1
|
Bardou P, Laguerre S, Maman Haddad S, Legoueix Rodriguez S, Laville E, Dumon C, Potocki-Veronese G, Klopp C. MINTIA: a metagenomic INserT integrated assembly and annotation tool. PeerJ 2021; 9:e11885. [PMID: 34692239 PMCID: PMC8483015 DOI: 10.7717/peerj.11885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 07/09/2021] [Indexed: 11/29/2022] Open
Abstract
The earth harbors trillions of bacterial species adapted to very diverse ecosystems thanks to specific metabolic function acquisition. Most of the genes responsible for these functions belong to uncultured bacteria and are still to be discovered. Functional metagenomics based on activity screening is a classical way to retrieve these genes from microbiomes. This approach is based on the insertion of large metagenomic DNA fragments into a vector and transformation of a host to express heterologous genes. Metagenomic libraries are then screened for activities of interest, and the metagenomic DNA inserts of active clones are extracted to be sequenced and analysed to identify genes that are responsible for the detected activity. Hundreds of metagenomics sequences found using this strategy have already been published in public databases. Here we present the MINTIA software package enabling biologists to easily generate and analyze large metagenomic sequence sets, retrieved after activity-based screening. It filters reads, performs assembly, removes cloning vector, annotates open reading frames and generates user friendly reports as well as files ready for submission to international sequence repositories. The software package can be downloaded from https://github.com/Bios4Biol/MINTIA.
Collapse
Affiliation(s)
- Philippe Bardou
- Sigenae, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | | | - Sarah Maman Haddad
- Sigenae, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | | | | | - Claire Dumon
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | - Christophe Klopp
- Sigenae, Genotoul Bioinfo, MIAT UR875, INRAE, Castanet Tolosan, France
| |
Collapse
|
2
|
Tauzin AS, Pereira MR, Van Vliet LD, Colin PY, Laville E, Esque J, Laguerre S, Henrissat B, Terrapon N, Lombard V, Leclerc M, Doré J, Hollfelder F, Potocki-Veronese G. Investigating host-microbiome interactions by droplet based microfluidics. Microbiome 2020; 8:141. [PMID: 33004077 PMCID: PMC7531118 DOI: 10.1186/s40168-020-00911-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 08/23/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Despite the importance of the mucosal interface between microbiota and the host in gut homeostasis, little is known about the mechanisms of bacterial gut colonization, involving foraging for glycans produced by epithelial cells. The slow pace of progress toward understanding the underlying molecular mechanisms is largely due to the lack of efficient discovery tools, especially those targeting the uncultured fraction of the microbiota. RESULTS Here, we introduce an ultra-high-throughput metagenomic approach based on droplet microfluidics, to screen fosmid libraries. Thousands of bacterial genomes can be covered in 1 h of work, with less than ten micrograms of substrate. Applied to the screening of the mucosal microbiota for β-N-acetylgalactosaminidase activity, this approach allowed the identification of pathways involved in the degradation of human gangliosides and milk oligosaccharides, the structural homologs of intestinal mucin glycans. These pathways, whose prevalence is associated with inflammatory bowel diseases, could be the result of horizontal gene transfers with Bacteroides species. Such pathways represent novel targets to study the microbiota-host interactions in the context of inflammatory bowel diseases, in which the integrity of the mucosal barrier is impaired. CONCLUSION By compartmentalizing experiments inside microfluidic droplets, this method speeds up and miniaturizes by several orders of magnitude the screening process compared to conventional approaches, to capture entire metabolic pathways from metagenomic libraries. The method is compatible with all types of (meta)genomic libraries, and employs a commercially available flow cytometer instead of a custom-made sorting system to detect intracellular or extracellular enzyme activities. This versatile and generic workflow will accelerate experimental exploration campaigns in functional metagenomics and holobiomics studies, to further decipher host-microbiota relationships. Video Abstract.
