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Demirjian C, Razavi N, Yu G, Mayjonade B, Zhang L, Lonjon F, Chardon F, Carrere S, Gouzy J, Genin S, Macho AP, Roux F, Berthomé R, Vailleau F. An atypical NLR gene confers bacterial wilt susceptibility in Arabidopsis. Plant Commun 2023; 4:100607. [PMID: 37098653 PMCID: PMC10504594 DOI: 10.1016/j.xplc.2023.100607] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 01/19/2023] [Accepted: 04/20/2023] [Indexed: 06/12/2023]
Abstract
Quantitative disease resistance (QDR) remains the most prevalent form of plant resistance in crop fields and wild habitats. Genome-wide association studies (GWAS) have proved to be successful in deciphering the quantitative genetic basis of complex traits such as QDR. To unravel the genetics of QDR to the devastating worldwide bacterial pathogen Ralstonia solanacearum, we performed a GWAS by challenging a highly polymorphic local mapping population of Arabidopsis thaliana with four R. solanacearum type III effector (T3E) mutants, identified as key pathogenicity determinants after a first screen on an A. thaliana core collection of 25 accessions. Although most quantitative trait loci (QTLs) were highly specific to the identity of the T3E mutant (ripAC, ripAG, ripAQ, and ripU), we finely mapped a common QTL located on a cluster of nucleotide-binding domain and leucine-rich repeat (NLR) genes that exhibited structural variation. We functionally validated one of these NLRs as a susceptibility factor in response to R. solanacearum, named it Bacterial Wilt Susceptibility 1 (BWS1), and cloned two alleles that conferred contrasting levels of QDR. Further characterization indicated that expression of BWS1 leads to suppression of immunity triggered by different R. solanacearum effectors. In addition, we showed a direct interaction between BWS1 and RipAC T3E, and BWS1 and SUPPRESSOR OF G2 ALLELE OF skp1 (SGT1b), the latter interaction being suppressed by RipAC. Together, our results highlight a putative role for BWS1 as a quantitative susceptibility factor directly targeted by the T3E RipAC, mediating negative regulation of the SGT1-dependent immune response.
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Affiliation(s)
- Choghag Demirjian
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Narjes Razavi
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Gang Yu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | - Lu Zhang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fabien Lonjon
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Fabien Chardon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Sébastien Carrere
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Jérome Gouzy
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Stéphane Genin
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Alberto P Macho
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fabrice Roux
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Richard Berthomé
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Fabienne Vailleau
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France.
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Pecrix Y, Sallet E, Moreau S, Bouchez O, Carrere S, Gouzy J, Jardinaud MF, Gamas P. DNA demethylation and hypermethylation are both required for late nodule development in Medicago. Nat Plants 2022; 8:741-749. [PMID: 35817824 DOI: 10.1038/s41477-022-01188-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Plant epigenetic regulations are involved in transposable element silencing, developmental processes and responses to the environment1-7. They often involve modifications of DNA methylation, particularly through the DEMETER (DME) demethylase family and RNA-dependent DNA methylation (RdDM)8. Root nodules host rhizobia that can fix atmospheric nitrogen for the plant's benefit in nitrogen-poor soils. The development of indeterminate nodules, as in Medicago truncatula, involves successive waves of gene activation9-12, control of which raises interesting questions. Using laser capture microdissection (LCM) coupled to RNA-sequencing (SYMbiMICS data11), we previously identified 4,309 genes (termed NDD) activated in the nodule differentiation and nitrogen fixation zones, 36% of which belong to co-regulated genomic regions dubbed symbiotic islands13. We found MtDME to be upregulated in the differentiation zone and required for nodule development, and we identified 474 differentially methylated regions hypomethylated in the nodule by analysing ~2% of the genome4. Here, we coupled LCM and whole-genome bisulfite sequencing for a comprehensive view of DNA methylation, integrated with gene expression at the tissue level. Furthermore, using CRISPR-Cas9 mutagenesis of MtDRM2, we showed the importance of RdDM for CHH hypermethylation and nodule development. We thus proposed a model of DNA methylation dynamics during nodule development.
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Affiliation(s)
- Y Pecrix
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
- CIRAD, UMR PVBMT, Saint-Pierre, La Réunion, France
| | - E Sallet
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - S Moreau
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - O Bouchez
- INRAE, US1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - S Carrere
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - J Gouzy
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - M-F Jardinaud
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - P Gamas
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France.
