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Accueil > Départements > Microbiologie > Muriel GONDRY : Enzymologie et Biosynthèse Peptidique Non Ribosomale

Publications

2019


  • N. Canu, M. Moutiez, P. Belin, et M. Gondry, « Cyclodipeptide synthases: a promising biotechnological tool for the synthesis of diverse 2,5-diketopiperazines », Natural Product Reports, août 2019.
    Résumé : Covering: Up to mid-2019Cyclodipeptide synthases (CDPSs) catalyse the formation of cyclodipeptides using aminoacylated-tRNA as substrates. The recent characterization of large sets of CDPSs has revealed that they can produce highly diverse products, and therefore have great potential for use in the production of different 2,5-diketopiperazines (2,5-DKPs). Sequence similarity networks (SSNs) are presented as a new, efficient way of classifying CDPSs by specificity and identifying new CDPS likely to display novel specificities. Several strategies for further increasing the diversity accessible with these enzymes are discussed here, including the incorporation of non-canonical amino acids by CDPSs and use of the remarkable diversity of 2,5-DKP-tailoring enzymes discovered in recent years.
    Mots-clés : BIOSYN, MICROBIO.

  • P. Dubois, I. Correia, F. Le Chevalier, S. Dubois, I. Jacques, N. Canu, M. Moutiez, R. Thai, M. Gondry, O. Lequin, et P. Belin, « Author Correction: Reprogramming Escherichia coli for the production of prenylated indole diketopiperazine alkaloids », Scientific Reports, vol. 9, nᵒ 1, p. 15009, oct. 2019.
    Résumé : An amendment to this paper has been published and can be accessed via a link at the top of the paper.
    Mots-clés : BIOSYN, MICROBIO.
    Pièce jointe Full Text 794.7 ko (source)

  • P. Dubois, I. Correia, F. Le Chevalier, S. Dubois, I. Jacques, N. Canu, M. Moutiez, R. Thai, M. Gondry, O. Lequin, et P. Belin, « Reprogramming Escherichia coli for the production of prenylated indole diketopiperazine alkaloids », Scientific Reports, vol. 9, nᵒ 1, p. 9208, juin 2019.
    Résumé : Prenylated indole diketopiperazine (DKP) alkaloids are important bioactive molecules or their precursors. In the context of synthetic biology, efficient means for their biological production would increase their chemical diversification and the discovery of novel bioactive compounds. Here, we prove the suitability of the Escherichia coli chassis for the production of prenylated indole DKP alkaloids. We used enzyme combinations not found in nature by co-expressing bacterial cyclodipeptide synthases (CDPSs) that assemble the DKP ring and fungal prenyltransferases (PTs) that transfer the allylic moiety from the dimethylallyl diphosphate (DMAPP) to the indole ring of tryptophanyl-containing cyclodipeptides. Of the 11 tested combinations, seven resulted in the production of eight different prenylated indole DKP alkaloids as determined by LC-MS/MS and NMR characterization. Two were previously undescribed. Engineering E. coli by introducing a hybrid mevalonate pathway for increasing intracellular DMAPP levels improved prenylated indole DKP alkaloid production. Purified product yields of 2-26 mg/L per culture were obtained from culture supernatants. Our study paves the way for the bioproduction of novel prenylated indole DKP alkaloids in a tractable chassis that can exploit the cyclodipeptide diversity achievable with CDPSs and the numerous described PT activities.
    Mots-clés : BIOSYN, MICROBIO.

