Abstract
In prokaryotes, protein phosphorylation plays a critical role in regulating a broad spectrum of biological processes and occurs mainly on various amino acids, including serine (S), threonine (T), tyrosine (Y), arginine (R), aspartic acid (D), histidine (H) and cysteine (C) residues of protein substrates. Through literature curation and public database integration, here we reported an updated database of phosphorylation sites (p-sites) in prokaryotes (dbPSP 2.0) that contains 19,296 experimentally identified p-sites in 8,586 proteins from 200 prokaryotic organisms, which belong to 12 phyla of two kingdoms, bacteria and archaea. To carefully annotate these phosphoproteins and p-sites, we integrated the knowledge from 88 publicly available resources that covers 9 aspects, namely, taxonomy annotation, genome annotation, function annotation, transcriptional regulation, sequence and structure information, family and domain annotation, interaction, orthologous information and biological pathway. In contrast to version 1.0 (~30 MB), dbPSP 2.0 contains ~9 GB of data, with a 300-fold increased volume. We anticipate that dbPSP 2.0 can serve as a useful data resource for further investigating phosphorylation events in prokaryotes. dbPSP 2.0 is free for all users to access at: http://dbpsp.biocuckoo.cn.
Highlights
As one of the most well-characterized and important post-translational modifications (PTMs), protein phosphorylation plays an essential role in almost all signalling pathways and biological processes, from eukaryotes to prokaryotes[1,2,3,4,5]
Later studies demonstrated that many proteins can be phosphorylated in eukaryotes, it was long debated whether protein phosphorylation exists in prokaryotes until the discovery of isocitrate dehydrogenase in Escherichia coli, the first identified prokaryotic phosphoprotein, in 19797,8
In contrast with eukaryotic phosphorylation, which occurs mainly at specific serine (S), threonine (T) and tyrosine (Y) residues of proteins[5], prokaryotic protein phosphorylation can occur at additional types of amino acids, such as arginine (R), aspartic acid (D), histidine (H) and cysteine (C)[1,9,10,11,12,13]
Summary
As one of the most well-characterized and important post-translational modifications (PTMs), protein phosphorylation plays an essential role in almost all signalling pathways and biological processes, from eukaryotes to prokaryotes[1,2,3,4,5]. This reversibly dynamic process is precisely modulated by protein kinases (PKs) and protein phosphatases (PPs), which are involved in linking or removing a phosphate group at specific residues of protein substrates[1,2,3,4,5]. Given the importance of phosphorylation in the regulation of protein functions[11,12,13], the identification of novel phosphorylation sites (p-sites) in proteins is fundamental for understanding the molecular mechanism and regulatory roles of prokaryotic phosphorylation
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