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Badouin H, Gladieux P, Gouzy J, Siguenza S, Aguileta G, Snirc A, Le Prieur S, Jeziorski C, Branca A, Giraud T. Widespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates. Mol Ecol 2017; 26:2041-2062. [DOI: 10.1111/mec.13976] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 12/15/2016] [Accepted: 12/19/2016] [Indexed: 12/11/2022]
Affiliation(s)
- H. Badouin
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; 91400 Orsay France
| | - P. Gladieux
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; 91400 Orsay France
- UMR BGPI; Campus International de Baillarguet; INRA; 34398 Montpellier France
| | - J. Gouzy
- Laboratoire des Interactions Plantes-Microorganismes (LIPM); UMR441; INRA; 31326 Castanet-Tolosan France
- Laboratoire des Interactions Plantes-Microorganismes (LIPM); UMR2594; CNRS; 31326 Castanet-Tolosan France
| | - S. Siguenza
- Laboratoire des Interactions Plantes-Microorganismes (LIPM); UMR441; INRA; 31326 Castanet-Tolosan France
- Laboratoire des Interactions Plantes-Microorganismes (LIPM); UMR2594; CNRS; 31326 Castanet-Tolosan France
| | - G. Aguileta
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; 91400 Orsay France
| | - A. Snirc
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; 91400 Orsay France
| | - S. Le Prieur
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; 91400 Orsay France
| | - C. Jeziorski
- Genotoul; GeT-PlaGe; INRA Auzeville 31326 Castanet-Tolosan France
- UAR1209; INRA Auzeville 31326 Castanet-Tolosan France
| | - A. Branca
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; 91400 Orsay France
| | - T. Giraud
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; 91400 Orsay France
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Fortuna TM, Snirc A, Badouin H, Gouzy J, Siguenza S, Esquerre D, Le Prieur S, Shykoff JA, Giraud T. Polymorphic Microsatellite Markers for the Tetrapolar Anther-Smut Fungus Microbotryum saponariae Based on Genome Sequencing. PLoS One 2016; 11:e0165656. [PMID: 27832131 PMCID: PMC5104459 DOI: 10.1371/journal.pone.0165656] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/14/2016] [Indexed: 01/06/2023] Open
Abstract
Background Anther-smut fungi belonging to the genus Microbotryum sterilize their host plants by aborting ovaries and replacing pollen by fungal spores. Sibling Microbotryum species are highly specialized on their host plants and they have been widely used as models for studies of ecology and evolution of plant pathogenic fungi. However, most studies have focused, so far, on M. lychnidis-dioicae that parasitizes the white campion Silene latifolia. Microbotryum saponariae, parasitizing mainly Saponaria officinalis, is an interesting anther-smut fungus, since it belongs to a tetrapolar lineage (i.e., with two independently segregating mating-type loci), while most of the anther-smut Microbotryum fungi are bipolar (i.e., with a single mating-type locus). Saponaria officinalis is a widespread long-lived perennial plant species with multiple flowering stems, which makes its anther-smut pathogen a good model for studying phylogeography and within-host multiple infections. Principal Findings Here, based on a generated genome sequence of M. saponariae we developed 6 multiplexes with a total of 22 polymorphic microsatellite markers using an inexpensive and efficient method. We scored these markers in fungal individuals collected from 97 populations across Europe, and found that the number of their alleles ranged from 2 to 11, and their expected heterozygosity from 0.01 to 0.58. Cross-species amplification was examined using nine other Microbotryum species parasitizing hosts belonging to Silene, Dianthus and Knautia genera. All loci were successfully amplified in at least two other Microbotryum species. Significance These newly developed markers will provide insights into the population genetic structure and the occurrence of within-host multiple infections of M. saponariae. In addition, the draft genome of M. saponariae, as well as one of the described markers will be useful resources for studying the evolution of the breeding systems in the genus Microbotryum and the evolution of specialization onto different plant species.
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Affiliation(s)
- Taiadjana M. Fortuna
- Laboratoire d’Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
- * E-mail:
| | - Alodie Snirc
- Laboratoire d’Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Hélène Badouin
- Laboratoire d’Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Jérome Gouzy
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France
| | - Sophie Siguenza
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France
| | - Diane Esquerre
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, F-31326, France
| | - Stéphanie Le Prieur
- Laboratoire d’Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Jacqui A. Shykoff
- Laboratoire d’Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Tatiana Giraud
- Laboratoire d’Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
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Bustos-Sanmamed P, Hudik E, Laffont C, Reynes C, Sallet E, Wen J, Mysore KS, Camproux AC, Hartmann C, Gouzy J, Frugier F, Crespi M, Lelandais-Brière C. A Medicago truncatula rdr6 allele impairs transgene silencing and endogenous phased siRNA production but not development. Plant Biotechnol J 2014; 12:1308-1318. [PMID: 25060922 DOI: 10.1111/pbi.12230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 06/02/2014] [Accepted: 06/12/2014] [Indexed: 06/03/2023]
Abstract
RNA-dependent RNA polymerase 6 (RDR6) and suppressor of gene silencing 3 (SGS3) act together in post-transcriptional transgene silencing mediated by small interfering RNAs (siRNAs) and in biogenesis of various endogenous siRNAs including the tasiARFs, known regulators of auxin responses and plant development. Legumes, the third major crop family worldwide, has been widely improved through transgenic approaches. Here, we isolated rdr6 and sgs3 mutants in the model legume Medicago truncatula. Two sgs3 and one rdr6 alleles led to strong developmental defects and impaired biogenesis of tasiARFs. In contrast, the rdr6.1 homozygous plants produced sufficient amounts of tasiARFs to ensure proper development. High throughput sequencing of small RNAs from this specific mutant identified 354 potential MtRDR6 substrates, for which siRNA production was significantly reduced in the mutant. Among them, we found a large variety of novel phased loci corresponding to protein-encoding genes or transposable elements. Interestingly, measurement of GFP expression revealed that post-transcriptional transgene silencing was reduced in rdr6.1 roots. Hence, this novel mis-sense mutation, affecting a highly conserved amino acid residue in plant RDR6s, may be an interesting tool both to analyse endogenous pha-siRNA functions and to improve transgene expression, at least in legume species.
