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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A comparative genomics study of Sinorhizobium spp. strains highlighting the molecular mechanisms underlying partner specificity in rhizobia-legume symbiosis / Mohamed Abdenour Rezzoug

Public ISBD Titre : A comparative genomics study of Sinorhizobium spp. strains highlighting the molecular mechanisms underlying partner specificity in rhizobia-legume symbiosis Type de document : document multimédia Auteurs : Mohamed Abdenour Rezzoug, Auteur ; Fathi Berrabah, Directeur de thèse ; Asma Rezzoug, Directeur de thèse Editeur : Laghouat : Université Amar Telidji - Département de biologie Année de publication : 2025 Importance : 50 p. Accompagnement : 1 disque optique numérique (CD-ROM) Note générale : Option : Microbiologie Langues : Anglais Mots-clés : Rhizobia  nodules  plant phenolic compounds  bacterial conjugation  symbiosis Résumé : Bacteria from the genus Sinorhizobium can form a symbiotic relationship with various leguminous plants, such as the model legume Medicago truncatula. This plant-microbe association induces the formation of specialized plant organs called root nodules, inside which the bacteria perform symbiotic nitrogen fixation (SNF). Among the methods of controlling the symbiotic process by the plant is the secretion of phenolic compounds (PCs), which acts as signaling molecules and have a potential role in modulating bacterial communities as a defense mechanism during symbiotic nodulation. This study aims to elucidate some of the molecular mechanisms involved in the selection of plant growth promoting Rhizobacteria (PGPR) by the host and factors determining symbiont specificity. Phenolic acid bioassays coupled with a comparison of the Pan-Genome of various Sinorhizobium spp. strains revealed key differences in gene features and distribution, especially in strain-specific genes found predominately within one of the symbiotic megaplasmids of S. meliloti, pSymA. Synteny analysis showed varying presence of rctB, a plasmid transfer transcription regulator. The gene was not present in two organisms, S. meliloti AK83 and S. medicae WSM419; these two strains were shown to be susceptible to the antimicrobial effect of gallic acid (GA), indicating the importance of plasmid conjugation during symbiosis. Transcriptome analysis further supported this idea. We found that genes directly involved in plasmid transfer, such as traA relaxases and Type IV Secretion System (T4SS) proteins, genes present in pSymA, were substantially up-regulated during the N2-fixation phase of root nodulation. Protein sequence comparison showed considerable dissimilarity in proteins encoded by pSymA compared to the rest of the genome. The similar localization of plasmid transfer genes and the majority of strain-specific genes indicates the importance of the megaplasmid in determining plant-microbe compatibility and N2-fixation effectiveness. This study provides insight into the molecular differences between various strains of Sinorhizobium spp. influencing their symbiotic prowess and the potential basis for the control mechanisms of plant-microbe interactions. note de thèses : Mémoire de master en en sciences biologiques A comparative genomics study of Sinorhizobium spp. strains highlighting the molecular mechanisms underlying partner specificity in rhizobia-legume symbiosis [document multimédia] / Mohamed Abdenour Rezzoug, Auteur ; Fathi Berrabah, Directeur de thèse ; Asma Rezzoug, Directeur de thèse . - Laghouat : Université Amar Telidji - Département de biologie, 2025 . - 50 p. + 1 disque optique numérique (CD-ROM). Option : Microbiologie Langues : Anglais Mots-clés : Rhizobia  nodules  plant phenolic compounds  bacterial conjugation  symbiosis Résumé : Bacteria from the genus Sinorhizobium can form a symbiotic relationship with various leguminous plants, such as the model legume Medicago truncatula. This plant-microbe association induces the formation of specialized plant organs called root nodules, inside which the bacteria perform symbiotic nitrogen fixation (SNF). Among the methods of controlling the symbiotic process by the plant is the secretion of phenolic compounds (PCs), which acts as signaling molecules and have a potential role in modulating bacterial communities as a defense mechanism during symbiotic nodulation. This study aims to elucidate some of the molecular mechanisms involved in the selection of plant growth promoting Rhizobacteria (PGPR) by the host and factors determining symbiont specificity. Phenolic acid bioassays coupled with a comparison of the Pan-Genome of various Sinorhizobium spp. strains revealed key differences in gene features and distribution, especially in strain-specific genes found predominately within one of the symbiotic megaplasmids of S. meliloti, pSymA. Synteny analysis showed varying presence of rctB, a plasmid transfer transcription regulator. The gene was not present in two organisms, S. meliloti AK83 and S. medicae WSM419; these two strains were shown to be susceptible to the antimicrobial effect of gallic acid (GA), indicating the importance of plasmid conjugation during symbiosis. Transcriptome analysis further supported this idea. We found that genes directly involved in plasmid transfer, such as traA relaxases and Type IV Secretion System (T4SS) proteins, genes present in pSymA, were substantially up-regulated during the N2-fixation phase of root nodulation. Protein sequence comparison showed considerable dissimilarity in proteins encoded by pSymA compared to the rest of the genome. The similar localization of plasmid transfer genes and the majority of strain-specific genes indicates the importance of the megaplasmid in determining plant-microbe compatibility and N2-fixation effectiveness. This study provides insight into the molecular differences between various strains of Sinorhizobium spp. influencing their symbiotic prowess and the potential basis for the control mechanisms of plant-microbe interactions. note de thèses : Mémoire de master en en sciences biologiques

