Advertisement

Evolutionary Ancestry of Eukaryotic Protein Kinases and Choline Kinases*

  • Author Footnotes
    1 Supported by University Graduate Fellowships from the University of British Columbia and Kinexus Bioinformatics Corporation.
    Shenshen Lai
    Footnotes
    1 Supported by University Graduate Fellowships from the University of British Columbia and Kinexus Bioinformatics Corporation.
    Affiliations
    From the Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5,
    Search for articles by this author
  • Author Footnotes
    1 Supported by University Graduate Fellowships from the University of British Columbia and Kinexus Bioinformatics Corporation.
    Javad Safaei
    Footnotes
    1 Supported by University Graduate Fellowships from the University of British Columbia and Kinexus Bioinformatics Corporation.
    Affiliations
    the Department of Computer Science, University of British Columbia, Vancouver, British Columbia V6T 1Z4, and
    Search for articles by this author
  • Steven Pelech
    Correspondence
    To whom correspondence should be addressed: Ste. 1, 8755 Ash St., Vancouver, British Columbia V6P 6T3, Canada. Tel.: 604-323-2547, Ext. 10; Fax: 604-323-2548;
    Affiliations
    From the Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5,

    the Kinexus Bioinformatics Corporation, Vancouver, British Columbia V6P 6T3, Canada
    Search for articles by this author
  • Author Footnotes
    * This work was supported by Kinexus. S. P. is the president, chief scientific officer and majority shareholder of Kinexus Bioinformatics Corporation, which offers proteomics services and products for sale.
    This article contains supplemental Tables S1–S9.
    1 Supported by University Graduate Fellowships from the University of British Columbia and Kinexus Bioinformatics Corporation.
Open AccessPublished:January 07, 2016DOI:https://doi.org/10.1074/jbc.M115.691428
      The reversible phosphorylation of proteins catalyzed by protein kinases in eukaryotes supports an important role for eukaryotic protein kinases (ePKs) in the emergence of nucleated cells in the third superkingdom of life. Choline kinases (ChKs) could also be critical in the early evolution of eukaryotes, because of their function in the biosynthesis of phosphatidylcholine, which is unique to eukaryotic membranes. However, the genomic origins of ePKs and ChKs are unclear. The high degeneracy of protein sequences and broad expansion of ePK families have made this fundamental question difficult to answer. In this study, we identified two class-I aminoacyl-tRNA synthetases with high similarities to consensus amino acid sequences of human protein-serine/threonine kinases. Comparisons of primary and tertiary structures supported that ePKs and ChKs evolved from a common ancestor related to glutaminyl aminoacyl-tRNA synthetases, which may have been one of the key factors in the successful of emergence of ancient eukaryotic cells from bacterial colonies.