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Affiliation(s)
- Pilar Bustos-Sanmamed
- CNRS, Institut des Sciences du Végétal (ISV), UPR2355, Labex SPS Saclay Plant Sciences, Gif-sur-Yvette Cedex, France
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Carle P, Saillard C, Carrère N, Carrère S, Duret S, Eveillard S, Gaurivaud P, Gourgues G, Gouzy J, Salar P, Verdin E, Breton M, Blanchard A, Laigret F, Bové JM, Renaudin J, Foissac X. Partial chromosome sequence of Spiroplasma citri reveals extensive viral invasion and important gene decay. Appl Environ Microbiol 2010; 76:3420-6. [PMID: 20363791 PMCID: PMC2876439 DOI: 10.1128/aem.02954-09] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Accepted: 03/25/2010] [Indexed: 11/20/2022] Open
Abstract
The assembly of 20,000 sequencing reads obtained from shotgun and chromosome-specific libraries of the Spiroplasma citri genome yielded 77 chromosomal contigs totaling 1,674 kbp (92%) of the 1,820-kbp chromosome. The largest chromosomal contigs were positioned on the physical and genetic maps constructed from pulsed-field gel electrophoresis and Southern blot hybridizations. Thirty-eight contigs were annotated, resulting in 1,908 predicted coding sequences (CDS) representing an overall coding density of only 74%. Cellular processes, cell metabolism, and structural-element CDS account for 29% of the coding capacity, CDS of external origin such as viruses and mobile elements account for 24% of the coding capacity, and CDS of unknown function account for 47% of the coding capacity. Among these, 21% of the CDS group into 63 paralog families. The organization of these paralogs into conserved blocks suggests that they represent potential mobile units. Phage-related sequences were particularly abundant and include plectrovirus SpV1 and SVGII3 and lambda-like SpV2 sequences. Sixty-nine copies of transposases belonging to four insertion sequence (IS) families (IS30, IS481, IS3, and ISNCY) were detected. Similarity analyses showed that 21% of chromosomal CDS were truncated compared to their bacterial orthologs. Transmembrane domains, including signal peptides, were predicted for 599 CDS, of which 58 were putative lipoproteins. S. citri has a Sec-dependent protein export pathway. Eighty-four CDS were assigned to transport, such as phosphoenolpyruvate phosphotransferase systems (PTS), the ATP binding cassette (ABC), and other transporters. Besides glycolytic and ATP synthesis pathways, it is noteworthy that S. citri possesses a nearly complete pathway for the biosynthesis of a terpenoid.
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Affiliation(s)
- Patricia Carle
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Colette Saillard
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Nathalie Carrère
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Sébastien Carrère
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Sybille Duret
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Sandrine Eveillard
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Patrice Gaurivaud
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Géraldine Gourgues
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Jérome Gouzy
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Pascal Salar
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Eric Verdin
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Marc Breton
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Alain Blanchard
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Frédéric Laigret
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Joseph-Marie Bové
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Joel Renaudin
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Xavier Foissac
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
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7
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Lelandais-Brière C, Naya L, Sallet E, Calenge F, Frugier F, Hartmann C, Gouzy J, Crespi M. Genome-wide Medicago truncatula small RNA analysis revealed novel microRNAs and isoforms differentially regulated in roots and nodules. Plant Cell 2009; 21:2780-96. [PMID: 19767456 PMCID: PMC2768930 DOI: 10.1105/tpc.109.068130] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Revised: 07/09/2009] [Accepted: 07/26/2009] [Indexed: 05/18/2023]
Abstract
Posttranscriptional regulation of a variety of mRNAs by small 21- to 24-nucleotide RNAs, notably the microRNAs (miRNAs), is emerging as a novel developmental mechanism. In legumes like the model Medicago truncatula, roots are able to develop a de novo meristem through the symbiotic interaction with nitrogen-fixing rhizobia. We used deep sequencing of small RNAs from root apexes and nodules of M. truncatula to identify 100 novel candidate miRNAs encoded by 265 hairpin precursors. New atypical precursor classes producing only specific 21- and 24-nucleotide small RNAs were found. Statistical analysis on sequencing reads abundance revealed specific miRNA isoforms in a same family showing contrasting expression patterns between nodules and root apexes. The differentially expressed conserved and nonconserved miRNAs may target a large variety of mRNAs. In root nodules, which show diverse cell types ranging from a persistent meristem to a fully differentiated central region, we discovered miRNAs spatially enriched in nodule meristematic tissues, vascular bundles, and bacterial infection zones using in situ hybridization. Spatial regulation of miRNAs may determine specialization of regulatory RNA networks in plant differentiation processes, such as root nodule formation.
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Affiliation(s)
- Christine Lelandais-Brière
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, F-91198 Gif-sur-Yvette Cedex, France
- Université Paris Diderot-Paris 7, 75205 Paris Cedex 13, France
| | - Loreto Naya
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, F-91198 Gif-sur-Yvette Cedex, France
| | - Erika Sallet
- Laboratoire des Interactions Plantes Micro-organismes, Unité Mixte de Recherche, Centre National de la Recherche Scientifique–Institut National de la Recherche Agronomique 2594/441, F- 31320 Castanet Tolosan, France
- Plateforme Bioinformatique du Génopole Toulouse Midi-Pyrénées, Groupement d'Intérêt Scientifique Toulouse Genopole, F-31320 Castanet Tolosan, France
| | - Fanny Calenge
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, F-91198 Gif-sur-Yvette Cedex, France
- Université Paris Diderot-Paris 7, 75205 Paris Cedex 13, France
| | - Florian Frugier
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, F-91198 Gif-sur-Yvette Cedex, France
| | - Caroline Hartmann
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, F-91198 Gif-sur-Yvette Cedex, France
- Université Paris Diderot-Paris 7, 75205 Paris Cedex 13, France
| | - Jérome Gouzy
- Laboratoire des Interactions Plantes Micro-organismes, Unité Mixte de Recherche, Centre National de la Recherche Scientifique–Institut National de la Recherche Agronomique 2594/441, F- 31320 Castanet Tolosan, France
| | - Martin Crespi
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, F-91198 Gif-sur-Yvette Cedex, France
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8
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Seddas PMA, Arias CM, Arnould C, van Tuinen D, Godfroy O, Benhassou HA, Gouzy J, Morandi D, Dessaint F, Gianinazzi-Pearson V. Symbiosis-related plant genes modulate molecular responses in an arbuscular mycorrhizal fungus during early root interactions. Mol Plant Microbe Interact 2009; 22:341-351. [PMID: 19245328 DOI: 10.1094/mpmi-22-3-0341] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
To gain further insight into the role of the plant genome in arbuscular mycorrhiza (AM) establishment, we investigated whether symbiosis-related plant genes affect fungal gene expression in germinating spores and at the appressoria stage of root interactions. Glomus intraradices genes were identified in expressed sequence tag libraries of mycorrhizal Medicago truncatula roots by in silico expression analyses. Transcripts of a subset of genes, with predicted functions in transcription, protein synthesis, primary or secondary metabolism, or of unknown function, were monitored in spores and germinating spores and during interactions with roots of wild-type or mycorrhiza-defective (Myc-) mutants of M. truncatula. Not all the fungal genes were active in quiescent spores but all were expressed when G. intraradices spores germinated in wild-type M. truncatula root exudates or when appressoria or arbuscules were formed in association with wild-type M. truncatula roots. Most of the fungal genes were upregulated or induced at the stage of appressorium development. Inactivation of the M. truncatula genes DMI1, DMI2/MtSYM2, or DMI3/MtSYM13 was associated with altered fungal gene expression (nonactivation or inhibition), modified appressorium structure, and plant cell wall responses, providing first evidence that cell processes modified by symbiosis-related plant genes impact on root interactions by directly modulating AM fungal activity.