2018



  • G. Bourgeois, J. Seguin, M. Babin, P. Belin, M. Moutiez, Y. Mechulam, M. Gondry, et E. Schmitt, « Structural basis for partition of the cyclodipeptide synthases into two subfamilies », Journal of Structural Biology, vol. 203, nᵒ 1, p. 17-26, juill. 2018.
    Résumé : Cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides that can be further used for the synthesis of diketopiperazines. It was shown that CDPSs fall into two subfamilies, NYH and XYP, characterized by the presence of specific sequence signatures. However, current understanding of CDPSs only comes from studies of enzymes from the NYH subfamily. The present study reveals the crystal structures of three CDPSs from the XYP subfamily. Comparison of the XYP and NYH enzymes shows that the two subfamilies mainly differ in the first half of their Rossmann fold. This gives a structural basis for the partition of CDPSs into two subfamilies. Despite these differences, the catalytic residues adopt similar positioning regardless of the subfamily suggesting that the XYP and NYH motifs correspond to two structural solutions to facilitate the reactivity of the catalytic serine residue.
    Mots-clés : Aminoacyl-tRNA synthetases, BIOSYN, Cyclodipeptides, Diketopiperazines, MICROBIO, Non-ribosomal peptide synthesis, Rossmann fold, Transfer RNA.

  • N. Canu, P. Belin, R. Thai, I. Correia, O. Lequin, J. Seguin, M. Moutiez, et M. Gondry, « Incorporation of Non-canonical Amino Acids into 2,5-Diketopiperazines by Cyclodipeptide Synthases », Angewandte Chemie (International Ed. in English), vol. 57, nᵒ 12, p. 3118-3122, mars 2018.
    Résumé : The manipulation of natural product biosynthetic pathways is a powerful means of expanding the chemical diversity of bioactive molecules. 2,5-diketopiperazines (2,5-DKPs) have been widely developed by medicinal chemists, but their biological production is yet to be exploited. We introduce an in vivo method for incorporating non-canonical amino acids (ncAAs) into 2,5-DKPs using cyclodipeptide synthases (CDPSs), the enzymes responsible for scaffold assembly in many 2,5-DKP biosynthetic pathways. CDPSs use aminoacyl-tRNAs as substrates. We exploited the natural ability of aminoacyl-tRNA synthetases to load ncAAs onto tRNAs. We found 26 ncAAs to be usable as substrates by CDPSs, leading to the enzymatic production of approximately 200 non-canonical cyclodipeptides. CDPSs constitute an efficient enzymatic tool for the synthesis of highly diverse 2,5-DKPs. Such diversity could be further expanded, for example, by using various cyclodipeptide-tailoring enzymes found in 2,5-DKP biosynthetic pathways.
    Mots-clés : biocatalysis, BIOSYN, biosynthesis, Cyclodipeptide synthases, cyclodipeptides, Diketopiperazines, MICROBIO, Natural product engineering, Non-canonical amino acid.

  • M. Gondry, I. B. Jacques, R. Thai, M. Babin, N. Canu, J. Seguin, P. Belin, J. - L. Pernodet, et M. Moutiez, « A Comprehensive Overview of the Cyclodipeptide Synthase Family Enriched with the Characterization of 32 New Enzymes », Frontiers in Microbiology, vol. 9, p. 46, 2018.
    Résumé : Cyclodipeptide synthases (CDPSs) use as substrates two amino acids activated as aminoacyl-tRNAs to synthesize cyclodipeptides in secondary metabolites biosynthetic pathways. Since the first description of a CDPS in 2002, the number of putative CDPSs in databases has increased exponentially, reaching around 800 in June 2017. They are likely to be involved in numerous biosynthetic pathways but the diversity of their products is still under-explored. Here, we describe the activity of 32 new CDPSs, bringing the number of experimentally characterized CDPSs to about 100. We detect 16 new cyclodipeptides, one of which containing an arginine which has never been observed previously. This brings to 75 the number of cyclodipeptides formed by CDPSs out of the possible 210 natural ones. We also identify several consensus sequences related to the synthesis of a specific cyclodipeptide, improving the predictive model of CDPS specificity. The improved prediction method enables to propose the main product synthesized for about 80% of the CDPS sequences available in databases and opens the way for the deciphering of CDPS-dependent pathways. Analysis of phylum distribution and predicted activity for all CDPSs identified in databases shows that the experimentally characterized set is representative of the whole family. Our work also demonstrates that some cyclodipeptides, precursors of diketopiperazines with interesting pharmacological properties and previously described as being synthesized by fungal non-ribosomal peptide synthetases, can also be produced by CDPSs in bacteria.
    Mots-clés : ACTINO, activity prediction, BIOSYN, Biosynthetic Pathways, MICROBIO, Secondary metabolites.

