Comparative analysis of the pathogenesis-related protein 10 gene family and their role during legume symbiosis / Toufik Yahia Takhi

Public ISBD Titre : Comparative analysis of the pathogenesis-related protein 10 gene family and their role during legume symbiosis Type de document : document multimédia Auteurs : Toufik Yahia Takhi, Auteur ; Fathi Berrabah, Directeur de thèse ; Véronique Gruber, Directeur de thèse Editeur : Laghouat : Université Amar Telidji - Département de biologie Année de publication : 2024 Importance : 55 p. Accompagnement : 1 disque optique numérique (CD-ROM) Note générale : Option : Microbiologie appliquée Langues : Anglais Mots-clés : PR10  Medicago  Nodule defense response  Nodule immunity  Symbiosis Résumé : Pathogenesis-related class 10 (PR10) proteins play various roles during plants’ growth and resistance to biotic and abiotic stress. However, little is known about their role in the context of legume-rhizobia symbiosis, particularly in nodules. This present study aims to bridge that gap by characterizing the various roles of PR10s in the nodules of Medicago truncatula (Medtr). Initially, phylogenetic analysis of PR10s revealed two distinct PR10 groups, PBI and PBII. The expression analysis performed on nodules of two Medtr mutants, symbiotic Cysteine-rich Kinase-Like (symCRK) and defective in nitrogen fixation 2 (dnf2), showed an upregulation of PR10s in symCRK and dnf2 mutant nodules compared to the WT, with PBI showing a higher expression than PBII. Collinearity analysis revealed three collinear PR10 gene pairs that all belong to PBI, suggesting that PR10s were possibly subjected to tandem gene duplication. The multiple sequence alignments of 500 nucleotides up-stream PR10 genes show a high conservation of 250 nucleotides in that site between PBI PR10 genes and a loss of this conservation in PBII PR10 genes. The conserved 250 up-stream nucleotides display a high density of putative binding sites for bZIP, NAC, and Myb transcription factors. Interestingly, molecular docking findings highlight that PBI PR10s bind phenolic compounds more efficiently than PBII. Moreover, multiple sequence alignments revealed that, unlike PBII PR10 proteins, PBI proteins have a high conservation of RNase motifs, which are important for the activation of programmed cell death during plant defenses. Finally, protein enrichment data revealed that PR10s can additionally accumulate in the different cellular compartments of nodules, including the cytoplasm, microsomes, and symbiosome. Altogether, our data show that PBI PR10s of M. truncatula are more conserved and highly functional during nodule defense responses compared to PBII PR10s. Thus, this study provides a valuable understanding of PR10s and their role during legume-rhizobia symbiosis. note de thèses : Mémoire de master en sciences biologiques Comparative analysis of the pathogenesis-related protein 10 gene family and their role during legume symbiosis [document multimédia] / Toufik Yahia Takhi, Auteur ; Fathi Berrabah, Directeur de thèse ; Véronique Gruber, Directeur de thèse . - Laghouat : Université Amar Telidji - Département de biologie, 2024 . - 55 p. + 1 disque optique numérique (CD-ROM). Option : Microbiologie appliquée Langues : Anglais Mots-clés : PR10  Medicago  Nodule defense response  Nodule immunity  Symbiosis Résumé : Pathogenesis-related class 10 (PR10) proteins play various roles during plants’ growth and resistance to biotic and abiotic stress. However, little is known about their role in the context of legume-rhizobia symbiosis, particularly in nodules. This present study aims to bridge that gap by characterizing the various roles of PR10s in the nodules of Medicago truncatula (Medtr). Initially, phylogenetic analysis of PR10s revealed two distinct PR10 groups, PBI and PBII. The expression analysis performed on nodules of two Medtr mutants, symbiotic Cysteine-rich Kinase-Like (symCRK) and defective in nitrogen fixation 2 (dnf2), showed an upregulation of PR10s in symCRK and dnf2 mutant nodules compared to the WT, with PBI showing a higher expression than PBII. Collinearity analysis revealed three collinear PR10 gene pairs that all belong to PBI, suggesting that PR10s were possibly subjected to tandem gene duplication. The multiple sequence alignments of 500 nucleotides up-stream PR10 genes show a high conservation of 250 nucleotides in that site between PBI PR10 genes and a loss of this conservation in PBII PR10 genes. The conserved 250 up-stream nucleotides display a high density of putative binding sites for bZIP, NAC, and Myb transcription factors. Interestingly, molecular docking findings highlight that PBI PR10s bind phenolic compounds more efficiently than PBII. Moreover, multiple sequence alignments revealed that, unlike PBII PR10 proteins, PBI proteins have a high conservation of RNase motifs, which are important for the activation of programmed cell death during plant defenses. Finally, protein enrichment data revealed that PR10s can additionally accumulate in the different cellular compartments of nodules, including the cytoplasm, microsomes, and symbiosome. Altogether, our data show that PBI PR10s of M. truncatula are more conserved and highly functional during nodule defense responses compared to PBII PR10s. Thus, this study provides a valuable understanding of PR10s and their role during legume-rhizobia symbiosis. note de thèses : Mémoire de master en sciences biologiques