Collapse
Affiliation(s)
- Alexandra S Tauzin
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31400, Toulouse, France
| | - Mariana Rangel Pereira
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- CAPES Foundation, Ministry of Education of Brazil, BrasÍlia, DF, 70040-020, Brazil
| | - Liisa D Van Vliet
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- Drop-Tech, Canterbury Court, Cambridge, CB4 3QU, UK
| | - Pierre-Yves Colin
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Elisabeth Laville
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31400, Toulouse, France
| | - Jeremy Esque
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31400, Toulouse, France
| | - Sandrine Laguerre
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31400, Toulouse, France
| | - Bernard Henrissat
- CNRS, UMR 7257, Aix-Marseille Université, F-13288, Marseille, France
- USC 1408 AFMB, INRAE, F-13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nicolas Terrapon
- CNRS, UMR 7257, Aix-Marseille Université, F-13288, Marseille, France
- USC 1408 AFMB, INRAE, F-13288, Marseille, France
| | - Vincent Lombard
- CNRS, UMR 7257, Aix-Marseille Université, F-13288, Marseille, France
- USC 1408 AFMB, INRAE, F-13288, Marseille, France
| | - Marion Leclerc
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, F-78350, Jouy-en-Josas, France
| | - Joël Doré
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, F-78350, Jouy-en-Josas, France
- Metagenopolis, INRAE, F-78350, Jouy-en-Josas, France
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
| | | |
Collapse
|
3
|
Dressaire C, Pobre V, Laguerre S, Girbal L, Arraiano CM, Cocaign-Bousquet M. PNPase is involved in the coordination of mRNA degradation and expression in stationary phase cells of Escherichia coli. BMC Genomics 2018; 19:848. [PMID: 30486791 PMCID: PMC6264599 DOI: 10.1186/s12864-018-5259-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 11/16/2018] [Indexed: 12/02/2022] Open
Abstract
Background Exoribonucleases are crucial for RNA degradation in Escherichia coli but the roles of RNase R and PNPase and their potential overlap in stationary phase are not well characterized. Here, we used a genome-wide approach to determine how RNase R and PNPase affect the mRNA half-lives in the stationary phase. The genome-wide mRNA half-lives were determined by a dynamic analysis of transcriptomes after transcription arrest. We have combined the analysis of mRNA half-lives with the steady-state concentrations (transcriptome) to provide an integrated overview of the in vivo activity of these exoribonucleases at the genome-scale. Results The values of mRNA half-lives demonstrated that the mRNAs are very stable in the stationary phase and that the deletion of RNase R or PNPase caused only a limited mRNA stabilization. Intriguingly the absence of PNPase provoked also the destabilization of many mRNAs. These changes in mRNA half-lives in the PNPase deletion strain were associated with a massive reorganization of mRNA levels and also variation in several ncRNA concentrations. Finally, the in vivo activity of the degradation machinery was found frequently saturated by mRNAs in the PNPase mutant unlike in the RNase R mutant, suggesting that the degradation activity is limited by the deletion of PNPase but not by the deletion of RNase R. Conclusions This work had identified PNPase as a central player associated with mRNA degradation in stationary phase. Electronic supplementary material The online version of this article (10.1186/s12864-018-5259-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Clémentine Dressaire
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Vânia Pobre
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | | | - Laurence Girbal
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
| | - Cecilia Maria Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
| | | |
Collapse
|
4
|
Laguerre S, González I, Nouaille S, Moisan A, Villa-Vialaneix N, Gaspin C, Bouvier M, Carpousis AJ, Cocaign-Bousquet M, Girbal L. Large-Scale Measurement of mRNA Degradation in Escherichia coli: To Delay or Not to Delay. Methods Enzymol 2018; 612:47-66. [PMID: 30502954 DOI: 10.1016/bs.mie.2018.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this study, we compared different computational methods used for genome-wide determination of mRNA half-lives in Escherichia coli with a special focus on the impact on considering a delay before the onset of mRNA decay after transcription arrest. A wide variety of datasets were analyzed coming from different technical methods for mRNA quantification (microarrays, RNA-seq, and RT-qPCR) and different bacterial growth conditions. The exponential decay of mRNA levels was fitted using both linear and exponential models and with or without a delay. We showed that for all the models, independently of mRNA quantification methods and growth conditions, ignoring the delay resulted in only a modest overestimation of the half-life. For approximately 80% of the mRNAs, differences in mRNA half-life values were less than 34s. The correlation between half-lives estimated with and without a delay was extremely high. However, the slope of the linear regression between the half-lives with and without a delay tended to decrease with the delay. For the few mRNAs for which taking into account the delay influenced the estimated half-life, the impact was dependent on the model and the growth condition. The smallest impact was obtained for the linear model.