  • E. Schmitt, G. Bourgeois, M. Gondry, et A. Aleksandrov, « Cyclization Reaction Catalyzed by Cyclodipeptide Synthases Relies on a Conserved Tyrosine Residue », Scientific Reports, vol. 8, nᵒ 1, p. 7031, mai 2018.
    Résumé : Cyclodipeptide synthases (CDPSs) form various cyclodipeptides from two aminoacyl tRNAs via a stepwise mechanism with the formation of a dipeptidyl enzyme intermediate. As a final step of the catalytic reaction, the dipeptidyl group undergoes intramolecular cyclization to generate the target cyclodipeptide product. In this work, we investigated the cyclization reaction in the cyclodipeptide synthase AlbC using QM/MM methods and free energy simulations. The results indicate that the catalytic Y202 residue is in its neutral protonated form, and thus, is not likely to serve as a general base during the reaction. We further demonstrate that the reaction relies on the conserved residue Y202 serving as a proton relay, and the direct proton transfer from the amino group to S37 of AlbC is unlikely. Calculations reveal that the hydroxyl group of tyrosine is more suitable for the proton transfer than hydroxyl groups of other amino acids, such as serine and threonine. Results also show that the residues E182, N40, Y178 and H203 maintain the correct conformation of the dipeptide needed for the cyclization reaction. The mechanism discovered in this work relies on the amino groups conserved among the entire CDPS family and, thus is expected to be universal among CDPSs.
    Mots-clés : BIOSYN, MICROBIO.

2017


  • A. Malabirade, J. Morgado-Brajones, S. Trépout, F. Wien, I. Marquez, J. Seguin, S. Marco, M. Velez, et V. Arluison, « Publisher Correction: Membrane association of the bacterial riboregulator Hfq and functional perspectives », Scientific Reports, vol. 7, nᵒ 1, p. 15651, nov. 2017.
    Résumé : A correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper.
    Mots-clés : BIOSYN, MICROBIO.

  • A. Malabirade, J. Morgado-Brajones, S. Trépout, F. Wien, I. Marquez, J. Seguin, S. Marco, M. Velez, et A. Véronique, « Membrane association of the bacterial riboregulator Hfq and functional perspectives », Scientific Reports, vol. 7, nᵒ 1, p. 10724, sept. 2017.
    Résumé : Hfq is a bacterial RNA binding protein that carries out several roles in genetic expression regulation, mainly at the post-transcriptional level. Previous studies have shown its importance in growth and virulence of bacteria. Here, we provide the direct observation of its ability to interact with membranes. This was established by co-sedimentation assay, cryo-transmission electron (cryo-TEM) and atomic force (AFM) microscopies. Furthermore, our results suggest a role for its C-terminus amyloidogenic domain in membrane disruption. Precisely, AFM images of lipid bilayers in contact with Hfq C-terminus fibrils show the emergence of holes with a size dependent on the time of interaction. Cryo-TEM observations also show that liposomes are in contact with clusters of fibrils, with occasional deformation of the vesicles and afterward the apparition of a multitude of tiny vesicles in the proximity of the fibrils, suggesting peptide-induced breakage of the liposomes. Finally, circular dichroism spectroscopy demonstrated a change in the secondary structure of Hfq C-terminus upon interaction with liposomes. Altogether, these results show an unexpected property of Hfq and suggest a possible new role for the protein, exporting sRNA outside of the bacterial cell.
    Mots-clés : BIOSYN, MICROBIO.

