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66 results for “Sinorhizobium meliloti”
................................................................................................................................................. Fig. 5. Phylogenetic tree based on 16S rRNA sequences (a) and gltA sequences (b) showing the position of strains R1T, R3, R4 and R6 in relation to the known Bartonella spp. The tree was rooted by using Brucella abortus (a) and Sinorhizobium meliloti (b) as the outgroup. in Bartonella schoenbuchii sp. nov., isolated from the blood of wild roe deer.
................................................................................................................................................. Fig. 5. Phylogenetic tree based on 16S rRNA sequences (a) and gltA sequences (b) showing the position of strains R1T, R3, R4 and R6 in relation to the known Bartonella spp. The tree was rooted by using Brucella abortus (a) and Sinorhizobium meliloti (b) as the outgroup.
Data from: Genome-wide sensitivity analysis of the microsymbiont Sinorhizobium meliloti to symbiotically important, defensin-like host peptides
The model legume species Medicago truncatula expresses more than 700 nodule-specific cysteine-rich (NCR) signaling peptides that mediate the differentiation of Sinorhizobium meliloti bacteria into nitrogen-fixing bacteroids. NCR peptides are essential for a successful symbiosis in legume plants of the inverted-repeat-lacking clade (IRLC) and show similarity to mammalian defensins. In addition to signaling functions, many NCR peptides exhibit antimicrobial activity in vitro and in vivo. Bacterial resistance to these antimicrobial activities is likely to be important for symbiosis. However, the mechanisms used by S. meliloti to resist antimicrobial activity of plant peptides are poorly understood. To address this, we applied a global genetic approach using transposon mutagenesis followed by high-throughput sequencing (Tn-seq) to identify S. meliloti genes and pathways that increase or decrease bacterial competitiveness during exposure to the well-studied cationic NCR247 peptide and also to the unrelated model antimicrobial peptide polymyxin B. We identified 78 genes and several diverse pathways whose interruption alters S. meliloti resistance to NCR247. These genes encode the following: (i) cell envelope polysaccharide biosynthesis and modification proteins, (ii) inner and outer membrane proteins, (iii) peptidoglycan (PG) effector proteins, and (iv) non-membrane-associated factors such as transcriptional regulators and ribosome-associated factors. We describe a previously uncharacterized yet highly conserved peptidase, which protects S. meliloti from NCR247 and increases competitiveness during symbiosis. Additionally, we highlight a considerable number of uncharacterized genes that provide the basis for future studies to investigate the molecular basis of symbiotic development as well as chronic pathogenic interactions.
Competitiveness prediction for nodule colonization in Sinorhizobium meliloti through combined in vitro tagged strain characterization and genome-wide association analysis
<p>Associations between leguminous plants and symbiotic nitrogen-fixing rhizobia are a classic example of mutualism between a eukaryotic host and a specific group of prokaryotic microbes. Although this symbiosis is in part species-specific, different rhizobial strains may colonise the same nodule. Some rhizobial strains are commonly known as better competitors than others, but detailed analyses that aim to predict rhizobial competitive abilities based on genomes are still scarce. Here, we performed a bacterial <em>genome-wide association (GWAS) analysis to define the </em>genomic determinants related to the competitive capabilities in the model rhizobial species <em>Sinorhizobium meliloti.</em> For this, 13 tester strains were GFP-tagged and assayed <i>vs.</i> 3 RFP-tagged reference competitor strains (<em>Rm1021, AK83, and BL225C) in a</em> <i>Medicago sativa</i> nodule occupancy test. Competition data and strain genomic sequences were employed to build a model for GWAS based on <i>k</i>-mers. Among the <i>k</i>-mers with the highest scores, 51 <i>k</i>-mers mapped on the genomes of four strains showing the highest competition phenotypes (> 60% single strain nodule occupancy; GR4, KH35c, KH46 and SM11) <i>vs.</i> BL225C. These <i>k</i>-mers were mainly located on the symbiosis-related megaplasmid pSymA, specifically on genes coding for transporters, proteins involved in the biosynthesis of cofactors and proteins related to metabolism (e.g., fatty acids). The same analysis was performed considering the sum of single and mixed nodules obtained in the competition assays <em>vs. </em>BL225C, retrieving <i>k</i>-mers mapped on the genes previously found and on <i>vir</i> genes. Therefore, the competition abilities seem to be linked to multiple genetic determinants and comprise several cellular components.</p>
The pan-epigenome of the symbiotic nitrogen fixing bacterium Sinorhizobium meliloti unravels unexpected variability of DNA-methylation profiles in closely related strains
