Caudovirales
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA172386 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Dna microarray technology was used to survey changes in gene expression in R. etli CFN42 in biofilm formation In these organisms, two main phases, biofilm and planktonic, have been identified. In this work, using microarray assays, we evaluated global gene expression in biofilm and planktonic growth phases in rich medium, in the bacterium Rhizobium etli CFN42.
2016-04-15 | GSE67656 | GEO
Project description:The NifA-RpoN complex is a master regulator of the nitrogen fixation genes in alpha-proteobacteria. Based on the complete Rhizobium etli genome sequence, we constructed the R. etli CFN42 oligonucleotide (70 mer) microarray, and utilized this tool to survey changes in gene expression in R. etli CFN42 wild type compared with NifA CFNX247 mutant strain in symbiosis with Phaseolus vulgaris. As expected, the genes associated with a NifA and RpoN binding sites were downregulated in the NifA mutant strain.
2010-05-15 | GSE20638 | GEO
Project description:Resendis-Antonio2007 - Genome-scale metabolic
network of Rhizobium etli (iOR363)
This model is described in the article:
Metabolic reconstruction and
modeling of nitrogen fixation in Rhizobium etli.
Resendis-Antonio O, Reed JL,
Encarnación S, Collado-Vides J, Palsson BØ.
PLoS Comput. Biol. 2007 Oct; 3(10):
1887-1895
Abstract:
Rhizobiaceas are bacteria that fix nitrogen during symbiosis
with plants. This symbiotic relationship is crucial for the
nitrogen cycle, and understanding symbiotic mechanisms is a
scientific challenge with direct applications in agronomy and
plant development. Rhizobium etli is a bacteria which provides
legumes with ammonia (among other chemical compounds), thereby
stimulating plant growth. A genome-scale approach, integrating
the biochemical information available for R. etli, constitutes
an important step toward understanding the symbiotic
relationship and its possible improvement. In this work we
present a genome-scale metabolic reconstruction (iOR363) for R.
etli CFN42, which includes 387 metabolic and transport
reactions across 26 metabolic pathways. This model was used to
analyze the physiological capabilities of R. etli during stages
of nitrogen fixation. To study the physiological capacities in
silico, an objective function was formulated to simulate
symbiotic nitrogen fixation. Flux balance analysis (FBA) was
performed, and the predicted active metabolic pathways agreed
qualitatively with experimental observations. In addition,
predictions for the effects of gene deletions during nitrogen
fixation in Rhizobia in silico also agreed with reported
experimental data. Overall, we present some evidence supporting
that FBA of the reconstructed metabolic network for R. etli
provides results that are in agreement with physiological
observations. Thus, as for other organisms, the reconstructed
genome-scale metabolic network provides an important framework
which allows us to compare model predictions with experimental
measurements and eventually generate hypotheses on ways to
improve nitrogen fixation.
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2015-07-30 | MODEL1507180006 | BioModels
Project description:89 small non-coding RNAs (ncRNAs) were identified in the soil-dwelling alpha-proteobacterium Rhizobium etli by comparing an extensive compilation of ncRNA predictions to intergenic expression data of a whole-genome tiling array. The differential expression levels of some of these ncRNAs during free-living growth and during interaction with the eukaryotic host plant may indicate a role in adaptation to changing environmental conditions.
2009-11-17 | GSE18580 | GEO
Project description:We report an small RNA sequencing (sRNA-seq) approach to identify host sRNAs involved in the nitrogen fixing symbiosis between Mesoamerican Phaseolus vulgaris and Rhizobium etli strains with different degrees in nodulation efficiency. This approach identified conserved and known microRNAs (miRNAs) differentially accumulated in Mesoamerican P. vulgaris roots in response to a highly efficient strain, to a less efficient one or to both strains.
2020-11-01 | GSE155414 | GEO
Project description:Clinical Enterobacter spp. isolates and Enterobacter-targeting bacteriophages
| PRJNA777034 | ENA
Project description:Unlike other bacteria, cell growth in rhizobiales is unipolar and asymmetric. The regulation of cell division, and its coordination with metabolic processes is an active field of research. In Rhizobium etli, gene RHE_PE00024, located in a secondary chromosome, is essential for growth. This gene encodes a hybrid histidine kinase sensor protein, participating in a, as yet undescribed, two-component signaling system. In this work, we show that a conditional knockdown mutant (cKD24) in RHE_PE00024 (hereby referred as rdsA, after rhizobium division and shape) generates a striking phenotype, characterized by cells with a round shape, with stochastic and uncoordinated cell division. A fraction of the cells showed also multiple ectopic polar growths, sometimes leading to growth from the old pole, a sector that is normally inactive for growth in a wild-type cell. Homodimerization of RdsA appears to be required for normal function. RNAseq analysis of mutant cKD24 reveals global changes, with differentially expressed genes in at least five biological processes: cell division, wall biogenesis, respiration, translation, and motility. These modifications may affect proper structuring of the divisome, as well as peptidoglycan synthesis. Together, these results indicate that the hybrid histidine kinase RdsA is an essential global regulator influencing cell division and cell shape in R. etli.
2021-09-22 | GSE184428 | GEO
Project description:Growth inhibition of Rhizobium etli and other organisms by exogenous OA has not been previously reported. We conducted genome-wide transcriptomic analysis to determine the possible mechanism by which OA exerts its growth-inhibitory effect on R. etli CE3. The observed changes fall into several broad categories. First, the decreased expression of genes involved in protein synthesis (including ribosomal genes), replication and energy production indicates that the cells arrest or at least slow their growth, which agrees with the observed growth arrest induced by OA. The upregulation of a key enzyme (PrsAch) for 5'-phosphoribosyl-1'-pyrophosphate (PRPP) synthesis suggests that cells exposed to OA suffer PRPP deprivation. We hypothesized that the PRPP pools were depleted as a result of an increase in the synthesis of OMP stimulated by exogenous OA. PRPP depletion would result in a marked decrease in purine synthesis, which would lead to an imbalance between purine and pyrimidine nucleotides, causing arrest of DNA synthesis and a lack of energetic nucleotides (ADP, ATP).
2013-10-12 | GSE46013 | GEO
Project description:Rhizobium etli R22G genome sequencing
| PRJNA330443 | ENA