Collapse
Affiliation(s)
| | | | | | - Annick Moisan
- MIAT, Université de Toulouse, INRA, Castanet-Tolosan, France
| | | | | | - Marie Bouvier
- LMGM, CBI, Université de Toulouse, CNRS, Toulouse, France
| | | | | | - Laurence Girbal
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| |
Collapse
|
5
|
Morin M, Ropers D, Letisse F, Laguerre S, Portais JC, Cocaign-Bousquet M, Enjalbert B. The post-transcriptional regulatory system CSR controls the balance of metabolic pools in upper glycolysis ofEscherichia coli. Mol Microbiol 2016; 100:686-700. [DOI: 10.1111/mmi.13343] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Manon Morin
- Université de Toulouse; INSA, UPS, INP; 135 Avenue de Rangueil F-31077 Toulouse France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, LISBP; F-31400 Toulouse France
- CNRS, UMR5504; F-31400 Toulouse France
- Inria Grenoble-Rhône-Alpes; 655 avenue de l'Europe 38334 Montbonnot Cedex France
| | - Delphine Ropers
- Inria Grenoble-Rhône-Alpes; 655 avenue de l'Europe 38334 Montbonnot Cedex France
| | - Fabien Letisse
- Université de Toulouse; INSA, UPS, INP; 135 Avenue de Rangueil F-31077 Toulouse France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, LISBP; F-31400 Toulouse France
- CNRS, UMR5504; F-31400 Toulouse France
| | - Sandrine Laguerre
- Université de Toulouse; INSA, UPS, INP; 135 Avenue de Rangueil F-31077 Toulouse France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, LISBP; F-31400 Toulouse France
- CNRS, UMR5504; F-31400 Toulouse France
| | - Jean-Charles Portais
- Université de Toulouse; INSA, UPS, INP; 135 Avenue de Rangueil F-31077 Toulouse France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, LISBP; F-31400 Toulouse France
- CNRS, UMR5504; F-31400 Toulouse France
| | - Muriel Cocaign-Bousquet
- Université de Toulouse; INSA, UPS, INP; 135 Avenue de Rangueil F-31077 Toulouse France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, LISBP; F-31400 Toulouse France
- CNRS, UMR5504; F-31400 Toulouse France
| | - Brice Enjalbert
- Université de Toulouse; INSA, UPS, INP; 135 Avenue de Rangueil F-31077 Toulouse France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, LISBP; F-31400 Toulouse France
- CNRS, UMR5504; F-31400 Toulouse France
| |
Collapse
|
6
|
Malbert Y, Pizzut-Serin S, Massou S, Cambon E, Laguerre S, Monsan P, Lefoulon F, Morel S, André I, Remaud-Simeon M. Extending the Structural Diversity of α-Flavonoid Glycosides with Engineered Glucansucrases. ChemCatChem 2014. [DOI: 10.1002/cctc.201402144] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
7
|
Esquerré T, Laguerre S, Turlan C, Carpousis AJ, Girbal L, Cocaign-Bousquet M. Dual role of transcription and transcript stability in the regulation of gene expression in Escherichia coli cells cultured on glucose at different growth rates. Nucleic Acids Res 2014; 42:2460-72. [PMID: 24243845 PMCID: PMC3936743 DOI: 10.1093/nar/gkt1150] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 10/23/2013] [Accepted: 10/25/2013] [Indexed: 11/13/2022] Open
Abstract
Microorganisms extensively reorganize gene expression to adjust growth rate to changes in growth conditions. At the genomic scale, we measured the contribution of both transcription and transcript stability to regulating messenger RNA (mRNA) concentration in Escherichia coli. Transcriptional control was the dominant regulatory process. Between growth rates of 0.10 and 0.63 h(-1), there was a generic increase in the bulk mRNA transcription. However, many transcripts became less stable and the median mRNA half-life decreased from 4.2 to 2.8 min. This is the first evidence that mRNA turnover is slower at extremely low-growth rates. The destabilization of many, but not all, transcripts at high-growth rate correlated with transcriptional upregulation of genes encoding the mRNA degradation machinery. We identified five classes of growth-rate regulation ranging from mainly transcriptional to mainly degradational. In general, differential stability within polycistronic messages encoded by operons does not appear to be affected by growth rate. We show here that the substantial reorganization of gene expression involving downregulation of tricarboxylic acid cycle genes and acetyl-CoA synthetase at high-growth rates is controlled mainly by transcript stability. Overall, our results demonstrate that the control of transcript stability has an important role in fine-tuning mRNA concentration during changes in growth rate.
