michaut M, Kerrien S, Montecchi-Palazzi L, Chauvat F, Cassier-Chauvat C, Aude JC, Legrain P, Hermjakob H. (2007).Inference and validation of Synechocystis protein interaction network using orthology. JOBIM. 229-234.

Molin M, Renault JP, Lagniel G, Pin S, Toledano M, Labarre J.  (2007). Ionizing radiation induces a Yap1-dependent peroxide stress response in yeast. Free Radic Biol Med. 43, 136-144.

Thorsen M, Lagniel G, Kristiansson E, Junot C, Nerman O, Labarre J, Tamas MJ.  (2007). Quantitative transcriptome, proteome and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiol Genomics. 30, 35-43.

Baudouin-Cornu P, Labarre J.  (2006). Regulation of the cadmium stress response through SCF-like ubiquitin ligases: comparison between Saccharomyces cerevisiae, Schizosaccharomyces pombe and mammalian cells Biochimie. 88, 1673-1685.

Baudouin-Cornu, P. and Bragg J.G. (2006) Analyzing proteomic, genomic and transcriptomic elemental compositions to uncover the intimate evolution of biopolymers. In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics (ed. L. Jorde, P. Little, M. Dunn, and S. Subramaniam). John Wiley & Sons

Tamás M., Labarre J., Toledano M. B. and Wysocki R. (2006) Mechanisms of toxic metal tolerance in yeast. In Topics in Current Genetics. Molecular Biology of Metal Homeostasis and Detoxification – From Microbes to Man. Eds Markus J. Tamas and Enrico Martinoia. Springer P395-435.

Lafaye A, Labarre J, Tabet JC, Ezan E, Junot C.  (2005). Liquid Chromatography-Mass Spectrometry and (15)N Metabolic Labeling for Quantitative Metabolic Profiling. Anal Chem. 77, 2026-2033.

Lafaye A, Junot C, Pereira Y, Lagniel G, Tabet JC, Ezan E, Labarre J.  (2005). Combined proteome and metabolite-profiling analyses reveal surprising insights into yeast sulfur metabolism. J Biol Chem. 280, 24723-24730.

Lefebvre C, Aude JC, Glemet E, Neri C.  (2005). Balancing protein similarity and gene co-expression reveals new links between genetic conservation and developmental diversity in invertebrates. Bioinformatics. 21, 1550-1558.

Mansour H, Cheval L, Elalouf JM, Aude JC, Alyanakian MA, Mougenot B, Doucet A, Deschenes G.  (2005). T-cell transcriptome analysis points up a thymic disorder in idiopathic nephrotic syndrome Kidney Int. 67, 2168-2177.

Desaint S, Luriau S, Aude JC, Rousselet G, Toledano MB.  (2004). Mammalian antioxidant defenses are not inducible by H2O2. J Biol Chem. 279, 31157-31163.

Fiévet J, Dillmann C, Lagniel G, Davanture M, Negroni L, Labarre J, De Vienne D.  (2004). Assessing factors for reliable quantitative proteomics based on two-dimensional gel electrophoresis. Proteomics. 4, 1939-1949.

Biteau B, Labarre J, Toledano MB.  (2003). ATP-dependent reduction of cysteine-sulphinic acid by S-cerevisiae sulphiredoxin. Nature. 425, 980-984.

Bonamy C, Labarre J, Cazaubon L, Jacob C, Le Bohec F, Reyes O, Leblon G.  (2003). The mobile element IS1207 of Brevibacterium lactofermentum ATCC21086: isolation and use in the construction of Tn5531, a versatile transposon for insertional mutagenesis of Corynebacterium glutamicum. J Biotechnol. 104, 301-309.

Bro C, Regenberg B, Lagniel G, Labarre J, Montero-Lomeli M, Nielsen J.  (2003). Transcriptional, proteomic and metabolic response to lithium in galactose-grown yeast cells. J Biol Chem. 278, 32141-32149.

Bebien M, Lagniel G, Garin J, Touati D, Vermeglio A, Labarre J.  (2002).  Involvement of superoxide dismutases in the response of Escherichia coli to selenium oxides. J Bacteriol.  184,  1556-1564.

Fauchon M, Lagniel G, Aude JC, Lombardia L, Soularue P, Petat C, Marguerie G, Sentenac A, Werner M, Labarre J.  (2002).  Sulfur-sparing in the yeast proteome in response to sulfur demand. Mol Cell.  9,  713-723.

Hasan R, Leroy C, Isnard AD, Labarre J, Boy-Marcotte E, Toledano MB.  (2002).  The control of the yeast H2O2 response by the Msn2/4 transcription factors. Mol Microbiol.  45,  233-245.

Lenssen E, Oberholzer U, Labarre J, De Virgilio C, Collart MA.  (2002).  Saccharomyces cerevisiae Ccr4-Not complex contributes to the control of Msn2p-dependent transcription by the Ras/cAMP pathway. Mol Microbiol.  43,  1023-1037.

Prouzet-Mauleon V, Monribot-Espagne C, Boucherie H, Lagniel G, Lopez S, Labarre J, Garin J, Lauquin GJ. (2002).  Identification in Saccharomyces cerevisiae of a new stable variant of alkyl hydroperoxide reductase 1 (Ahp1) induced by oxidative stress. J Biol Chem.  277,  4823-4830.

Louis A, Ollivier E, Aude JC, Risler JL.  (2001). Massive sequence comparisons as a help in annotating genomic sequences. Genome Res. 11, 1296-1303.

Spector D, Labarre J, Toledano MB.  (2001). A genetic investigation of the essential role of glutathione. Mutations in the proline biosynthesis pathway are the only suppressors of glutathione auxotrophy in yeast. J Biol Chem. 276, 7011-7016.

Vido K, Spector D, Lagniel G, Lopez S, Toledano MB, Labarre J.  (2001). A proteome analysis of the cadmium response in Saccharomyces cerevisiae. J Biol Chem. 276, 8469-8474.