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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M.... / Nour Wissam Boudhalaa

Public ISBD Titre : M.... Type de document : document multimédia Auteurs : Nour Wissam Boudhalaa, Auteur ; Faiza Hamini, Directeur de thèse ; Fathi Berrabah, Directeur de thèse Editeur : Laghouat : Université Amar Telidji - Département d'agronomie Année de publication : 2025 Importance : 28 p. Accompagnement : 1 disque optique numérique (CD-ROM) Note générale : Option : Applied microbiology Langues : Français Note de contenu : In order to obtain a diploma - a startup/a patent of invention within the framework of the decree n°1275 of September 27, 2022 note de thèses : Mémoire de master en en sciences biologiques M.... [document multimédia] / Nour Wissam Boudhalaa, Auteur ; Faiza Hamini, Directeur de thèse ; Fathi Berrabah, Directeur de thèse . - Laghouat : Université Amar Telidji - Département d'agronomie, 2025 . - 28 p. + 1 disque optique numérique (CD-ROM). Option : Applied microbiology Langues : Français Note de contenu : In order to obtain a diploma - a startup/a patent of invention within the framework of the decree n°1275 of September 27, 2022 note de thèses : Mémoire de master en en sciences biologiques

Protection of Alfalfa from salt stress using Endophytic bacteria / Rania Berkai

Public ISBD Titre : Protection of Alfalfa from salt stress using Endophytic bacteria Type de document : document multimédia Auteurs : Rania Berkai, Auteur ; Fathi Berrabah, Directeur de thèse ; Asma Rezzoug, Directeur de thèse Editeur : Laghouat : Université Amar Telidji - Département de biologie Année de publication : 2024 Importance : 54 p. Accompagnement : 1 disque optique numérique (CD-ROM) Note générale : Option : Microbiologie appliquée Langues : Anglais Mots-clés : Plant microbiome  Salt stress  Endophytic bacteria  PGPR  Genes Résumé : Endophytes are microorganisms mostly bacteria present asymptomatically in plants and can exercise several beneficial activities for their hosts. There are many reports currently that microorganisms isolated from the extreme environments have great biotechnological applications in medicine, agriculture, and industry. Alfalfa is a fodder legume of great S116) were studied for their ability to reduce Medicago sativa salt stress. Results show different levels in responses of M. sativa alfalfa. Genomic analyses were performed using selectedeconomic importance, but its productivity is often affected by salt stress in arid and semi-arid regions. Endophytic bacteria, which colonize the internal tissues of plants in a symbiotic manner, represent a promising solution for improving the salt tolerance of alfalfa. To improve alfalfa salt stress resistance, four endophytic bacteria (M17, M50, S113 and strains M17 that show a good protection from salt stress. M17 is identified as Pseudomonas aeruginosastrain, Comparative genomic for both strains is illustrated. For Pseudomonas strains (M17): two strains associated with plants and two non-associated with plant, one phytopathogens and Human pathogen). The results shows 521 common genes and synteny analyses revelas a high conservation between the bacteria associated with plants. Pseudomonas which indicate a mechanism to protect plants from salt and other abiotic and biotic stresses. note de thèses : Mémoire de master en sciences biologiques Protection of Alfalfa from salt stress using Endophytic bacteria [document multimédia] / Rania Berkai, Auteur ; Fathi Berrabah, Directeur de thèse ; Asma Rezzoug, Directeur de thèse . - Laghouat : Université Amar Telidji - Département de biologie, 2024 . - 54 p. + 1 disque optique numérique (CD-ROM). Option : Microbiologie appliquée Langues : Anglais Mots-clés : Plant microbiome  Salt stress  Endophytic bacteria  PGPR  Genes Résumé : Endophytes are microorganisms mostly bacteria present asymptomatically in plants and can exercise several beneficial activities for their hosts. There are many reports currently that microorganisms isolated from the extreme environments have great biotechnological applications in medicine, agriculture, and industry. Alfalfa is a fodder legume of great S116) were studied for their ability to reduce Medicago sativa salt stress. Results show different levels in responses of M. sativa alfalfa. Genomic analyses were performed using selectedeconomic importance, but its productivity is often affected by salt stress in arid and semi-arid regions. Endophytic bacteria, which colonize the internal tissues of plants in a symbiotic manner, represent a promising solution for improving the salt tolerance of alfalfa. To improve alfalfa salt stress resistance, four endophytic bacteria (M17, M50, S113 and strains M17 that show a good protection from salt stress. M17 is identified as Pseudomonas aeruginosastrain, Comparative genomic for both strains is illustrated. For Pseudomonas strains (M17): two strains associated with plants and two non-associated with plant, one phytopathogens and Human pathogen). The results shows 521 common genes and synteny analyses revelas a high conservation between the bacteria associated with plants. Pseudomonas which indicate a mechanism to protect plants from salt and other abiotic and biotic stresses. note de thèses : Mémoire de master en sciences biologiques

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Study of Arabidopsis thaliana response to salt stress and endophytic bacteria / Hanane Benferhat

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Study of Arabidopsis thaliana salt stress protection by beneficial bacteria / Nour Elhorra Bentria

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

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