Collapse
Affiliation(s)
- Thomas Esquerré
- Université de Toulouse; INSA, UPS, INP; LISBP, 135, avenue de Rangueil, 31077 Toulouse, France, INRA, UMR792 Ingénierie des systèmes biologiques et des procédés, 31400 Toulouse, France, CNRS, UMR5504, 31400 Toulouse, France and Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre National de la Recherche Scientifique et Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse, France
| | - Sandrine Laguerre
- Université de Toulouse; INSA, UPS, INP; LISBP, 135, avenue de Rangueil, 31077 Toulouse, France, INRA, UMR792 Ingénierie des systèmes biologiques et des procédés, 31400 Toulouse, France, CNRS, UMR5504, 31400 Toulouse, France and Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre National de la Recherche Scientifique et Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse, France
| | - Catherine Turlan
- Université de Toulouse; INSA, UPS, INP; LISBP, 135, avenue de Rangueil, 31077 Toulouse, France, INRA, UMR792 Ingénierie des systèmes biologiques et des procédés, 31400 Toulouse, France, CNRS, UMR5504, 31400 Toulouse, France and Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre National de la Recherche Scientifique et Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse, France
| | - Agamemnon J. Carpousis
- Université de Toulouse; INSA, UPS, INP; LISBP, 135, avenue de Rangueil, 31077 Toulouse, France, INRA, UMR792 Ingénierie des systèmes biologiques et des procédés, 31400 Toulouse, France, CNRS, UMR5504, 31400 Toulouse, France and Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre National de la Recherche Scientifique et Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse, France
| | - Laurence Girbal
- Université de Toulouse; INSA, UPS, INP; LISBP, 135, avenue de Rangueil, 31077 Toulouse, France, INRA, UMR792 Ingénierie des systèmes biologiques et des procédés, 31400 Toulouse, France, CNRS, UMR5504, 31400 Toulouse, France and Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre National de la Recherche Scientifique et Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse, France
| | - Muriel Cocaign-Bousquet
- Université de Toulouse; INSA, UPS, INP; LISBP, 135, avenue de Rangueil, 31077 Toulouse, France, INRA, UMR792 Ingénierie des systèmes biologiques et des procédés, 31400 Toulouse, France, CNRS, UMR5504, 31400 Toulouse, France and Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre National de la Recherche Scientifique et Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse, France
| |
Collapse
|
8
|
Cecchini DA, Laville E, Laguerre S, Robe P, Leclerc M, Doré J, Henrissat B, Remaud-Siméon M, Monsan P, Potocki-Véronèse G. Functional metagenomics reveals novel pathways of prebiotic breakdown by human gut bacteria. PLoS One 2013; 8:e72766. [PMID: 24066026 PMCID: PMC3774763 DOI: 10.1371/journal.pone.0072766] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 07/13/2013] [Indexed: 11/18/2022] Open
Abstract
The human intestine hosts a complex bacterial community that plays a major role in nutrition and in maintaining human health. A functional metagenomic approach was used to explore the prebiotic breakdown potential of human gut bacteria, including non-cultivated ones. Two metagenomic libraries, constructed from ileum mucosa and fecal microbiota, were screened for hydrolytic activities on the prebiotic carbohydrates inulin, fructo-oligosaccharides, xylo-oligosaccharides, galacto-oligosaccharides and lactulose. The DNA inserts of 17 clones, selected from the 167 hits that were identified, were pyrosequenced in-depth, yielding in total 407, 420 bp of metagenomic DNA. From these sequences, we discovered novel prebiotic degradation pathways containing carbohydrate transporters and hydrolysing enzymes, for which we provided the first experimental proof of function. Twenty of these proteins are encoded by genes that are also present in the gut metagenome of at least 100 subjects, whatever are their ages or their geographical origin. The sequence taxonomic assignment indicated that still unknown bacteria, for which neither culture conditions nor genome sequence are available, possess the enzymatic machinery to hydrolyse the prebiotic carbohydrates tested. The results expand the vision on how prebiotics are metabolized along the intestine, and open new perspectives for the design of functional foods.