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Affiliation(s)
- Pascale M A Seddas
- UMR 1088 INRA/5184 CNRS/Université de Bourgogne, Plante-Microbe-Environnement, INRA-CMSE, BP 86510, 21065 Dijon Cedex, France.
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9
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Saillard C, Carle P, Duret-Nurbel S, Henri R, Killiny N, Carrère S, Gouzy J, Bové JM, Renaudin J, Foissac X. The abundant extrachromosomal DNA content of the Spiroplasma citri GII3-3X genome. BMC Genomics 2008; 9:195. [PMID: 18442384 PMCID: PMC2386487 DOI: 10.1186/1471-2164-9-195] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Accepted: 04/28/2008] [Indexed: 11/24/2022] Open
Abstract
Background Spiroplama citri, the causal agent of citrus stubborn disease, is a bacterium of the class Mollicutes and is transmitted by phloem-feeding leafhopper vectors. In order to characterize candidate genes potentially involved in spiroplasma transmission and pathogenicity, the genome of S. citri strain GII3-3X is currently being deciphered. Results Assembling 20,000 sequencing reads generated seven circular contigs, none of which fit the 1.8 Mb chromosome map or carried chromosomal markers. These contigs correspond to seven plasmids: pSci1 to pSci6, with sizes ranging from 12.9 to 35.3 kbp and pSciA of 7.8 kbp. Plasmids pSci were detected as multiple copies in strain GII3-3X. Plasmid copy numbers of pSci1-6, as deduced from sequencing coverage, were estimated at 10 to 14 copies per spiroplasma cell, representing 1.6 Mb of extrachromosomal DNA. Genes encoding proteins of the TrsE-TraE, Mob, TraD-TraG, and Soj-ParA protein families were predicted in most of the pSci sequences, in addition to members of 14 protein families of unknown function. Plasmid pSci6 encodes protein P32, a marker of insect transmissibility. Plasmids pSci1-5 code for eight different S. citri adhesion-related proteins (ScARPs) that are homologous to the previously described protein P89 and the S. kunkelii SkARP1. Conserved signal peptides and C-terminal transmembrane alpha helices were predicted in all ScARPs. The predicted surface-exposed N-terminal region possesses the following elements: (i) 6 to 8 repeats of 39 to 42 amino acids each (sarpin repeats), (ii) a central conserved region of 330 amino acids followed by (iii) a more variable domain of about 110 amino acids. The C-terminus, predicted to be cytoplasmic, consists of a 27 amino acid stretch enriched in arginine and lysine (KR) and an optional 23 amino acid stretch enriched in lysine, aspartate and glutamate (KDE). Plasmids pSci mainly present a linear increase of cumulative GC skew except in regions presenting conserved hairpin structures. Conclusion The genome of S. citri GII3-3X is characterized by abundant extrachromosomal elements. The pSci plasmids could not only be vertically inherited but also horizontally transmitted, as they encode proteins usually involved in DNA element partitioning and cell to cell DNA transfer. Because plasmids pSci1-5 encode surface proteins of the ScARP family and pSci6 was recently shown to confer insect transmissibility, diversity and abundance of S. citri plasmids may essentially aid the rapid adaptation of S. citri to more efficient transmission by different insect vectors and to various plant hosts.
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Affiliation(s)
- Colette Saillard
- Université Victor Ségalen Bordeaux 2, UMR 1090 Génomique Diversité Pouvoir Pathogène, BP 81, F-33883 Villenave d'Ornon, France.
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10
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Journet EP, van Tuinen D, Gouzy J, Crespeau H, Carreau V, Farmer MJ, Niebel A, Schiex T, Jaillon O, Chatagnier O, Godiard L, Micheli F, Kahn D, Gianinazzi-Pearson V, Gamas P. Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis. Nucleic Acids Res 2002; 30:5579-92. [PMID: 12490726 PMCID: PMC140066 DOI: 10.1093/nar/gkf685] [Citation(s) in RCA: 174] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2002] [Revised: 10/18/2002] [Accepted: 10/18/2002] [Indexed: 11/13/2022] Open
Abstract
We report on a large-scale expressed sequence tag (EST) sequencing and analysis program aimed at characterizing the sets of genes expressed in roots of the model legume Medicago truncatula during interactions with either of two microsymbionts, the nitrogen-fixing bacterium Sinorhizobium meliloti or the arbuscular mycorrhizal fungus Glomus intraradices. We have designed specific tools for in silico analysis of EST data, in relation to chimeric cDNA detection, EST clustering, encoded protein prediction, and detection of differential expression. Our 21 473 5'- and 3'-ESTs could be grouped into 6359 EST clusters, corresponding to distinct virtual genes, along with 52 498 other M.truncatula ESTs available in the dbEST (NCBI) database that were recruited in the process. These clusters were manually annotated, using a specifically developed annotation interface. Analysis of EST cluster distribution in various M.truncatula cDNA libraries, supported by a refined R test to evaluate statistical significance and by 'electronic northern' representation, enabled us to identify a large number of novel genes predicted to be up- or down-regulated during either symbiotic root interaction. These in silico analyses provide a first global view of the genetic programs for root symbioses in M.truncatula. A searchable database has been built and can be accessed through a public interface.
