Abstract
The repertoire of RNA-binding proteins (RBPs) in bacteria play a crucial role in their survival, and interactions with the host machinery, but there is little information, record or characterisation in bacterial genomes. As a first step towards this, we have chosen the bacterial model system Escherichia coli, and organised all RBPs in this organism into a comprehensive database named EcRBPome. It contains RBPs recorded from 614 complete E. coli proteomes available in the RefSeq database (as of October 2018). The database provides various features related to the E. coli RBPs, like their domain architectures, PDB structures, GO and EC annotations etc. It provides the assembly, bioproject and biosample details of each strain, as well as cross-strain comparison of occurrences of various RNA-binding domains (RBDs). The percentage of RBPs, the abundance of the various RBDs harboured by each strain have been graphically represented in this database and available alongside other files for user download. To the best of our knowledge, this is the first database of its kind and we hope that it will be of great use to the biological community.
Highlights
RNA-binding proteins (RBPs) are important regulators of cellular function, being involved in processes at the transcriptional, post-transcriptional, translational, as well as post-translational levels
The most widely used of the RBP repositories, RBPDB [6], reports experimentally observed RNA-binding sites that have been manually curated from literature, but was last updated in 2012
On the analysis of the NADP-bound structure of this protein (PDB code: 2O7P), it was seen that RibD uses a different site to bind the oxidised NADP+ cofactor, which does not overlap with the RNA-binding site that we have proposed here
Summary
RNA-binding proteins (RBPs) are important regulators of cellular function, being involved in processes at the transcriptional, post-transcriptional, translational, as well as post-translational levels. They mediate transport, stabilisation, metabolism and degradation of transcripts within the cell [1]. The most widely used of the RBP repositories, RBPDB [6], reports experimentally observed RNA-binding sites that have been manually curated from literature, but was last updated in 2012. This database houses information from H. sapiens, M. musculus, D. melanogaster and C. elegans, but not from E. coli. The ATtRACT database [7], reported in
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