RNA-Sequencing of spinach tissues with contrasting oxalate contents
Ontology highlight
ABSTRACT:
ORGANISM(S): Spinacia oleracea
PROVIDER: GSE146711 | GEO | 2021/05/18
REPOSITORIES: GEO
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Project description:RNA-Sequencing of spinach tissues with contrasting oxalate contents
| PRJNA611735 | ENA
Project description:Purpose: The goals of this study are to compare differentially expressed transcripts in roots and leaves of spinach plants grown under nitrogen replete and deplete conditions using transcriptome profiling (RNA-seq)
2020-04-08 | GSE145943 | GEO
Project description:Food-borne illness arising for Shiga-toxigenic Escherichia coli is often linked to consumption of fruit and vegetables as the bacteria have the ability to interact with plants and use them as alternative or secondary hosts. Attachment of the bacteria to host tissue is one of the first steps in the interaction, and, as with mammalian hosts, has shown to be mediated by a combination of non-specific and specific adhesin-mediated interactions. We took a high-throughput positive-selection approach to investigate adherence mechanisms for E. coli O157:H7 isolate Sakai by inoculating a BAC clone library onto spinach, which was quantified by microarray hybridisation and gene loci enrichment measured using a Bayesian hierarchical model. The screen involved four successive rounds of adherence to spinach roots, resulting in 115 CDS credible candidates, covered by seven contiguous genomic regions. Two candidates regions selected for functional assessment included a chaperone-usher fimbrial gene cluster (loc6) and the type two secretion system (T2SS). The TS22 was found to significantly enhance binding to spinach roots and leaves, demonstrated with a BAC-T2SS clone and by mutagenesis of the secretin protein, EtpD. Both etpD and the inner membrane anchor protein gene etpC were expressed at 18 degree celsius, and expression of etpD was demonstrated for STEC (Sakai) resident in the apoplastic spaces in spinach leaf tissue. Together, these data indicate a novel function for STEC T2SS in adherence to plant tissue. Experiment 1: screening E coli O157:H7 Sakai genes for adherence to spinach roots. A BAC library of Sakai clones in an E coli DH10B background (which has poor root adherence) defined as the 'Input pool', was incubated with spinach roots for 4 rounds of enrichment, defined as the 'Output pool'. Control samples (defined as 'Input control' & 'Output control') were cultures of pV41 vector only. DNA extractions from test pools were labelled with Cy3 throughout. DH10B DNA was used for grid alignment and labelled with Cy5 throughout.
2019-11-20 | E-MTAB-5923 | biostudies-arrayexpress
Project description:Food-borne illness arising for Shiga-toxigenic Escherichia coli is often linked to consumption of fruit and vegetables as the bacteria have the ability to interact with plants and use them as alternative or secondary hosts. Attachment of the bacteria to host tissue is one of the first steps in the interaction, and, as with mammalian hosts, has shown to be mediated by a combination of non-specific and specific adhesin-mediated interactions. We took a high-throughput positive-selection approach to investigate adherence mechanisms for E. coli O157:H7 isolate Sakai by inoculating a BAC clone library onto spinach, which was quantified by microarray hybridisation and gene loci enrichment measured using a Bayesian hierarchical model. The screen involved four successive rounds of adherence to spinach roots, resulting in 115 CDS credible candidates, covered by seven contiguous genomic regions. Two candidates regions selected for functional assessment included a chaperone-usher fimbrial gene cluster (loc6) and the type two secretion system (T2SS). The TS22 was found to significantly enhance binding to spinach roots and leaves, demonstrated with a BAC-T2SS clone and by mutagenesis of the secretin protein, EtpD. Both etpD and the inner membrane anchor protein gene etpC were expressed at 18 degree celsius, and expression of etpD was demonstrated for STEC (Sakai) resident in the apoplastic spaces in spinach leaf tissue. Together, these data indicate a novel function for STEC T2SS in adherence to plant tissue. Experiment 2: full replicated control screen. Conditions as for Experiment 1 (E-MTAB-5923), but no spinach root present. Two BAC clones (BAC2B5 & BAC2B24) used for additional positive controls.
2019-11-20 | E-MTAB-5924 | biostudies-arrayexpress
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Project description:Elevated temperature limits plant growth and reproduction and poses a growing threat to agriculture. Plant heat stress response is highly conserved and fine-tuned in multiple pathways. Spinach (Spinacia oleracea L.) is a cold tolerant but heat sensitive green leafy vegetable. In this study, heat adaptation mechanisms in spinach sibling inbred heat-tolerant line Sp75 were investigated using physiology, proteomics, and phosphoproteomics approaches. The abundance patterns of 911 heat stress-responsive proteins, and phosphorylation level changes of 48 phosphopeptides representing 45 phosphoproteins indicated that heat induced calcium-mediated signaling, ROS homeostasis, endomembrane trafficking, and cross-membrane transport pathways, as well as > 15 transcription regulation factors. Although photosynthesis was inhibited, diverse primary and secondary metabolisms were employed for enhancing thermotolerance, such as glycolysis, pentose phosphate pathway, amino acid metabolism, fatty acid metabolism, nucleotide metabolism, vitamin metabolism, and isoprenoid biosynthesis. These data constitutes a heat stress-responsive metabolic atlas in spinach, which will springboard further investigation into the sophisticated molecular mechanism of plant heat adaptation and inform spinach molecular breeding initiatives.
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Project description:Verotoxigenic Escherichia coli (VTEC) are a leading cause of food-borne illness. Fruit and vegetables are recognised as an important source of the pathogen and can account for ~ 25 % of food-borne VTEC outbreaks, globally. The ability of VTEC to colonise leaves and roots of leafy vegetables, spinach (Spinacia oleracea) and lettuce (Lactuca sativa), was compared. The highest levels of colonisation occurred in the roots and rhizosphere, whereas colonisation of the leaves was lower and significantly different between the species. Colonisation of the leaves of prickly lettuce (L. serriola), a wild relative of domesticated lettuce, was especially poor. Differential VTEC gene expression in spinach extracts was markedly different for three tissue types, with little overlap. Comparison of expression in the same tissue type, cell wall polysaccharides, for lettuce and spinach also showed substantial differences, again with virtually no overlap. The transcriptional response was largely dependent on temperatures that are relevant to plant growth, not warm-blooded animals. The data show that VTEC adaptation to plant hosts and subsequent colonisation potential is underpinned by wholescale changes in gene expression that are specific to both plant tissue type and to the species.
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Project description:Verotoxigenic Escherichia coli (VTEC) are a leading cause of food-borne illness. Fruit and vegetables are recognised as an important source of the pathogen and can account for ~ 25 % of food-borne VTEC outbreaks, globally. The ability of VTEC to colonise leaves and roots of leafy vegetables, spinach (Spinacia oleracea) and lettuce (Lactuca sativa), was compared. The highest levels of colonisation occurred in the roots and rhizosphere, whereas colonisation of the leaves was lower and significantly different between the species. Colonisation of the leaves of prickly lettuce (L. serriola), a wild relative of domesticated lettuce, was especially poor. Differential VTEC gene expression in spinach extracts was markedly different for three tissue types, with little overlap. Comparison of expression in the same tissue type, cell wall polysaccharides, for lettuce and spinach also showed substantial differences, again with virtually no overlap. The transcriptional response was largely dependent on temperatures that are relevant to plant growth, not warm-blooded animals. The data show that VTEC adaptation to plant hosts and subsequent colonisation potential is underpinned by wholescale changes in gene expression that are specific to both plant tissue type and to the species.
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