Novel Families of Putative Protein Kinases in Bacteria and Archaea: Evolution of the “Eukaryotic” Protein Kinase Superfamily

Abstract

The central role of serine/threonine and tyrosine protein kinases in signal transduction and cellular regulation in eukaryotes is well established and widely documented. Considerably less is known about the prevalence and role of these protein kinases in bacteria and archaea. In order to examine the evolutionary origins of the eukaryotic-type protein kinase (ePK) superfamily, we conducted an extensive analysis of the proteins encoded by the completely sequenced bacterial and archaeal genomes. We detected five distinct families of known and predicted putative protein kinases with representatives in bacteria and archaea that share a common ancestry with the eukaryotic protein kinases. Four of these protein families have not been identified previously as protein kinases. From the phylogenetic distribution of these families, we infer the existence of an ancestral protein kinase(s) prior to the divergence of eukaryotes, bacteria, and archaea.For many years after the discovery of protein phosphorylation, the prevailing view was that phosphorylation of proteins on serine, threonine, and tyrosine residues was a phenomenon restricted to the eukaryotes, in which these modifications perform important regulatory functions (Hanks et al. 1988;Hunter 1995). In bacteria, an analogous regulatory role was attributed to the two-component sensor kinases and the phosphoenolpyruvatedependent phosphotransferase systems, which typically catalyze the phosphorylation of proteins on histidine and aspartate residues, respectively (Saier et al. 1990). Further experimental work has brought to light exceptions to these paradigms. Evidence of bacterial Koshland 1978, 1981) and archaeal (Skorko 1984; proteins containing phosphoserine, phosphothreonine, or phosphotyrosine residues has accumulated over the past two decades, and elements of the twocomponent sensor kinase system have been detected in archaea and eukaryotes (Loomis et al. 1997).Several unusual mechanisms of Ser/Thr or Tyr protein phosphorylation have been recognized in prokaryotes, but they do not appear universally in bacteria or archaebacteria. There are examples of histidine kinase-related proteins in Bacillus subtilis (Yang et al. 1996) and the eukaryotic mitochondrion (Popov et al. 1992) that mediate phosphoserine formation. In addition, there have been reports of Ser/Thr or Tyr autophosphorylating proteins in bacteria (Ostrovsky and Maloy 1995;Grangeasse et al. 1997).Recently, genes encoding proteins homologous to eukaryotic Ser/Thr protein kinases have been identified in several bacteria (Kennelly and Potts 1996) and archaea (Smith and King 1995). Myxococcus xanthus encodes numerous paralogous Ser/Thr kinases that show highly significant sequence similarity to one another (Munoz-Dorado et al. 1993). The best characterized of these proteins, Pkn2, has been shown to play a regulatory role in secretion (Udo et al. 1995). Protein kinases of the Pkn2 type have also been recognized in a number of other bacteria (Zhang 1996).To evaluate the entire repertoire of potential protein k...

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