Abstract
BackgroundSer/Thr/Tyr kinases (STYKs) commonly found in eukaryotes have been recently reported in many bacterial species. Recent studies elucidating their cellular functions have established their roles in bacterial growth and development. However functions of a large number of bacterial STYKs still remain elusive. The organisation of domains in a large dataset of bacterial STYKs has been investigated here in order to recognise variety in domain combinations which determine functions of bacterial STYKs.ResultsUsing sensitive sequence and profile search methods, domain organisation of over 600 STYKs from 125 prokaryotic genomes have been examined. Kinase catalytic domains of STYKs tethered to a wide range of enzymatic domains such as phosphatases, HSP70, peptidyl prolyl isomerases, pectin esterases and glycoproteases have been identified. Such distinct preferences for domain combinations are not known to be present in either the Histidine kinase or the eukaryotic STYK families. Domain organisation of STYKs specific to certain groups of bacteria has also been noted in the current anlaysis. For example, Hydrophobin like domains in Mycobacterial STYK and penicillin binding domains in few STYKs of Gram-positive organisms and FHA domains in cyanobacterial STYKs. Homologues of characterised substrates of prokaryotic STYKs have also been identified.ConclusionThe domains and domain architectures of most of the bacterial STYKs identified are very different from the known domain organisation in STYKs of eukaryotes. This observation highlights distinct biological roles of bacterial STYKs compared to eukaryotic STYKs. Bacterial STYKs reveal high diversity in domain organisation. Some of the modular organisations conserved across diverse bacterial species suggests their central role in bacterial physiology. Unique domain architectures of few other groups of STYKs reveal recruitment of functions specific to the species.
Highlights
Ser/Thr/Tyr kinases (STYKs) commonly found in eukaryotes have been recently reported in many bacterial species
The analysis suggests that the bacterial homologues form a distinct class of protein kinases as indicated by the highest similarity (20–30% sequence identity) of their catalytic kinase domain with the generic kinase profiles rather than any individual subfamily profile of eukaryotic protein kinases. i.e., the percent sequence identities of bacterial kinases with specific sub-families of eukaryotic Ser/Thr/Tyr kinase like sequences (STYKs) is lower
All the archaeal genomes analysed have at least one STYK, which belongs to the RIO1 family [19]
Summary
Ser/Thr/Tyr kinases (STYKs) commonly found in eukaryotes have been recently reported in many bacterial species. Recent studies elucidating their cellular functions have established their roles in bacterial growth and development. The variations in functional states of the proteins are brought about by covalent and non-covalent molecular interactions. Phosphorylation events lead to changes in the electrostatic interactions and ionisation states of residues at the catalytic site as exemplified by regulation of isocitrate dehydrogenases and HMG-CoA reductase [1,2]. Covalent attachment of the phosphoryl groups to various proteins is catalysed by protein kinases. These enzymes transfer a phosphate group from adenosine tri phosphate (ATP) onto an acceptor amino acid in a substrate protein. In addition to nucleoside triphosphates as donors of the phosphate groups, certain class of phosphorylating enzymes makes use of either phosphoenzyme intermediates or low molecular weight metabolites such as phosphoenol pyruvate, acetyl phosphate or carbamoyl phosphates and polyphosphates as donors [57]
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