  • M. Moutiez, P. Belin, et M. Gondry, « Aminoacyl-tRNA-Utilizing Enzymes in Natural Product Biosynthesis », Chemical Reviews, janv. 2017.
    Résumé : Aminoacyl-tRNAs were long thought to be involved solely in ribosome-dependent protein synthesis and essential primary metabolism processes, such as targeted protein degradation and peptidoglycan synthesis. About 10 years ago, an aminoacyl-tRNA-dependent enzyme involved in the biosynthesis of the antibiotic valanimycin was discovered in a Streptomyces strain. Far from being an isolated case, this discovery has been followed by the description of an increasing number of aminoacyl-tRNA-dependent enzymes involved in secondary metabolism. This review describes the three groups of aminoacyl-tRNA-dependent enzymes involved in the synthesis of natural products. Each group is characterized by a particular chemical reaction, and its members are predicted to share a specific fold. The three groups are cyclodipeptide synthases involved in diketopiperazine synthesis, LanB-like dehydratases involved in the posttranslational modification of ribosomal peptides, and transferases from various biosynthesis pathways.
    Mots-clés : BIOSYN, MICROBIO.


  • C. Tellier-Lebegue, E. Dizet, E. Ma, X. Veaute, E. Coïc, J. - B. Charbonnier, et L. Maloisel, « The translesion DNA polymerases Pol ζ and Rev1 are activated independently of PCNA ubiquitination upon UV radiation in mutants of DNA polymerase δ », PLOS Genetics, vol. 13, nᵒ 12, p. e1007119, déc. 2017.

2015


  • I. B. Jacques, M. Moutiez, J. Witwinowski, E. Darbon, C. Martel, J. Seguin, E. Favry, R. Thai, A. Lecoq, S. Dubois, J. - L. Pernodet, M. Gondry, et P. Belin, « Analysis of 51 cyclodipeptide synthases reveals the basis for substrate specificity », Nature Chemical Biology, vol. 11, nᵒ 9, p. 721-727, sept. 2015.
    Résumé : Cyclodipeptide synthases (CDPSs) constitute a family of peptide bond-forming enzymes that use aminoacyl-tRNAs for the synthesis of cyclodipeptides. Here, we describe the activity of 41 new CDPSs. We also show that CDPSs can be classified into two main phylogenetically distinct subfamilies characterized by specific functional subsequence signatures, named NYH and XYP. All 11 previously characterized CDPSs belong to the NYH subfamily, suggesting that further special features may be yet to be discovered in the other subfamily. CDPSs synthesize a large diversity of cyclodipeptides made up of 17 proteinogenic amino acids. The identification of several CDPSs having the same specificity led us to determine specificity sequence motifs that, in combination with the phylogenetic distribution of CDPSs, provide a first step toward being able to predict the cyclodipeptides synthesized by newly discovered CDPSs. The determination of the activity of ten more CDPSs with predicted functions constitutes a first experimental validation of this predictive approach.
    Mots-clés : ACTINO, Amino Acid Motifs, Bacterial Proteins, BIOCELL, BIOSYN, Computational Biology, Cyclization, Databases, Genetic, Dipeptides, Escherichia coli, Fungal Proteins, gene expression, MICROBIO, Molecular Sequence Data, Peptide Biosynthesis, Nucleic Acid-Independent, Peptide Synthases, Peptides, Cyclic, Phylogeny, Protein Structure, Tertiary, Recombinant Proteins, RNA, Transfer, Amino Acyl, Substrate Specificity.
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Publications Principales avant 2015

Moutiez M., Schmitt E., Seguin J., Thai R., Favry E., Belin P., Mechulam Y., Gondry M. (2014). Unravelling the mechanism of non-ribosomal peptide synthesis by cyclodipeptide synthases. Nat. Commun. 5:5141 doi : 10.1038/ncomms6141

Moutiez M., Seguin J., Fonvielle M., Belin P., Jacques I.B., Favry E., Arthur M., Gondry M. (2014). Specificity determinants for the two tRNA substrates of the cyclodipeptide synthase AlbC from Streptomyces noursei. Nucl. Acids Res. 42, 7247–7258
http://nar.oxfordjournals.org/content/42/11/7247.long