      Introduction

      Protein kinases play a pivotal role in communicating intracellular signals in eukaryotes. The family of eukaryotic protein kinases (ePKs)
      The abbreviations used are: ePK, eukaryotic protein kinase; AMPK, AMP-dependent protein kinase; ChK, choline kinase; GlnRS, glutaminyl-tRNA synthetase; GluRS, glutamyl-tRNA synthetase; PTK, protein-tyrosine kinase; STK, protein-serine/threonine kinase.
      comprises at least 568 human members, which accounts for more than 2% of the protein coding genes of the entire human genome (
      • Manning G.
      • Whyte D.B.
      • Martinez R.
      • Hunter T.
      • Sudarsanam S.
      The protein kinase complement of the human genome.
      ). These kinases are highly conserved both in their primary amino acid sequences (
      • Hanks S.K.
      • Quinn A.M.
      • Hunter T.
      The protein kinase family: conserved features and deduced phylogeny of the catalytic domains.
      ) and in the three-dimensional structures (
      • Taylor S.S.
      • Radzio-Andzelm E.
      Three protein kinase structures define a common motif.
      ) of their catalytic domains. Because of the central regulatory roles and the high conservation of the ePKs, the ancestry of these enzymes has become an important question in the study of the evolution of eukaryotic organisms.
      The majority of the kinases among the ePKs are responsible for the phosphorylation of proteins on serine or threonine residues, whereas a smaller group of protein kinases catalyzes their tyrosine phosphorylation. This branch of protein-tyrosine kinases (PTKs) arose from protein-serine/threonine kinases (STKs), which is believed to be an important event in early metazoan evolution (
      • Darnell Jr., J.E.
      Phosphotyrosine signaling and the single cell:metazoan boundary.
      ,
      • Rokas A.
      • Krüger D.
      • Carroll S.B.
      Animal evolution and the molecular signature of radiations compressed in time.
      ). Of all the STKs, there is another lumped group of diverse kinases that are described as atypical protein kinases. With little sequence identity and structural similarity to typical protein kinases, these atypical protein kinases are suggested to have diverged early in evolution and have distinct evolutionary histories (
      • Leonard C.J.
      • Aravind L.
      • Koonin E.V.
      Novel families of putative protein kinases in bacteria and archaea: evolution of the “eukaryotic” protein kinase superfamily.
      ,
      • Middelbeek J.
      • Clark K.
      • Venselaar H.
      • Huynen M.A.
      • van Leeuwen F.N.
      The α-kinase family: an exceptional branch on the protein kinase tree.
      ). Despite the atypical protein kinases and recently derived PTKs, the rest of the typical protein kinases constitutes a major lineage in protein kinase evolution.
      Eukaryotic life is believed to have evolved between 1.7 and 2.7 billion years ago, and no living representatives of the earliest eukaryotes survive today. Consequently, the actual origin of protein kinases is difficult to establish with a high degree of confidence. Firstly, protein sequences are highly degenerate, which makes the detection of sequence similarities difficult even at the superfamily level (
      • Murzin A.G.
      • Brenner S.E.
      • Hubbard T.
      • Chothia C.
      SCOP: a structural classification of proteins database for the investigation of sequences and structures.
      ). Secondly, the ePKs comprise a group of very broadly expanded proteins. Loss and expansion of kinase-relatedness tree branches occur in various species, as well as insertions and deletions inside their catalytic domains. To investigate these problems, we developed novel strategies using consensus sequences from precise amino acid sequence alignments as the initial query in BLAST searches and compared top hits from multiple species. Our conclusions are supported by protein primary and tertiary structure comparisons. Our findings offer new insights into the evolution of ePKs and choline kinases (ChKs) in ancient eukaryotes. The molecular paleontology approach undertaken in this study also provides a broadly applicable strategy to generally investigate the origins of large protein domain families.