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Affiliation(s)
- Etienne-Pascal Journet
- Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, CNRS-INRA, Laboratoire de Biométrie et Intelligence Artificielle, INRA, 31326 Castanet-Tolosan Cedex, France.
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11
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Salanoubat M, Genin S, Artiguenave F, Gouzy J, Mangenot S, Arlat M, Billault A, Brottier P, Camus JC, Cattolico L, Chandler M, Choisne N, Claudel-Renard C, Cunnac S, Demange N, Gaspin C, Lavie M, Moisan A, Robert C, Saurin W, Schiex T, Siguier P, Thébault P, Whalen M, Wincker P, Levy M, Weissenbach J, Boucher CA. Genome sequence of the plant pathogen Ralstonia solanacearum. Nature 2002; 415:497-502. [PMID: 11823852 DOI: 10.1038/415497a] [Citation(s) in RCA: 608] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ralstonia solanacearum is a devastating, soil-borne plant pathogen with a global distribution and an unusually wide host range. It is a model system for the dissection of molecular determinants governing pathogenicity. We present here the complete genome sequence and its analysis of strain GMI1000. The 5.8-megabase (Mb) genome is organized into two replicons: a 3.7-Mb chromosome and a 2.1-Mb megaplasmid. Both replicons have a mosaic structure providing evidence for the acquisition of genes through horizontal gene transfer. Regions containing genetically mobile elements associated with the percentage of G+C bias may have an important function in genome evolution. The genome encodes many proteins potentially associated with a role in pathogenicity. In particular, many putative attachment factors were identified. The complete repertoire of type III secreted effector proteins can be studied. Over 40 candidates were identified. Comparison with other genomes suggests that bacterial plant pathogens and animal pathogens harbour distinct arrays of specialized type III-dependent effectors.
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Affiliation(s)
- M Salanoubat
- Genoscope and CNRS UMR-8030, 2 rue Gaston Crémieux, CP5706, 91057 Evry Cedex, France
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12
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Capela D, Barloy-Hubler F, Gouzy J, Bothe G, Ampe F, Batut J, Boistard P, Becker A, Boutry M, Cadieu E, Dréano S, Gloux S, Godrie T, Goffeau A, Kahn D, Kiss E, Lelaure V, Masuy D, Pohl T, Portetelle D, Pühler A, Purnelle B, Ramsperger U, Renard C, Thébault P, Vandenbol M, Weidner S, Galibert F. Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021. Proc Natl Acad Sci U S A 2001; 98:9877-82. [PMID: 11481430 PMCID: PMC55546 DOI: 10.1073/pnas.161294398] [Citation(s) in RCA: 269] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sinorhizobium meliloti is an alpha-proteobacterium that forms agronomically important N(2)-fixing root nodules in legumes. We report here the complete sequence of the largest constituent of its genome, a 62.7% GC-rich 3,654,135-bp circular chromosome. Annotation allowed assignment of a function to 59% of the 3,341 predicted protein-coding ORFs, the rest exhibiting partial, weak, or no similarity with any known sequence. Unexpectedly, the level of reiteration within this replicon is low, with only two genes duplicated with more than 90% nucleotide sequence identity, transposon elements accounting for 2.2% of the sequence, and a few hundred short repeated palindromic motifs (RIME1, RIME2, and C) widespread over the chromosome. Three regions with a significantly lower GC content are most likely of external origin. Detailed annotation revealed that this replicon contains all housekeeping genes except two essential genes that are located on pSymB. Amino acid/peptide transport and degradation and sugar metabolism appear as two major features of the S. meliloti chromosome. The presence in this replicon of a large number of nucleotide cyclases with a peculiar structure, as well as of genes homologous to virulence determinants of animal and plant pathogens, opens perspectives in the study of this bacterium both as a free-living soil microorganism and as a plant symbiont.
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Affiliation(s)
- D Capela
- Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, Unité Mixte de Recherche (UMR) 215 Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique, Castanet Tolosan Cedex, France
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13
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Finan TM, Weidner S, Wong K, Buhrmester J, Chain P, Vorhölter FJ, Hernandez-Lucas I, Becker A, Cowie A, Gouzy J, Golding B, Pühler A. The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti. Proc Natl Acad Sci U S A 2001; 98:9889-94. [PMID: 11481431 PMCID: PMC55548 DOI: 10.1073/pnas.161294698] [Citation(s) in RCA: 249] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Analysis of the 1,683,333-nt sequence of the pSymB megaplasmid from the symbiotic N(2)-fixing bacterium Sinorhizobium meliloti revealed that the replicon has a high gene density with a total of 1,570 protein-coding regions, with few insertion elements and regions duplicated elsewhere in the genome. The only copies of an essential arg-tRNA gene and the minCDE genes are located on pSymB. Almost 20% of the pSymB sequence carries genes encoding solute uptake systems, most of which were of the ATP-binding cassette family. Many previously unsuspected genes involved in polysaccharide biosynthesis were identified and these, together with the two known distinct exopolysaccharide synthesis gene clusters, show that 14% of the pSymB sequence is dedicated to polysaccharide synthesis. Other recognizable gene clusters include many involved in catabolic activities such as protocatechuate utilization and phosphonate degradation. The functions of these genes are consistent with the notion that pSymB plays a major role in the saprophytic competence of the bacteria in the soil environment.