Jacques I., Seguin J., Moutiez M., Favry E., Gondry M., Belin P. (2014). Expanding the diversity of diketopiperazines biosynthesized by cyclodipeptide synthases. New Biotechnol. 31S, S74-S75 doi : 110.1016/j.nbt.2014.05.1782

Fonvielle M., Le Du M.-H., Lequin O., Lecoq A., Jacquet M., Thai R., Dubois S., Grach G., Gondry M., Belin P. (2013). Substrate and reaction specificity of Mycobacterium tuberculosis cytochrome P450 CYP121 : insights from biochemical studies and crystal structures. J. Biol. Chem. 288, 17347-17359
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3682536/

Nozach H., Fruchart-Gaillard C., Fenaille F., Beau F., Ramos O.H., Douzi B., Saez N.J., Moutiez M., Servent D., Gondry M., Thai R., Cuniasse P., Vincentelli R., Dive V. (2013). High throughput screening identifies disulfide isomerase DsbC as a very efficient partner for recombinant expression of small disulfide-rich proteins in E. coli. Microb. Cell Fact. 12, 37
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3668227/

Gueneau E., Dherin C., Legrand P., Tellier-Lebegue C., Gilquin B., Bonnesoeur P., Londino F., Quemener C., Le Du M.-H., Marquez J. A., Moutiez M., Gondry M., Boiteux S., Charbonnier J.-B. (2013). Structures of the MutLa C-terminal domain reveal how Mlh1 recruits exonuclease I and contributes to PMS1 endonuclease active site. Nat. Struct. Mol. Biol. 20, 461-468

Belin P., Moutiez M., Lautru S., Seguin J., Pernodet J.-L., Gondry M. (2012). The nonribosomal synthesis of diketopiperazines in tRNA-dependent cyclodipeptide synthase pathways. Nat. Prod. Rep. 29, 961-979

Seguin J., Moutiez M., Li Y., Belin P., Lecoq A., Fonvielle M., Charbonnier J.-B., Pernodet J.-L., Gondry M. (2011). Nonribosomal peptide synthesis in animals : the cyclodipeptide synthase of Nematostella. Chem. Biol. 18, 1362-1368
http://www.sciencedirect.com/science/article/pii/S1074552111003516

Sauguet L., Moutiez M., Li Y., Belin P., Seguin J., Le Du M.-H., Thai R., Masson C., Fonvielle M., Pernodet J.-L., Charbonnier J.-B., Gondry M. (2011). Cyclodipeptide synthases, a family of class-I aminoacyl-tRNA synthetase-like enzymes involved in non-ribosomal peptide synthesis. Nucl. Acids Res. 39, 4475-4489
http://nar.oxfordjournals.org/content/39/10/4475.long

Gondry M., Sauguet L., Belin P., Thai R., Amouroux R., Tellier C., Tuphile K, Jacquet M., Braud S., Courçon M., Masson C., Dubois S., Lautru S., Lecoq A., Hashimoto S.-i, Genet R., Pernodet J.-L. (2009). Cyclodipeptide synthases are a family of tRNA-dependent peptide bond-forming enzymes. Nat. Chem. Biol. 5, 414-420

Belin P., Le Du M.-H., Fielding A., Lequin O, Jacquet M., Charbonnier J.-B., Lecoq A., Thai R., Courçon M., Masson C., Dugave C., Genet R., Pernodet J.-L., Gondry M. (2009). Identification and structural basis of the reaction catalyzed by CYP121, an essential cytochrome P450 in Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 106, 7426-7431
http://www.pnas.org/content/106/18/7426.long

Juguet M., Lautru S., Francou F.-X., Nezbedová S., Leblond P., Gondry M., Pernodet J.-L. (2009). An iterative nonribosomal peptide synthetase assembles the pyrrole-amide antibiotic congocidine in Streptomyces ambofaciens. Chem. Biol. 16, 421-431
http://www.sciencedirect.com/science/article/pii/S1074552109001136

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