Collapse
Affiliation(s)
- Davide A. Cecchini
- Université de Toulouse, Institut National des Sciences Appliquées, Université Paul Sabatier, Institut National Polytechnique, Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France
- UMR5504, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Toulouse, France
| | - Elisabeth Laville
- Université de Toulouse, Institut National des Sciences Appliquées, Université Paul Sabatier, Institut National Polytechnique, Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France
- UMR5504, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Toulouse, France
| | - Sandrine Laguerre
- Université de Toulouse, Institut National des Sciences Appliquées, Université Paul Sabatier, Institut National Polytechnique, Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France
- UMR5504, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Toulouse, France
| | | | - Marion Leclerc
- Institut National de la Recherche Agronomique, Micalis, UMR1319, Jouy en Josas Cedex, France
| | - Joël Doré
- Institut National de la Recherche Agronomique, Micalis, UMR1319, Jouy en Josas Cedex, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, Centre National de la Recherche Scientifique, Universités Aix-Marseille I & II, Marseille, France
| | - Magali Remaud-Siméon
- Université de Toulouse, Institut National des Sciences Appliquées, Université Paul Sabatier, Institut National Polytechnique, Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France
- UMR5504, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Toulouse, France
| | - Pierre Monsan
- Université de Toulouse, Institut National des Sciences Appliquées, Université Paul Sabatier, Institut National Polytechnique, Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France
- UMR5504, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Toulouse, France
| | - Gabrielle Potocki-Véronèse
- Université de Toulouse, Institut National des Sciences Appliquées, Université Paul Sabatier, Institut National Polytechnique, Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France
- UMR5504, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Toulouse, France
- * E-mail:
| |
Collapse
|
9
|
Bastien G, Arnal G, Bozonnet S, Laguerre S, Ferreira F, Fauré R, Henrissat B, Lefèvre F, Robe P, Bouchez O, Noirot C, Dumon C, O’Donohue M. Mining for hemicellulases in the fungus-growing termite Pseudacanthotermes militaris using functional metagenomics. Biotechnol Biofuels 2013; 6:78. [PMID: 23672637 PMCID: PMC3662619 DOI: 10.1186/1754-6834-6-78] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 04/24/2013] [Indexed: 05/10/2023]
Abstract
BACKGROUND The metagenomic analysis of gut microbiomes has emerged as a powerful strategy for the identification of biomass-degrading enzymes, which will be no doubt useful for the development of advanced biorefining processes. In the present study, we have performed a functional metagenomic analysis on comb and gut microbiomes associated with the fungus-growing termite, Pseudacanthotermes militaris. RESULTS Using whole termite abdomens and fungal-comb material respectively, two fosmid-based metagenomic libraries were created and screened for the presence of xylan-degrading enzymes. This revealed 101 positive clones, corresponding to an extremely high global hit rate of 0.49%. Many clones displayed either β-d-xylosidase (EC 3.2.1.37) or α-l-arabinofuranosidase (EC 3.2.1.55) activity, while others displayed the ability to degrade AZCL-xylan or AZCL-β-(1,3)-β-(1,4)-glucan. Using secondary screening it was possible to pinpoint clones of interest that were used to prepare fosmid DNA. Sequencing of fosmid DNA generated 1.46 Mbp of sequence data, and bioinformatics analysis revealed 63 sequences encoding putative carbohydrate-active enzymes, with many of these forming parts of sequence clusters, probably having carbohydrate degradation and metabolic functions. Taxonomic assignment of the different sequences revealed that Firmicutes and Bacteroidetes were predominant phyla in the gut sample, while microbial diversity in the comb sample resembled that of typical soil samples. Cloning and expression in E. coli of six enzyme candidates identified in the libraries provided access to individual enzyme activities, which all proved to be coherent with the primary and secondary functional screens. CONCLUSIONS This study shows that the gut microbiome of P. militaris possesses the potential to degrade biomass components, such as arabinoxylans and arabinans. Moreover, the data presented suggests that prokaryotic microorganisms present in the comb could also play a part in the degradation of biomass within the termite mound, although further investigation will be needed to clarify the complex synergies that might exist between the different microbiomes that constitute the termitosphere of fungus-growing termites. This study exemplifies the power of functional metagenomics for the discovery of biomass-active enzymes and has provided a collection of potentially interesting biocatalysts for further study.