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Affiliation(s)
- T M Finan
- Department of Biology, McMaster University, Hamilton, ON, Canada.
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14
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Barnett MJ, Fisher RF, Jones T, Komp C, Abola AP, Barloy-Hubler F, Bowser L, Capela D, Galibert F, Gouzy J, Gurjal M, Hong A, Huizar L, Hyman RW, Kahn D, Kahn ML, Kalman S, Keating DH, Palm C, Peck MC, Surzycki R, Wells DH, Yeh KC, Davis RW, Federspiel NA, Long SR. Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid. Proc Natl Acad Sci U S A 2001; 98:9883-8. [PMID: 11481432 PMCID: PMC55547 DOI: 10.1073/pnas.161294798] [Citation(s) in RCA: 208] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The symbiotic nitrogen-fixing soil bacterium Sinorhizobium meliloti contains three replicons: pSymA, pSymB, and the chromosome. We report here the complete 1,354,226-nt sequence of pSymA. In addition to a large fraction of the genes known to be specifically involved in symbiosis, pSymA contains genes likely to be involved in nitrogen and carbon metabolism, transport, stress, and resistance responses, and other functions that give S. meliloti an advantage in its specialized niche.
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Affiliation(s)
- M J Barnett
- Department of Biological Sciences, and Howard Hughes Medical Institute, Stanford University, CA 94305, USA
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15
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Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P, Bothe G, Boutry M, Bowser L, Buhrmester J, Cadieu E, Capela D, Chain P, Cowie A, Davis RW, Dreano S, Federspiel NA, Fisher RF, Gloux S, Godrie T, Goffeau A, Golding B, Gouzy J, Gurjal M, Hernandez-Lucas I, Hong A, Huizar L, Hyman RW, Jones T, Kahn D, Kahn ML, Kalman S, Keating DH, Kiss E, Komp C, Lelaure V, Masuy D, Palm C, Peck MC, Pohl TM, Portetelle D, Purnelle B, Ramsperger U, Surzycki R, Thebault P, Vandenbol M, Vorholter FJ, Weidner S, Wells DH, Wong K, Yeh KC, Batut J. The composite genome of the legume symbiont Sinorhizobium meliloti. Science 2001; 293:668-72. [PMID: 11474104 DOI: 10.1126/science.1060966] [Citation(s) in RCA: 835] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The scarcity of usable nitrogen frequently limits plant growth. A tight metabolic association with rhizobial bacteria allows legumes to obtain nitrogen compounds by bacterial reduction of dinitrogen (N2) to ammonium (NH4+). We present here the annotated DNA sequence of the alpha-proteobacterium Sinorhizobium meliloti, the symbiont of alfalfa. The tripartite 6.7-megabase (Mb) genome comprises a 3.65-Mb chromosome, and 1.35-Mb pSymA and 1.68-Mb pSymB megaplasmids. Genome sequence analysis indicates that all three elements contribute, in varying degrees, to symbiosis and reveals how this genome may have emerged during evolution. The genome sequence will be useful in understanding the dynamics of interkingdom associations and of life in soil environments.
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Affiliation(s)
- F Galibert
- UMR6061-CNRS, Laboratoire de Génétique et Développement, Faculté de Médecine, 2 avenue du Pr. Léon Bernard, F-35043 Rennes cedex, France
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16
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Abstract
The Sinorhizobium meliloti genome consists of three replicons. This bacterium forms an intricate symbiotic relationship with the roots of certain legumes and is considered as an agriculturally important nitrogen-fixer. A consortium of 6 European laboratories was organized to sequence its single chromosome (3.7 Mb), whereas the other two elements (pSyma 1.4 Mb and pSymb 1.7 Mb) will be sequenced by other groups.
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Affiliation(s)
- F Galibert
- UPR 41 CNRS Recombinaisons Génétiques, Faculté de Médecine, Rennes, France.
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17
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Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ, Zdobnov EM. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res 2001; 29:37-40. [PMID: 11125043 PMCID: PMC29841 DOI: 10.1093/nar/29.1.37] [Citation(s) in RCA: 704] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Signature databases are vital tools for identifying distant relationships in novel sequences and hence for inferring protein function. InterPro is an integrated documentation resource for protein families, domains and functional sites, which amalgamates the efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. Each InterPro entry includes a functional description, annotation, literature references and links back to the relevant member database(s). Release 2.0 of InterPro (October 2000) contains over 3000 entries, representing families, domains, repeats and sites of post-translational modification encoded by a total of 6804 different regular expressions, profiles, fingerprints and Hidden Markov Models. Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1,000,000 hits from 462,500 proteins in SWISS-PROT and TrEMBL). The database is accessible for text- and sequence-based searches at http://www.ebi.ac.uk/interpro/. Questions can be emailed to interhelp@ebi.ac.uk.
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Affiliation(s)
- R Apweiler
- EMBL Outstation - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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18
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Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ, Zdobnov EM. InterPro--an integrated documentation resource for protein families, domains and functional sites. Bioinformatics 2000; 16:1145-50. [PMID: 11159333 DOI: 10.1093/bioinformatics/16.12.1145] [Citation(s) in RCA: 228] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION InterPro is a new integrated documentation resource for protein families, domains and functional sites, developed initially as a means of rationalising the complementary efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. RESULTS Merged annotations from PRINTS, PROSITE and Pfam form the InterPro core. Each combined InterPro entry includes functional descriptions and literature references, and links are made back to the relevant parent database(s), allowing users to see at a glance whether a particular family or domain has associated patterns, profiles, fingerprints, etc. Merged and individual entries (i.e. those that have no counterpart in the companion resources) are assigned unique accession numbers. Release 1.2 of InterPro (June 2000) contains over 3000 entries, representing families, domains, repeats and sites of post-translational modification (PTMs) encoded by 6581 different regular expressions, profiles, fingerprints and Hidden Markov Models (HMMs). Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1000000 hits from 264333 different proteins out of 384572 in SWISS-PROT and TrEMBL).