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Identification and study of endophytic bacteria in the model plant Medicago truncatula / Fatima Zahra Djokhdem

Public ISBD Titre : Identification and study of endophytic bacteria in the model plant Medicago truncatula Type de document : document multimédia Auteurs : Fatima Zahra Djokhdem, Auteur ; Fathi Berrabah, Directeur de thèse ; Véronique Gruber, Directeur de thèse Editeur : Laghouat : Université Amar Telidji - Département de biologie Année de publication : 2023 Importance : 50 p. Accompagnement : 1 disque optique numérique (CD-ROM) Note générale : Option : Basic and applied microbiology (Microbiologie appliquée) Langues : Anglais Résumé : In this study, the effects of endophytes on the Medicago-Sinorhizobium symbiosis and the interaction between Medicago and endophyte bacteria were studied. For this, soil from organic farms or the desert was used to create a collection of endophytic bacterial strains. The capacity of 46 of them to infect Medicago R108 and A17 roots under axenic conditions was investigated. Five strains (M17, M18, M50, M67.2 and BT-37) among the forty validated bacteria were selected for molecular identification .We studied the potential effects of the PGPR of the strain studied, the analysis of the response of Medicago to salt stress in the presence or in the absence of endophytes was evaluated. The results indicate the presence of various effects of the tested strain on the protection of Medicago against abiotic stress. Interestingly, the less infectious strain may possess the highest protection against salt stress. the qPCR analysis of the PR10, PR5 and NDR1-Like genes after inoculation of the A17 ecotype by the endophytes showed Different levels of immune stimulation are observed depending on the strain used. Interestingly, the expressions of the PR10 genes are correlated with the level of tissue occupancy by endophytes .Finally, we have studied the impact of endophytes on the Medicago-Sinorhizobium symbiosis, a co-inoculation of Medicago with the strain studied and the rhizobium was carried out. Our preliminary data suggest that endophytes have a weak impact on the initiation of the symbiotic interaction. endophytes tested are able to infect nodules and reduce nitrogen-fixing capacity. Interestingly, Lysinibaccillus sp. These show the lowest root colonization ability, display the highest nodule infection rates. This observation underlies the difference between nodule and roots and could be explained by the difference in immunity and/or metabolic status. Finally we were able to demonstrate that infection rates do not seem to be correlated with nitrogen fixation. note de thèses : Mémoire de master en sciences biologiques Identification and study of endophytic bacteria in the model plant Medicago truncatula [document multimédia] / Fatima Zahra Djokhdem, Auteur ; Fathi Berrabah, Directeur de thèse ; Véronique Gruber, Directeur de thèse . - Laghouat : Université Amar Telidji - Département de biologie, 2023 . - 50 p. + 1 disque optique numérique (CD-ROM). Option : Basic and applied microbiology (Microbiologie appliquée) Langues : Anglais Résumé : In this study, the effects of endophytes on the Medicago-Sinorhizobium symbiosis and the interaction between Medicago and endophyte bacteria were studied. For this, soil from organic farms or the desert was used to create a collection of endophytic bacterial strains. The capacity of 46 of them to infect Medicago R108 and A17 roots under axenic conditions was investigated. Five strains (M17, M18, M50, M67.2 and BT-37) among the forty validated bacteria were selected for molecular identification .We studied the potential effects of the PGPR of the strain studied, the analysis of the response of Medicago to salt stress in the presence or in the absence of endophytes was evaluated. The results indicate the presence of various effects of the tested strain on the protection of Medicago against abiotic stress. Interestingly, the less infectious strain may possess the highest protection against salt stress. the qPCR analysis of the PR10, PR5 and NDR1-Like genes after inoculation of the A17 ecotype by the endophytes showed Different levels of immune stimulation are observed depending on the strain used. Interestingly, the expressions of the PR10 genes are correlated with the level of tissue occupancy by endophytes .Finally, we have studied the impact of endophytes on the Medicago-Sinorhizobium symbiosis, a co-inoculation of Medicago with the strain studied and the rhizobium was carried out. Our preliminary data suggest that endophytes have a weak impact on the initiation of the symbiotic interaction. endophytes tested are able to infect nodules and reduce nitrogen-fixing capacity. Interestingly, Lysinibaccillus sp. These show the lowest root colonization ability, display the highest nodule infection rates. This observation underlies the difference between nodule and roots and could be explained by the difference in immunity and/or metabolic status. Finally we were able to demonstrate that infection rates do not seem to be correlated with nitrogen fixation. note de thèses : Mémoire de master en sciences biologiques