      Discussion

      A few eukaryotic protein kinase-like genes have been identified in archaebacteria (
      • Smith R.F.
      • King K.Y.
      Identification of a eukaryotic-like protein kinase gene in Archaebacteria.
      ) and prokaryotes (
      • Tyagi N.
      • Anamika K.
      • Srinivasan N.
      A framework for classification of prokaryotic protein kinases.
      ,
      • Pérez J.
      • Castañeda-García A.
      • Jenke-Kodama H.
      • Müller R.
      • Muñoz-Dorado J.
      Eukaryotic-like protein kinases in the prokaryotes and the myxobacterial kinome.
      ). The widespread distribution of protein kinase genes has led to suggestions that the ancestry of these catalytic domains predated the divergence of the three domains of life (
      • Leonard C.J.
      • Aravind L.
      • Koonin E.V.
      Novel families of putative protein kinases in bacteria and archaea: evolution of the “eukaryotic” protein kinase superfamily.
      ). However, these eukaryotic-like protein kinases lack some of the essential motifs of ePKs. Other studies have indicated that some of the eukaryotic-like protein kinases had distinct evolutionary histories, which might be even more ancient than ePKs (
      • Ortiz-Lombardía M.
      • Pompeo F.
      • Boitel B.
      • Alzari P.M.
      Crystal structure of the catalytic domain of the PknB serine/threonine kinase from Mycobacterium tuberculosis.
      ,
      • Scheeff E.D.
      • Bourne P.E.
      Structural evolution of the protein kinase-like superfamily.
      ).
      Signal transduction in prokaryotes is mainly conducted through the two-component system by histidine kinases instead of by protein-serine/threonine or protein-tyrosine kinases. These histidine kinases commonly possesses a conserved C-terminal kinase core domain that features the phospho-accepting histidine as well as homology boxes (H-, N-, D-, F-, G-, and X-) that are not evident in typical eukaryotic protein kinases and display no resemblance to the highly conserved kinase catalytic subdomains in ePKs (
      • Grebe T.W.
      • Stock J.B.
      The histidine protein kinase superfamily.
      ).
      With recent data generated from the sequencing of many whole genomes, it is believed that genes actively undergo horizontal transfers across species, which contribute significantly to the flows of genes in evolution (
      • Kannan N.
      • Taylor S.S.
      • Zhai Y.
      • Venter J.C.
      • Manning G.
      Structural and functional diversity of the microbial kinome.
      ,
      • Syvanen M.
      Evolutionary implications of horizontal gene transfer.
      ). Horizontal gene transfers most likely account for many of the eukaryotic-like protein kinases that have been identified in bacteria. These proteins, such as the PknB kinases (
      • Keeling P.J.
      • Palmer J.D.
      Horizontal gene transfer in eukaryotic evolution.
      ,
      • Kennelly P.J.
      Protein kinases and protein phosphatases in prokaryotes: a genomic perspective.
      ) and the aminoglycoside phosphotransferase APH(3′)-IIIa (
      • Daigle D.M.
      • McKay G.A.
      • Thompson P.R.
      • Wright G.D.
      Aminoglycoside antibiotic phosphotransferases are also serine protein kinases.
      ,
      • Walsh C.
      Molecular mechanisms that confer antibacterial drug resistance.
      ), are usually limited to a few branches of the entire bacterial kingdom. Thus, ePKs are still likely to have a eukaryotic origin.
      The human protein kinase complement is a well studied group of regulatory enzymes that is expanded broadly in relatedness trees in all investigated eukaryotes. As a result, we selected all of the human STK catalytic domains and precisely aligned them to generate a representative consensus sequence for ancient ePKs. The strategy of comparing BLAST results from various well studied organisms and aligning the extremely conserved key residues made it possible to detect long distant relationships. The supportive results from primary sequence analysis and structural comparison provide high confidence in the evolutionary linkages between glutaminyl-tRNA synthetase, protein kinases, and choline/ethanolamine kinases.
      This contention could be further supported in future studies by site-directed mutagenesis experiments, ideally starting with the deduced consensus sequence of GlnRS or possibly human glutaminyl aminoacyl-tRNA synthetase as this would be technically easier. Based on our comparisons of the consensus sequences of the ePKs and GlnRS shown in Table 2, there are at least 8 highly conserved amino acids found in the catalytic subdomains of ePKs that were missing in GlnRS. Replacement of these amino acid residues in GlnRS with those that are conserved in the ePKs in their catalytic subdomains and that are generally involved in ATP binding and catalysis would be a first step. Additional amino acid residue replacements may be needed for improving recognition of the protein substrate. Our Protein Kinase Substrate Prediction Algorithm Version 2.0 predicts substrate-determining residues that might also be altered to improve the prospects of successful conversion of a GlnRS into a protein kinase (
      • Safaei J.
      • Maǔch J.
      • Gupta A.
      • Stacho L.
      • Pelech S.
      Prediction of 492 human protein kinase substrate specificities.
      ,
      • Theobald D.L.
      A formal test of the theory of universal common ancestry.
      ).
      Our results indicated that ePKs and ChKs share a common ancestor, which is consistent with previous three-dimensional structure studies on these proteins. GlnRS exhibited higher sequence identities with ePKs and ChKs than these did with each other, as well as moderate structural similarities. It appears to be the contemporary gene most closely related to the ancestor of both ePK and ChK. Although GlnRS appears exclusively in eukarya and archaea, the aminoacyl-tRNA synthetases comprise a most ancient group of genes that are believed to undergo horizontal transfers early in evolution and gave rise to many of the contemporary genes (
      • Safaei J.
      • Maǔch J.
      • Gupta A.
      • Stacho L.
      • Pelech S.
      Prediction of 492 human protein kinase substrate specificities.
      ,
      • Brown J.R.
      • Douady C.J.
      • Italia M.J.
      • Marshall W.E.
      • Stanhope M.J.
      Universal trees based on large combined protein sequence data sets.
      ). We are compelled to believe that ePKs and ChKs also have an early eukaryotic origin and that both played an important part in early evolution of highly complex eukaryotic cells.
      Here we propose that ePKs and ChKs arose from a common ancestor that is an ancient gene involved in the mRNA translation process as an aminoacyl-tRNA ligase. The emergence of ChKs offered additional phospholipid constituents for construction of more complex membrane structures that provide for intracellular compartmentalization as well as sources of intracellular mediators of signaling. At the same time, ePKs made the communication among different compartments more specific and efficient, which facilitated the specialization of various organelles. The emergence of protein kinases and choline/ethanolamine kinases may well have been critical to the development and success of eukaryotic organisms.