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Affiliation(s)
- R Apweiler
- EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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Corpet F, Servant F, Gouzy J, Kahn D. ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res 2000; 28:267-9. [PMID: 10592243 PMCID: PMC102458 DOI: 10.1093/nar/28.1.267] [Citation(s) in RCA: 264] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/1999] [Accepted: 10/08/1999] [Indexed: 11/13/2022] Open
Abstract
ProDom contains all protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases (http://www. toulouse.inra.fr/prodom.html ). ProDom-CG results from a similar domain analysis as applied to completed genomes (http://www.toulouse. inra.fr/prodomCG.html ). Recent improvements to the ProDom database and its server include: scaling up to include sequences from TrEMBL, addition of Pfam-A entries to the set of expert validated families, assignment of stable accession numbers, consistency indicators for domain families, domain arrangements of sub-families and links to Pfam-A.
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Affiliation(s)
- F Corpet
- Laboratoire de Génétique Cellulaire, INRA/CNRS, BP 27, F-31326 Castanet-Tolosan, Cedex, France
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Abstract
MOTIVATION Multiple alignments of protein sequences are the basis of structural and functional analysis of protein families. It is however difficult even for an expert biologist to comprehend an alignment of more than 50 to 100 homologous sequences. RESULTS This paper presents a browser for the analysis of multiple alignments of large numbers of protein sequences. Phylogenetic trees and consensus sequences are computed and used to summarise the alignments; these data are stored in a structure called Rich Family Description. Summary alignments and trees are displayed in HTML pages and can be developed or reduced by the user. This browser is used to display the ProDom domain families on the Web. Its zooming facilities allow extracting information from alignments of more than 1000 homologous sequences.
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Affiliation(s)
- F Corpet
- Laboratoire de Génétique Cellulaire, Centre INRA de Toulouse, Castanet, France.
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Capela D, Barloy-Hubler F, Gatius MT, Gouzy J, Galibert F. A high-density physical map of Sinorhizobium meliloti 1021 chromosome derived from bacterial artificial chromosome library. Proc Natl Acad Sci U S A 1999; 96:9357-62. [PMID: 10430947 PMCID: PMC17787 DOI: 10.1073/pnas.96.16.9357] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [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: 11/18/2022] Open
Abstract
As part of the European Sinorhizobium meliloti (strain 1021) chromosome sequencing project, four genomic bacterial artificial chromosome (BAC) libraries have been constructed, one of which was mainly used for chromosome mapping. This library consists of 1,824 clones with an average insert size of 80 kilobases and represents approximately 20-fold total genome coverage [6.8 megabases (Mbs)]. PCR screening of 384 BAC clones with 447 chromosomal markers (PCR primer pairs), consisting of 73 markers representing 118 genes (40 individual genes and 78 genes clustered in 23 operons), two markers from the rrn operon (three loci), four markers from insertion sequences (approximately 16 loci) and 368 sequence-tagged sites allowed the identification of 252 chromosomal BAC clones and the construction of a high-density physical map of the whole 3.7-Mb chromosome of S. meliloti. An average of 5.5 overlapping and colinear BAC clones per marker, correlated with a low rate of deleted or rearranged clones (0.8%) indicate a solid BAC contigation and a correct mapping. Systematic BLASTX analysis of sequence-tagged site marker sequences allowed prediction of a biological function for a number of putative ORFs. Results are available at. This map, whose resolution averages one marker every 9 kilobases, should provide a valuable tool for further sequencing, functional analysis, and positional cloning.
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Affiliation(s)
- D Capela
- Laboratoire Recombinaisons Génétiques, Centre National de la Recherche Scientifique-UPR41, 2 Avenue du Pr Léon Bernard, 35043 Rennes Cedex, France
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Abstract
We present the outcome of a systematic analysis of protein domain shuffling in 17 completed microbial genomes. This analysis has been performed using MKDOM Version 2, a completely new version of the domain clustering program MKDOM based on PSI-BLAST recursive homology searches. It allows to delineate the most frequent protein domain building blocks, which domains are found specifically in Bacteria, Archaea or yeast, and which domains are shared between two or all three domains of life. The latter are good candidates as the basic protein building blocks underlying all forms of cellular life. Statistics of multi-domain proteins indicate that some organisms such as Bacillus subtilis or Mycobacterium tuberculosis contain an abnormally high number of large multi-domain proteins. We also provide examples of highly shuffled or circularly permutated domains. A WWW graphical interface has been made available to interactively browse domain arrangements of proteins in all 17 genomes, at http:@www.toulouse.inra.fr/prodomCG.html.
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Affiliation(s)
- J Gouzy
- Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, I.N.R.A./C.N.R.S., BP27, Castanet-Tolosan, France
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Abstract
The ProDom database contains protein domain families generated from the SWISS-PROT database by automated sequence comparisons. The current version was built with a new improved procedure based on recursive PSI-BLAST homology searches. ProDom can be searched on the World Wide Web to study domain arrangements within either known families or new proteins, with the help of a user-friendly graphical interface (http://www.toulouse.inra.fr/prodom.html). Recent improvements to the ProDom server include: ProDom queries under the SRS Sequence Retrieval System; links to the PredictProtein server; phylogenetic trees and condensed multiple alignments for a better representation of large domain families, with zooming in and out capabilities. In addition, a similar server was set up to display the outcome of whole genome domain analysis as applied to 17 completed microbial genomes (http://www.toulouse.inra.fr/prodomCG.html ).