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Understanding phenols function during tripartite interaction between legume- rhizobia and endophytic bacteria / Maroua Makhloufi

Public ISBD Titre : Understanding phenols function during tripartite interaction between legume- rhizobia and endophytic bacteria Type de document : document multimédia Auteurs : Maroua Makhloufi, Auteur ; Fathi Berrabah, Directeur de thèse ; Véronique Gruber, Directeur de thèse Editeur : Laghouat : Université Amar Telidji - Département de biologie Année de publication : 2024 Importance : 42 p. Accompagnement : 1 disque optique numérique (CD-ROM) Note générale : Option : Microbiologie appliquée Langues : Anglais Mots-clés : Nodule  immunity  Phenols  Sinorhizobium  Symbiosis Résumé : Rhizobia can live inside the nodule plant under the control of several genes that regulate immunity. Five genes were identified that have a crucial role in immunity repression including RSD, SymCRK, NAD1 and NIN-16. A mutation in these genes results in the formation of necrotic nodules characterised by the activation of the immune response and the induction of defence related proteins and with the accumulation of phenolic compounds (PCs). Little is known about phenolic accumulation during nodule defence response, our study aims to understand the regulation of these phenols inside the nodule and the role of PCs during the legume-rhizobium symbiosis. Analysis of RNAseq data was performed to identify the genes involved in the biosynthesis of PCs. As result, many gene families were determined to be up-regulated, and a conserved up-regulated PCs metabolic pathway was identified between rsd, symCRK, nad1 and nin-16 mutants. The phylogenetic analysis of two up-regulated genes family; chalcone synthase and caffeic acid O methyltransferase, indicates that probably one group of each family evolved to control the immune response in nodules. In addition, an alignment of three nucleotide sequences of three genes, two genes from the chalcone synthase family and one gene from the PR10 family in the 5’-UTR upstream region shows the presence of a conserved nucleotide block, indicating the presence of common transcription factors regulating PCs biosynthetic genes. To understand the role of PCs during immunity response, antimicrobial activity of selected PCs was tested on Sinorhzibium medicae WSM419 and endophytic bacteria. The results show significant inhibition of S. medicae WSM419, which indicates high sensitivity of the symbionte to PCs. Our data support the hypothesis that PCs accumulation compromises the symbionte survival inside the nodule. note de thèses : Mémoire de master en sciences biologiques Understanding phenols function during tripartite interaction between legume- rhizobia and endophytic bacteria [document multimédia] / Maroua Makhloufi, Auteur ; Fathi Berrabah, Directeur de thèse ; Véronique Gruber, Directeur de thèse . - Laghouat : Université Amar Telidji - Département de biologie, 2024 . - 42 p. + 1 disque optique numérique (CD-ROM). Option : Microbiologie appliquée Langues : Anglais Mots-clés : Nodule  immunity  Phenols  Sinorhizobium  Symbiosis Résumé : Rhizobia can live inside the nodule plant under the control of several genes that regulate immunity. Five genes were identified that have a crucial role in immunity repression including RSD, SymCRK, NAD1 and NIN-16. A mutation in these genes results in the formation of necrotic nodules characterised by the activation of the immune response and the induction of defence related proteins and with the accumulation of phenolic compounds (PCs). Little is known about phenolic accumulation during nodule defence response, our study aims to understand the regulation of these phenols inside the nodule and the role of PCs during the legume-rhizobium symbiosis. Analysis of RNAseq data was performed to identify the genes involved in the biosynthesis of PCs. As result, many gene families were determined to be up-regulated, and a conserved up-regulated PCs metabolic pathway was identified between rsd, symCRK, nad1 and nin-16 mutants. The phylogenetic analysis of two up-regulated genes family; chalcone synthase and caffeic acid O methyltransferase, indicates that probably one group of each family evolved to control the immune response in nodules. In addition, an alignment of three nucleotide sequences of three genes, two genes from the chalcone synthase family and one gene from the PR10 family in the 5’-UTR upstream region shows the presence of a conserved nucleotide block, indicating the presence of common transcription factors regulating PCs biosynthetic genes. To understand the role of PCs during immunity response, antimicrobial activity of selected PCs was tested on Sinorhzibium medicae WSM419 and endophytic bacteria. The results show significant inhibition of S. medicae WSM419, which indicates high sensitivity of the symbionte to PCs. Our data support the hypothesis that PCs accumulation compromises the symbionte survival inside the nodule. note de thèses : Mémoire de master en sciences biologiques

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