Project description:Recombinant aRNase J from P. abyssi, with C-terminal (His)6-tag (aRNase J-His), was produced, purified and used as baits for AP-MS experiments. In order to discriminate specific protein interaction from column background, we performed mock AP-MS analyses with P. abyssi cell extracts in absence of protein bait. In addition, to determine if some interactions are mediated through RNA or DNA, we implemented a nuclease treatment after incubating the cell extract with the bait. The co-purified partners were identified by bottom-up proteomic techniques coupled with mass spectrometry.

2020-01-21 | PXD015856 | Pride

RNA at 92 °C: the non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi.

Project description:The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi is investigated using the RNA-seq technology. A dedicated computational pipeline analyzes RNA-seq reads and prior genome annotation to identify small RNAs, untranslated regions of mRNAs, and cis-encoded antisense transcripts. Unlike other archaea, such as Sulfolobus and Halobacteriales, P. abyssi produces few leaderless mRNA transcripts. Antisense transcription is widespread (215 transcripts) and targets protein-coding genes that are less conserved than average genes. We identify at least three novel H/ACA-like guide RNAs among the newly characterized non-coding RNAs. Long 5' UTRs in mRNAs of ribosomal proteins and amino-acid biosynthesis genes strongly suggest the presence of cis-regulatory leaders in these mRNAs. We selected a high-interest subset of non-coding RNAs based on their strong promoters, high GC-content, phylogenetic conservation, or abundance. Some of the novel small RNAs and long 5' UTRs display high GC contents, suggesting unknown structural RNA functions. However, we were surprised to observe that most of the high-interest RNAs are AU-rich, which suggests an absence of stable secondary structure in the high-temperature environment of P. abyssi. Yet, these transcripts display other hallmarks of functionality, such as high expression or high conservation, which leads us to consider possible RNA functions that do not require extensive secondary structure.

2014-05-31 | GSE58131 | GEO

Camelina sativa cultivar:MT5

Project description:Camelina sativa MT5 Gene Expression Profiling - MT5-8D-1 transcriptome

| PRJNA497622 | ENA

Camelina sativa cultivar:MT5

Project description:Camelina sativa MT5 Gene Expression Profiling - MT5-8D-2 transcriptome

| PRJNA497623 | ENA

Camelina sativa cultivar:MT5

Project description:Camelina sativa MT5 Gene Expression Profiling - MT5-12D-1 transcriptome

| PRJNA497628 | ENA

Camelina sativa cultivar:MT5

Project description:Camelina sativa MT5 Gene Expression Profiling - MT5-12D-2 transcriptome

| PRJNA497629 | ENA

Camelina sativa cultivar:MT5

Project description:Camelina sativa MT5 Gene Expression Profiling - MT5-12D-3 transcriptome

| PRJNA497630 | ENA

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