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Affiliation(s)
- F Corpet
- Laboratoire de Génétique Cellulaire, INRA, BP27, F-31326 Castanet-Tolosan cedex, France.
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Abstract
The ProDom database contains protein domain families generated from the SWISS-PROT database by automated sequence comparisons. It can be searched on the World Wide Web (http://protein.toulouse.inra. fr/prodom.html ) or by E-mail (prodom@toulouse.inra.fr) to study domain arrangements within known families or new proteins. Strong emphasis has been put on the graphical user interface which allows for interactive analysis of protein homology relationships. Recent improvements to the server include: ProDom search by keyword; links to PROSITE and PDB entries; more sensitive ProDom similarity search with BLAST or WU-BLAST; alignments of query sequences with homologous ProDom domain families; and links to the SWISS-MODEL server (http: //www.expasy.ch/swissmod/SWISS-MODEL.html ) for homology based 3-D domain modelling where possible.
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Affiliation(s)
- F Corpet
- Laboratoire de Génétique Cellulaire and Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, INRA/CNRS, BP 27, F-31326 Castanet-Tolosan Cedex, France
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Gouzy J, Eugéne P, Greene EA, Kahn D, Corpet F. XDOM, a graphical tool to analyse domain arrangements in any set of protein sequences. Comput Appl Biosci 1997; 13:601-8. [PMID: 9475988 DOI: 10.1093/bioinformatics/13.6.601] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
MOTIVATION To extract the maximum possible information from a set of protein sequences, its modular organization must be known and clearly displayed. This is important both for structural and functional analysis. RESULTS This paper presents an algorithm and a graphical interface called XDOM which performs a systematic analysis of the modular organization of any set of protein sequences. The algorithm is an automatic method to identify putative domains from sequence comparisons. The graphical tool displays the proteins as a set of linked boxes, corresponding to its domains. The method has been tested on a family of bacterial proteins and on whole genomes. It is currently applied to the complete SWISS-PROT database to build the PRODOM database. AVAILABILITY XDOM is available free of charge by anonymous ftp:¿¿ftp://ftp.toulouse.inra.fr/pub/xdom¿ ¿. The ProDom database can be consulted at ¿¿http://protein.toulouse.inra.fr/prodom.html¿¿.
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Affiliation(s)
- J Gouzy
- Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, INRA/CNRS, Castanet-Tolosan, France. [mailto:]
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Chevalet C, Gouzy J, SanCristobal-Gaudy M. Regional assignment of genetic markers using a somatic cell hybrid panel: a WWW interactive program available for the pig genome. Comput Appl Biosci 1997; 13:69-73. [PMID: 9088711 DOI: 10.1093/bioinformatics/13.1.69] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
MOTIVATION Quick and easy gene mapping by the use of a panel of cytogenetically characterized somatic cell hybrids is possible, even if some discordant experimental results arise. RESULTS An interactive program is proposed and is made available on a WWW site to users of a somatic cell hybrid panel. Assignments to chromosomes and subchromosomal regions are based on likelihood calculations and Bayes' theorem, and a confidence level is provided. The method is illustrated in the case of the pig genome.
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Affiliation(s)
- C Chevalet
- Laboratoire de Génétique Cellulaire, Institut National de la Recherche Agronomique BP 27, Tolosan, France.
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Affiliation(s)
- J Gouzy
- Institut National de la Becherche Agronomique, LBMRPM, Castanet Tolosan, France
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Gouzy J, Cluzel B, Artieres J. [A case of schwannoma of the floor of the mouth]. JFORL J Fr Otorhinolaryngol Audiophonol Chir Maxillofac 1972; 21:501-4. [PMID: 4264659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Gouzy J, Mouillaux J, Drevet D. [A case of sudden deafness with auditory recuperation monitored by automatic audiometry]. J Fr Otorhinolaryngol Audiophonol Chir Maxillofac (1967) 1969; 18:691-7. [PMID: 4249639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Gouzy J, Bernard G, Voilque G, Mouillaux J. [The maxillary sinus, route of approach to various projectiles deep in the face]. J Fr Otorhinolaryngol Audiophonol Chir Maxillofac (1967) 1969; 18:105-10. [PMID: 4245843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Gouzy J, Stipon J, Drevet D. [Changes in the tympanic membarne caused by blast effect and their anatomical development. A propos of 200 cases]. J Fr Otorhinolaryngol Audiophonol Chir Maxillofac (1967) 1968; 17:469-75. [PMID: 4236839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Gouzy J, Prudhon C, Voilque G. [A case of fibrous osteodysplasia of the upper maxilla]. J Fr Otorhinolaryngol Audiophonol Chir Maxillofac (1967) 1968; 17:79-84. [PMID: 4231450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Gouzy J, Meunier JL, Voilque G, Mouillaux J. [A particular case of cranio-facial dysostosis with bilateral deafness of perception]. Rev Laryngol Otol Rhinol (Bord) 1966; 87:1037-46. [PMID: 5992131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Gouzy J, Meunier JL, Stipon JP. [Foreign body in the esophagus. Removal by thoracotomy 5 months after ingestion]. J Fr Otorhinolaryngol Chir Maxillofac 1966; 15:777-82. [PMID: 5957573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Gouzy J, Meunier JL, Stipon JP. [Unusual aspect of 2 benign tumors of the oral cavity]. J Fr Otorhinolaryngol Chir Maxillofac 1966; 15:785-92. [PMID: 5957574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Bonjean M, Gouzy J, Ramaniraka G. [Launois-Bensaude adenolipomatosis]. Lyon Med 1966; 216:192-3. [PMID: 5916438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Gouzy J, Piquet JJ, Costa J. [Apropos of a voluminous ethmofrontal osteoma]. J Fr Otorhinolaryngol Chir Maxillofac 1965; 14:317-25. [PMID: 5848786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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