      Author Contributions

      S. P. conceived the project. S. L. and S. P. designed and performed most of the analyses. J. S. carried out the Pfam domain alignments and kinase domain evolutionary conservation analyses. S. L. wrote the initial draft of the manuscript, and S. P. completed the final version. S. L. and S. P. prepared the figures and tables. All authors analyzed the results and approved the final version of the manuscript.

      References

        • Manning G.
        • Whyte D.B.
        • Martinez R.
        • Hunter T.
        • Sudarsanam S.
        The protein kinase complement of the human genome.
        Science. 2002; 298: 1912-1934
        • Hanks S.K.
        • Quinn A.M.
        • Hunter T.
        The protein kinase family: conserved features and deduced phylogeny of the catalytic domains.
        Science. 1988; 241: 42-52
        • Taylor S.S.
        • Radzio-Andzelm E.
        Three protein kinase structures define a common motif.
        Structure. 1994; 2: 345-355
        • Darnell Jr., J.E.
        Phosphotyrosine signaling and the single cell:metazoan boundary.
        Proc. Natl. Acad. Sci. U.S.A. 1997; 94: 11767-11769
        • Rokas A.
        • Krüger D.
        • Carroll S.B.
        Animal evolution and the molecular signature of radiations compressed in time.
        Science. 2005; 310: 1933-1938
        • Leonard C.J.
        • Aravind L.
        • Koonin E.V.
        Novel families of putative protein kinases in bacteria and archaea: evolution of the “eukaryotic” protein kinase superfamily.
        Genome Res. 1998; 8: 1038-1047
        • Middelbeek J.
        • Clark K.
        • Venselaar H.
        • Huynen M.A.
        • van Leeuwen F.N.
        The α-kinase family: an exceptional branch on the protein kinase tree.
        Cell. Mol. Life Sci. 2010; 67: 875-890
        • Murzin A.G.
        • Brenner S.E.
        • Hubbard T.
        • Chothia C.
        SCOP: a structural classification of proteins database for the investigation of sequences and structures.
        J. Mol. Biol. 1995; 247: 536-540
        • Ortiz-Lombardía M.
        • Pompeo F.
        • Boitel B.
        • Alzari P.M.
        Crystal structure of the catalytic domain of the PknB serine/threonine kinase from Mycobacterium tuberculosis.
        J. Biol. Chem. 2003; 278: 13094-13100
        • Camacho C.
        • Coulouris G.
        • Avagyan V.
        • Ma N.
        • Papadopoulos J.
        • Bealer K.
        • Madden T.L.
        BLAST+: architecture and applications.
        BMC Bioinformatics. 2009; 10: 421
        • Kelley L.A.
        • Sternberg M.J.
        Protein structure prediction on the Web: a case study using the Phyre server.
        Nat. Protoc. 2009; 4: 363-371
        • Ye Y.
        • Godzik A.
        Flexible structure alignment by chaining aligned fragment pairs allowing twists.
        Bioinformatics. 2003; 19: ii246-ii255
        • Holland R.C.
        • Down T.A.
        • Pocock M.
        • Prlić A.
        • Huen D.
        • James K.
        • Foisy S.
        • Dräger A.
        • Yates A.
        • Heuer M.
        • Schreiber M.J.
        BioJava: an open-source framework for bioinformatics.
        Bioinformatics. 2008; 24: 2096-2097
        • Finn R.D.
        • Mistry J.
        • Tate J.
        • Coggill P.
        • Heger A.
        • Pollington J.E.
        • Gavin O.L.
        • Gunasekaran P.
        • Ceric G.
        • Forslund K.
        • Holm L.
        • Sonnhammer E.L.L.
        • Eddy S.R.
        • Bateman A.
        The Pfam protein families database.
        Nucleic Acids Res. 2010; 38: D211-D222
        • Sonnhammer E.L.
        • Eddy S.R.
        • Durbin R.
        Pfam: a comprehensive database of protein domain families based on seed alignments.
        Proteins. 1997; 28: 405-420
        • Peisach D.
        • Gee P.
        • Kent C.
        • Xu Z.