<p>Supplementary Dataset S1. Genome coverage data and assignment of contigs to <em>S. meliloti</em> 1021 genome replicons. MS Excel file format (.xlsx file)</p> <p>Supplementary Dataset S2. Folder containing summary pangenome statistics, core and accessory orthologs, alignments and R script. Zip archive</p> <p>Supplementary Dataset S3. Number motifs and methylated motifs identified and their ratio. Data on number of motifs (RAW), number of methylated motifs (METH), fraction of methylated motifs (RATIO) related to functional features (CDSid, tIG and US sequences) and to replicons (CHR, chromosome; PA, pSymA; PB, pSymB and other) are reported. Red color in columns from “other” indicate missing data (i.e., absence of replicons other than chromosome, pSymA, pSymB). .xlsx file</p>
Data from: Genome-wide sensitivity analysis of the microsymbiont Sinorhizobium meliloti to symbiotically important, defensin-like host peptides
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Competitiveness prediction for nodule colonization in Sinorhizobium meliloti through combined in vitro tagged strain characterization and genome-wide association analysis
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Gene expression data of Sinorhizobium meliloti-alfalfa initiation of symbiosis
<p>Rhizobia are ecologically important, facultative plant symbiotic microbes. In nature there exists large variability in the association of rhizobial strains and host plants of the same species. Here, we evaluated whether plant and rhizobial genotypes influence the initial transcriptional response of rhizobium following perception of host plant. RNA-sequencing of the model rhizobium <i>Sinorhizobium meliloti</i> exposed to root exudates or luteolin was performed in a combination of three <i>S. meliloti</i> strains and three <i>Medicago sativa</i> varieties. The response to root exudates involved hundreds of changes in the rhizobium transcriptome. Of the differentially expressed genes, expression of 35% were influenced by strain genotype, 16% by the plant genotype, and 29% by strain x host plant genotype interactions. We also examined the response of a hybrid <i>S. meliloti</i> strain, in which the symbiotic megaplasmid (~ 20% of the genome) was mobilized between two of the above-mentioned strains. Dozens of genes were up-regulated in the hybrid strain, indicative of nonadditive variation in the transcriptome. In conclusion, this study demonstrated that transcriptional responses of rhizobia upon perception of legumes is influenced by the genotypes of both symbiotic partners, and their interaction, a wide spectrum of genetic determinants involved in the phenotypic variation of plant-rhizobium symbiosis.</p>
Gene expression data of Sinorhizobium meliloti-alfalfa initiation of symbiosis
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Global analysis of cell cycle gene expression of the legume symbiont Sinorhizobium meliloti
GEO Series GSE54208. Sinorhizobium meliloti 1021; Sinorhizobium meliloti. 31 samples. Type: Expression profiling by array.
Directional RNA sequencing of mRNA from Sinorhizobium meliloti cells grown with limiting phosphate and with excess phosphate.
GEO Series GSE43558. Sinorhizobium meliloti. 4 samples. Type: Expression profiling by high throughput sequencing.
A Sinorhizobium meliloti IAA-overproducing strain improves phosphate solubilization and Medicago plant yield
GEO Series GSE21745. Sinorhizobium meliloti; Sinorhizobium meliloti 1021. 36 samples. Type: Expression profiling by array.
Sinorhizobium meliloti cells: untreated 1021 wild type strain vs. RD64 strain
GEO Series GSE21744. Sinorhizobium meliloti; Sinorhizobium meliloti 1021. 6 samples. Type: Expression profiling by array.
Sinorhizobium meliloti cells: untreated 1021 strain vs. 1021 treated with indole-3-acetic acid (IAA)
GEO Series GSE21737. Sinorhizobium meliloti; Sinorhizobium meliloti 1021. 6 samples. Type: Expression profiling by array.
A consolidated analysis of the physiological and molecular responses induced under acid stress in the legume symbiont model soil bacterium Sinorhizobium meliloti
GEO Series GSE74449. Sinorhizobium meliloti; Sinorhizobium meliloti 1021. 1 samples. Type: Expression profiling by array.
Sinorhizobium meliloti cells: untreated 1021 strain vs. 1021 treated with 2,4-dichlorophenoxyacetic acid (2,4-D)
GEO Series GSE21735. Sinorhizobium meliloti; Sinorhizobium meliloti 1021. 6 samples. Type: Expression profiling by array.
Sinorhizobium meliloti cells: untreated 1021 strain vs. 1021 treated with indole-3-carboxylic acid (ICA)
GEO Series GSE21740. Sinorhizobium meliloti 1021; Sinorhizobium meliloti. 6 samples. Type: Expression profiling by array.
Temporal changes in the transcriptome (RNA-seq) and genome-wide chromatin accessibility (ATAC-seq) after Sinorhizobium meliloti LCO treatment, in Medicago truncatula roots
GEO Series GSE154845. Medicago truncatula. 32 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Sinorhizobium meliloti cells: untreated 1021 strain vs. 1021 treated with indole (IND)
GEO Series GSE21742. Sinorhizobium meliloti; Sinorhizobium meliloti 1021. 6 samples. Type: Expression profiling by array.
Host plant peptides elicit a transcriptional response to control the Sinorhizobium meliloti cell cycle during symbiosis
GEO Series GSE54244. Sinorhizobium meliloti 1021; Sinorhizobium meliloti. 31 samples. Type: Expression profiling by array.
Sinorhizobium meliloti cells: untreated 1021 strain vs. 1021 treated with tryptophan (Trp)
GEO Series GSE21743. Sinorhizobium meliloti; Sinorhizobium meliloti 1021. 6 samples. Type: Expression profiling by array.
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