Collapse
Affiliation(s)
- Géraldine Bastien
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, Toulouse F-31077, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse F-31400, France
- CNRS, UMR5504, Toulouse F-31400, France
| | - Grégory Arnal
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, Toulouse F-31077, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse F-31400, France
- CNRS, UMR5504, Toulouse F-31400, France
| | - Sophie Bozonnet
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, Toulouse F-31077, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse F-31400, France
- CNRS, UMR5504, Toulouse F-31400, France
| | - Sandrine Laguerre
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, Toulouse F-31077, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse F-31400, France
- CNRS, UMR5504, Toulouse F-31400, France
| | - Fernando Ferreira
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, Toulouse F-31077, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse F-31400, France
- CNRS, UMR5504, Toulouse F-31400, France
| | - Régis Fauré
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, Toulouse F-31077, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse F-31400, France
- CNRS, UMR5504, Toulouse F-31400, France
| | | | - Fabrice Lefèvre
- LibraGen, 3 rue des Satellites, Bâtiment Canal Biotech I, Toulouse F-31400, France
| | - Patrick Robe
- LibraGen, 3 rue des Satellites, Bâtiment Canal Biotech I, Toulouse F-31400, France
| | - Olivier Bouchez
- INRA, UMR444 Laboratoire de Génétique Cellulaire, Castanet-Tolosan F31326, France
- GeT-PlaGe, Genotoul, Centre INRA, Castanet-Tolosan F31326, France
| | - Céline Noirot
- INRA, UR 875, Bioinfo, GenoToul, 24 Chemin de Borderouge, CS 52627, Castanet Tolosan F-31326, France
| | - Claire Dumon
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, Toulouse F-31077, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse F-31400, France
- CNRS, UMR5504, Toulouse F-31400, France
| | - Michael O’Donohue
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, Toulouse F-31077, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse F-31400, France
- CNRS, UMR5504, Toulouse F-31400, France
| |
Collapse
|
10
|
Brison Y, Laguerre S, Lefoulon F, Morel S, Monties N, Potocki-Véronèse G, Monsan P, Remaud-Simeon M. Branching pattern of gluco-oligosaccharides and 1.5kDa dextran grafted by the α-1,2 branching sucrase GBD-CD2. Carbohydr Polym 2013; 94:567-76. [DOI: 10.1016/j.carbpol.2013.01.064] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 01/20/2013] [Accepted: 01/21/2013] [Indexed: 12/01/2022]
|
11
|
Grimaud F, Lancelon-Pin C, Rolland-Sabaté A, Roussel X, Laguerre S, Viksø-Nielsen A, Putaux JL, Guilois S, Buléon A, D’Hulst C, Potocki-Véronèse G. In Vitro Synthesis of Hyperbranched α-Glucans Using a Biomimetic Enzymatic Toolbox. Biomacromolecules 2013; 14:438-47. [DOI: 10.1021/bm301676c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Florent Grimaud
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil,
F-31077 Toulouse, France
- UMR792 Ingénierie des
Systèmes Biologiques et des Procédés, INRA, F-31400 Toulouse, France
- CNRS, UMR5504, F-31400
Toulouse, France
| | - Christine Lancelon-Pin
- CERMAV-CNRS, BP 53, F-38041 Grenoble cedex 9, France
(affiliated with Université
Joseph Fourier, member of Institut de Chimie Moléculaire de
Grenoble and Institut Carnot PolyNat)
| | | | - Xavier Roussel
- UGSF, UMR 8576, Université Lille1, sciences et technologies, Bât. C9, F-59655
Villeneuve d’Ascq, France
| | - Sandrine Laguerre
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil,
F-31077 Toulouse, France
- UMR792 Ingénierie des
Systèmes Biologiques et des Procédés, INRA, F-31400 Toulouse, France
- CNRS, UMR5504, F-31400
Toulouse, France
| | | | - Jean-Luc Putaux
- CERMAV-CNRS, BP 53, F-38041 Grenoble cedex 9, France
(affiliated with Université
Joseph Fourier, member of Institut de Chimie Moléculaire de
Grenoble and Institut Carnot PolyNat)
| | - Sophie Guilois
- UR1268 Biopolymères Interactions
Assemblages, INRA, F-44300 Nantes, France
| | - Alain Buléon
- UR1268 Biopolymères Interactions
Assemblages, INRA, F-44300 Nantes, France
| | - Christophe D’Hulst
- UGSF, UMR 8576, Université Lille1, sciences et technologies, Bât. C9, F-59655