        The crystal structure of choline kinase reveals a eukaryotic protein kinase fold.
        Structure. 2003; 11: 703-713
        • Lamour V.
        • Quevillon S.
        • Diriong S.
        • N′Guyen V.C.
        • Lipinski M.
        • Mirande M.
        Evolution of the Glx-tRNA synthetase family: the glutaminyl enzyme as a case of horizontal gene transfer.
        Proc. Natl. Acad. Sci. U.S.A. 1994; 91: 8670-8674
        • Saha R.
        • Dasgupta S.
        • Basu G.
        • Roy S.
        A chimaeric glutamyl:glutaminyl-tRNA synthetase: implications for evolution.
        Biochem. J. 2009; 417: 449-455
        • Siatecka M.
        • Rozek M.
        • Barciszewski J.
        • Mirande M.
        Modular evolution of the Glx-tRNA synthetase family-rooting of the evolutionary tree between the bacteria and archaea/eukarya branches.
        Eur. J. Biochem. 1998; 256: 80-87
        • Carling D.
        • Aguan K.
        • Woods A.
        • Verhoeven A.J.
        • Beri R.K.
        • Brennan C.H.
        • Sidebottom C.
        • Davison M.D.
        • Scott J.
        Mammalian AMP-activated protein kinase is homologous to yeast and plant protein kinases involved in the regulation of carbon metabolism.
        J. Biol. Chem. 1994; 269: 11442-11448
        • Manning G.
        • Plowman G.D.
        • Hunter T.
        • Sudarsanam S.
        Evolution of protein kinase signaling from yeast to man.
        Trends Biochem. Sci. 2002; 27: 514-520
        • Smith R.F.
        • King K.Y.
        Identification of a eukaryotic-like protein kinase gene in Archaebacteria.
        Protein Sci. 1995; 4: 126-129
        • Tyagi N.
        • Anamika K.
        • Srinivasan N.
        A framework for classification of prokaryotic protein kinases.
        PLoS ONE. 2010; 5: e10608
        • Pérez J.
        • Castañeda-García A.
        • Jenke-Kodama H.
        • Müller R.
        • Muñoz-Dorado J.
        Eukaryotic-like protein kinases in the prokaryotes and the myxobacterial kinome.
        Proc. Natl. Acad. Sci. U.S.A. 2008; 105: 15950-15955
        • Scheeff E.D.
        • Bourne P.E.
        Structural evolution of the protein kinase-like superfamily.
        PLoS Comput. Biol. 2005; 1: e49
        • Grebe T.W.
        • Stock J.B.
        The histidine protein kinase superfamily.
        Adv. Microb. Physiol. 1999; 41: 139-227
        • Kannan N.
        • Taylor S.S.
        • Zhai Y.
        • Venter J.C.
        • Manning G.
        Structural and functional diversity of the microbial kinome.
        PLoS Biol. 2007; 5: e17
        • Syvanen M.
        Evolutionary implications of horizontal gene transfer.
        Annu. Rev. Genet. 2012; 46: 341-358
        • Keeling P.J.
        • Palmer J.D.
        Horizontal gene transfer in eukaryotic evolution.
        Nat. Rev. Genet. 2008; 9: 605-618
        • Kennelly P.J.
        Protein kinases and protein phosphatases in prokaryotes: a genomic perspective.
        FEMS Microbiol. Lett. 2002; 206: 1-8
        • Daigle D.M.
        • McKay G.A.
        • Thompson P.R.
        • Wright G.D.
        Aminoglycoside antibiotic phosphotransferases are also serine protein kinases.
        Chem. Biol. 1999; 6: 11-18
        • Walsh C.
        Molecular mechanisms that confer antibacterial drug resistance.
        Nature. 2000; 406: 775-781
        • Safaei J.
        • Maǔch J.
        • Gupta A.
        • Stacho L.
        • Pelech S.
        Prediction of 492 human protein kinase substrate specificities.
        Proteome Sci. 2011; 9: S6
        • Theobald D.L.
        A formal test of the theory of universal common ancestry.
        Nature. 2010; 465: 219-222
        • Brown J.R.
        • Douady C.J.
        • Italia M.J.
        • Marshall W.E.
        • Stanhope M.J.
        Universal trees based on large combined protein sequence data sets.
        Nat. Genet. 2001; 28: 281-285