VVX_LinDeg
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB30113 | ENA |
REPOSITORIES: ENA
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Project description:Chemical signaling in the plant microbiome can have drastic effects on microbial community structure, and on host growth and development. Previously, we demonstrated that the auxin metabolic signal interference performed by the bacterial genus Variovorax via a novel auxin degradation locus was essential for maintaining stereotypic root development in an ecologically-relevant bacterial synthetic community. Here, we dissect the Variovorax auxin degradation locus to define the genes necessary and sufficient for indole-3-acetic acid (IAA) degradation and signal interference. We determine the crystal structures and binding properties of the operon’s MarR-family repressor with IAA and other auxins. We identify auxin-degradation operons across the bacterial tree of life and define two distinct types based on gene content and metabolic products: iac-like and iad-like. We solve the structures of MarRs from representatives of each auxin degradation operon type, establishing that each have distinct IAA binding pockets. Comparison of representative IAA degrading strains from diverse bacterial genera show that while all degrade IAA, only strains containing iad-like auxin degrading operons interfere with auxin signaling in a complex synthetic community context. This suggests that iad-like operon containing strains, including Variovorax species, play a key ecological role in modulating auxins in the plant microbiome.
2022-08-11 | GSE210968 | GEO
Project description:The goal of this study was to optimize protein extraction methods to study root-associated bacteria in Arabidopsis. For this we inoculated Arabidopsis seedlings grown in agar plates with a synthetic community (SynSom) composed of four different strains (Variovorax paradoxus, Arthrobacter sp, Agrobacterium sp. and Pseudomonas sp.. Twelve days after inoculation we extracted proteins from the roots using six different protein extraction methods each in triplicates. These methods were a combination of different extraction buffers (SDS or Triton-based) and mechanical disruption methods (bead-beating, N2 grinding, glass homogenizer and freeze-thaw cycles) We found that bead-beating the roots with lysing matrix E in SDT lysis buffer yielded the highest numbers of microbial protein identification and enhanced the detection of proteins derived from gram positive bacteria.
2022-09-08 | PXD026330 | Pride
Project description:We isolated an efficient tetracycline degrading strain Sphingobacterium sp. WM1. To investigate gene expression patterns during tetracycline degradation by strain WM1, we conducted a comparative transcriptomic analysis using cultures of strain WM1 with and without tetracycline addition. The RNA-Seq data revealed that 90.44-96.56% of the reads mapped to the genome of Sphingobacterium sp. WM1 across all samples. Differentially expressed genes (DEGs) analysis (|log2FC| >2; p < 0.01) showed that 693 genes were significantly up-regulated and 592 genes were significantly down-regulated.
2023-09-21 | GSE234909 | GEO
Project description:We isolated an efficient doxycycline degrading strain Chryseobacterium sp. WX1. To investigate gene expression patterns during doxycyclinedegradation by strain WX1, we conducted a comparative transcriptomic analysis using cultures of strain WX1 with and without doxycycline addition. The RNA-Seq data revealed that 90.44-96.56% of the reads mapped to the genome of Chryseobacterium sp. WX1 across all samples. Differentially expressed genes (DEGs) analysis (|log2FC| >2; p < 0.01) showed that 693 genes were significantly up-regulated and 592 genes were significantly down-regulated.
2023-09-12 | GSE242785 | GEO
Project description:This study examines the transcriptomic response of biofilms of the PAH-degrading Sphingomonas sp. LH128 on solute stress when actively degrading and growing on the PAH compound. To address the effect of solute stress on bacterial physiology and transcriptomic response, NaCl was used as osmolyte. Both acute and chronic solute stress was invoked to assess differences in short-term and long-term responses.
2012-06-18 | GSE38296 | GEO
Project description:Wood-degrading fungi play a critical role in global carbon cycling, and their varied mechanisms for deconstruction offer pathways for industrial bioconversion. In this study, we used comparative genomics to isolate upregulation patterns among fungi with brown rot (carbohydrate-selective) or white rot (lignin-degrading) nutritional modes. Specifically, we used whole-transcriptome profiling to compare early, middle, and late decay stages on wood wafers, matching differentially-expressed gene (DEG) patterns with fungal growth and enzyme activities. This approach highlighted 34 genes uniquely upregulated in early brown rot stages, with notable candidates involved in generating reactive oxygen species (ROS) as a pretreatment mechanism during brown rot. This approach further isolated 18 genes in late brown rot stages that may be adapted to handle oxidatively-reacted lignocellulose components. By summing gene expression levels in functional classes, we also identified a broad and reliable distinction in glycoside hydrolase (GH) versus lignocellulose oxidative (LOX) transcript counts that may reflect the energy investment burden of lignin-degrading machinery among white rot fungi.
2018-01-05 | GSE108189 | GEO
Project description:To determine specific miRNAs for Th17 cells, we performed comparative miRNA screening of activated CD4+ T, polyclonal Th17 (Th17 poly) and OVA-specific Th17 (Th17 Ag-sp) cell skewed cultures or Th17 Ag-sp sorted cells. The expression of miRNAs analyzed by microarray revealed 27 miRNAs exclusively expressed in culture or sorted Th17 Ag-sp cell subset.
2021-01-01 | GSE109992 | GEO
Project description:Side population (SP) cells harbor malignant phenotypes, such as sphere forming capacity, single cell clonogenicity and in vivo tumorigenicity. These malignant phenotypes are related to a poor prognosis for women with ovarian cancer. The aim of this study was to identify key factor(s) that increase the proportion of ovarian cancer SP cells through a functional genomics screen. A library of 81 000 shRNAs targeting 15 000 genes was transfected into CH1 and SKOV3 cells, followed by SP analysis. We found that suppression of MSL3, ZNF691, VPS45, ITGB3BP, TLE2, and ZNF498 markedly increased the proportion of SP cells. Newly generated SP cells exhibit significantly greater capacity for sphere formation, single cell clonogenicity, and in vivo tumorigenicity. On the contrary, overexpression of MSL3, VPS45, ITGB3BP, TLE2, and ZNF498 significantly decreased the proportion of SP cells, sphere formation capacity and single cell clonogenicity. In ovarian cancer cases, low expression of MSL3, ZNF691 and VPS45 was related to poor prognosis. Suppression of these six genes tended to increase some stem cell-related pathways, and significantly enhanced activity of the hedgehog pathway. Cyclopamine, a hedgehog pathway inhibitor, significantly decreased the number of newly generated SP cells and their sphere forming ability. Our results provide new information regarding molecular mechanisms favoring SP cells and suggest that Hedgehog signaling may provide a viable target for improving ovarian cancer survival.
2018-07-24 | GSE117480 | GEO