Villeneuve d’Ascq, France
| | - Gabrielle Potocki-Véronèse
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil,
F-31077 Toulouse, France
- UMR792 Ingénierie des
Systèmes Biologiques et des Procédés, INRA, F-31400 Toulouse, France
- CNRS, UMR5504, F-31400
Toulouse, France
| |
Collapse
|
12
|
Song L, Laguerre S, Dumon C, Bozonnet S, O'Donohue MJ. A high-throughput screening system for the evaluation of biomass-hydrolyzing glycoside hydrolases. Bioresour Technol 2010; 101:8237-43. [PMID: 20579873 DOI: 10.1016/j.biortech.2010.05.097] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Revised: 05/08/2010] [Accepted: 05/28/2010] [Indexed: 05/14/2023]
Abstract
To implement a protein engineering strategy for the improvement of enzyme performance on biomass, a straightforward, robust high-throughput method was devised and tested with recombinant GH11 xylanase as acting on wheat straw. The method requires automated liquid handling equipment, but avoids the need for specialized milling and powder weighing devices and the use of labour intensive steps such as manual cutting of pipette tips. After expression in Escherichia coli cells grown in microtiter plates, recombinant xylanase was released into the culture medium and used directly for biomass hydrolysis. Reactions were monitored using a micro-3,5-dinitrosalicylic acid assay. The cumulative error of the method was less than 15%. To validate the method, randomly generated xylanase mutants were analyzed. This allowed the detection of one mutant, which produced a 74% increase in hydrolysis compared to the parental enzyme. Closer analysis revealed that this increase in activity was correlated with a twofold increase in xylanase expression.
Collapse
Affiliation(s)
- Letian Song
- Université de Toulouse, INSA, UPS, INP, France
| | | | | | | | | |
Collapse
|
13
|
Cambon E, Piamtongkam R, Bordes F, Duquesne S, Laguerre S, Nicaud JM, Marty A. A new Yarrowia lipolytica expression system: An efficient tool for rapid and reliable kinetic analysis of improved enzymes. Enzyme Microb Technol 2010. [DOI: 10.1016/j.enzmictec.2010.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
14
|
Rothenberg ML, Cox JV, Butts C, Navarro M, Bang YJ, Goel R, Gollins S, Siu LL, Laguerre S, Cunningham D. Capecitabine plus oxaliplatin (XELOX) versus 5-fluorouracil/folinic acid plus oxaliplatin (FOLFOX-4) as second-line therapy in metastatic colorectal cancer: a randomized phase III noninferiority study. Ann Oncol 2008; 19:1720-6. [PMID: 18550577 DOI: 10.1093/annonc/mdn370] [Citation(s) in RCA: 154] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND To demonstrate the noninferiority of capecitabine plus oxaliplatin (XELOX) versus 5-fluorouracil/folinic acid and oxaliplatin (FOLFOX-4) as second-line therapy in patients with metastatic colorectal cancer after prior irinotecan-based chemotherapy. PATIENTS AND METHODS A total of 627 patients were randomly assigned to receive XELOX (n = 313) or FOLFOX-4 (n = 314) following disease progression/recurrence or intolerance to irinotecan-based chemotherapy. The primary end point was progression-free survival (PFS). RESULTS PFS for XELOX was noninferior to FOLFOX-4 [hazard ratio (HR) = 0.97; 95% confidence interval (CI) 0.83-1.14] in the intention-to-treat (ITT) population. Median PFS was 4.7 months with XELOX versus 4.8 months with FOLFOX-4. The robustness of the primary analysis was supported by multivariate and subgroup analyses. Median overall survival in the ITT population was 11.9 months with XELOX versus 12.5 months with FOLFOX-4 (HR = 1.02; 95% CI 0.86-1.21). Treatment-related grade 3/4 adverse events occurred in 50% of XELOX- and 65% of FOLFOX-4-treated patients. Whereas grade 3/4 neutropenia (35% versus 5% with XELOX) and febrile neutropenia (4% versus < 1%) were more common with FOLFOX-4, grade 3/4 diarrhea (19% versus 5% with FOLFOX-4) and grade 3 hand-foot syndrome (4% versus < 1%) were more common with XELOX. CONCLUSION XELOX is noninferior to FOLFOX-4 when administered as second-line treatment in patients with metastatic colorectal cancer.
Collapse
Affiliation(s)
- M L Rothenberg
- Division of Hematology/Oncology, Vanderbilt-Ingram Cancer Center, Nashville, TN 37232-6307, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|