Comparative analysis of nascent transcription among plant species
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays Selaginella moellendorffii Arabidopsis thaliana Carica papaya Chlamydomonas reinhardtii Hordeum vulgare Physcomitrium patens Drosophila melanogaster
PROVIDER: GSE233927 | GEO | 2023/09/28
REPOSITORIES: GEO
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Project description:Transcriptional regulation of gene expression is a major mechanism utilized by plants to confer phenotypic plasticity, yet compared to archaebacteria, eubacteria, and other eukaryotes, very little is known about the design principles of plant transcription. We generated an extensive catalog of nascent and steady state transcripts in Arabidopsis thaliana seedlings using global nuclear run-on sequencing (GRO-seq), 5'GRO-seq and RNA-seq and reanalyzed published maize data to capture the general characteristics of plant transcription. De novo annotation of nascent transcripts enabled accurate start site annotations and revealed novel unstable transcripts. Coding and non-coding transcripts exhibit comparable promoter chromatin configurations. Motif analysis revealed new regulatory DNA elements including a conserved 'TGT core promoter motif' and unreported transcription factor (TF) binding sites. Mapping of engaged RNA polymerases revealed a lack of enhancer RNAs, promoter proximal pausing, and divergent transcription in Arabidopsis and maize, which are commonly present in humans and yeast. In contrast, Arabidopsis and maize genes accumulate RNA polymerases adjacent to the polyadenylation site immediately downstream of genes, a trend that correlated with increasing gene length and coincided with hypomethylation of CpG residues. Lack of promoter proximal pausing and a higher correlation of nascent and steady state transcripts indicates Arabidopsis regulates transcription predominantly at the level of initiation. Together, these findings provide insight into plant transcriptional mechanisms, but also eukaryotic transcription in general.
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Project description:Phytopathogenic Rathayibacter species are unique bacterial plant pathogens as they are obligately vectored by plant parasitic Anguinid nematodes to the developing seedheads of forage grasses and cereals. This understudied group of plant associated Actinomycetes includes the neurotoxigenic Plant Pathogen Select Agent, R. toxicus, which causes annual ryegrass toxicity in grazing livestock. The complexRathayibacter disease cycle requires intimate interactions with the nematode cuticle and plant hosts, which warrants an increased understanding of the secretory and surface-associated proteins that mediate these diverse eukaryotic interactions. Here we present the first comparative secretome analysis for this complex, nematode vectoredRathayibacter genera that compares three agronomically damaging Rathayibacterspecies, R. toxicus, R. iranicus, and R. tritici. The exoproteomic comparison identified 1,423 unique proteins between the three species using LC-MS/MS. Of the uniquely identified proteins, 94 homologous proteins were conserved between the three Rathayibacter exoproteomes and comprised between 43.4 to 58.6% of total protein abundance. Comparative analyses revealed both conserved and uniquely expressed extracellular proteins, which, interestingly, had more similarities to extracellular proteins commonly associated with bacterial animal pathogens than classical plant pathogens. This comparative exoproteome analysis will facilitate the characterization of proteins essential for vector and host colonization and assist in the development of diagnostic targets.
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Project description:Microbiological, genomic and transcriptomic analyses were used to examine three species from the bacterial genus Caldicellulosiruptor with respect to their capacity to convert the carbohydrate content of lignocellulosic biomass at 70°C to simple sugars, acetate, lactate, CO2 and H2. C. bescii, C. kronotskyensis and C. saccharolyticus solubilized 38%, 36% and 29% (by weight) of unpretreated switchgrass (5 g/l), repectively, which was about half of the concentration of crystalline cellulose (Avicel, 5 g/l) that was solubilized under the same conditions. The lower yields with C. saccharolyticus were unexpected, given that its genome encodes the same GH9-GH48 multi-domain cellulase (CelA) found in the other two species. However, the genome of C. saccharolyticus lacks two other cellulases with GH48 domains, which could be responsible for its lower levels of solubilization. Transcriptomes for growth of each species comparing Cellulose to switchgrass showed that many carbohydrate ABC transporters and multi-domain extracellular glycoside hydrolases were differentially regulated, reflecting the heterogeneity of lignocellulose. However, significant differences in transcription levels for conserved genes among the three species were noted, indicating unexpectedly diverse regulatory strategies for deconstruction for these closely related bacteria. Genes encoding the Che-type chemotaxis system and flagella biosynthesis were up-regulated in C. kronotskyensis and C. bescii during growth on cellulose, implicating motility in substrate utilization. The results here show that capacity for plant biomass deconstruction varies across Caldicellulosiruptor species and depends in a complex way on GH genome inventory, substrate composition, and gene regulation.
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Project description:Microbiological, genomic and transcriptomic analyses were used to examine three species from the bacterial genus Caldicellulosiruptor with respect to their capacity to convert the carbohydrate content of lignocellulosic biomass at 70°C to simple sugars, acetate, lactate, CO2 and H2. C. bescii, C. kronotskyensis and C. saccharolyticus solubilized 38%, 36% and 29% (by weight) of unpretreated switchgrass (5 g/l), repectively, which was about half of the concentration of crystalline cellulose (Avicel, 5 g/l) that was solubilized under the same conditions. The lower yields with C. saccharolyticus were unexpected, given that its genome encodes the same GH9-GH48 multi-domain cellulase (CelA) found in the other two species. However, the genome of C. saccharolyticus lacks two other cellulases with GH48 domains, which could be responsible for its lower levels of solubilization. Transcriptomes for growth of each species comparing Cellulose to switchgrass showed that many carbohydrate ABC transporters and multi-domain extracellular glycoside hydrolases were differentially regulated, reflecting the heterogeneity of lignocellulose. However, significant differences in transcription levels for conserved genes among the three species were noted, indicating unexpectedly diverse regulatory strategies for deconstruction for these closely related bacteria. Genes encoding the Che-type chemotaxis system and flagella biosynthesis were up-regulated in C. kronotskyensis and C. bescii during growth on cellulose, implicating motility in substrate utilization. The results here show that capacity for plant biomass deconstruction varies across Caldicellulosiruptor species and depends in a complex way on GH genome inventory, substrate composition, and gene regulation. A dye swap was completed with each of three Caldicellulosiruptor species: C. bescii, C. kronotskyensis and C. saccharolyticus growing on cellulose and switchgrass. Half of the RNA sample for one condition was labeled with Cy3 and the other half Cy5. The two differentially labeled samples were run on two different slides and analyzed to investigate differences in transcription during growth on cellulose and switchgrass.
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