Biol729 – The kinomes of model organisms

Phylogenetic comparison of the human kinome with those of yeast ( S. cerevisiae), worm (C. elegans) and fly (D. melanogaster) confirms that most kinase families are shared among metazoans and reveals classes that are expanded in each lineage.

 Of 189 subfamilies of protein kinases present in human, 51 are found in all four eukaryotic kinomes – these presumably serve functions that are essential for a eukaryotic cell.  An additional 93 subfamilies are present in human, fly and worm (i.e. not yeast) implying that these evolved to fulfil distinct functions in early metazoan (multicellular) evolution.  More that 95% of human kinases have direct orthologs in mouse.  The function of human kinases can be inferred from family members in model organisms. However there is no functional data available for 4 families with orthologues in human, fly and worm - they must have fundamental roles in metazoans about which we are still ignorant.

Group FamiliesSubfamiliesYeastWormFlyHuman Human pseudogenes Novel human kinases AGC CAMK CK CMGC Other STE Tyrosine kinase Tyrosine kinase-like RGC Protein kinase distribution by major groups in human and model systems

 The human genome has ~ twice as many kinases as those of the fly or worm. This expansion is not uniform. The expanded families function predominantly in processes that are more advanced in human, such as the nervous and immune systems, angiogenesis and haemopoiesis.  All human kinase genes have been mapped to chromosomal loci. Although the overall kinase distribution is similar in density to that of other genes, many pairs of closely related genes from the same families map closely to each other, indicating that they may have arisen through local duplications.  Most of these duplicated genes are from families that are highly expanded in human compared with worm and fly, supporting a recent origin.  28 inactive kinases belong to families where all members are inactive in human, fly, worm and even in yeast. i.e. nearly 10 % of all kinase domains appear to lack catalytic activity.

Dictyostelium discoideum – a slime mould.

The Dictyostelium kinome  Dictyostelium discoideum is an organism with both unicellular and multicellular forms.  Dictyostelium amoebae live in soil where they consume smaller microbes. Nutritional stress drives cells to aggregate. Aggregates differentiate into multicellular fruiting bodies containing spores.  Dictyostelium therefore shows a number of characteristics of complex eukaryotes.  The genome encodes ~ 12,500 protein-coding genes (twice the number in yeast). The rarity of alternative splicing simplifies the proteome compared with those of vertebrates.

The 285 Dictyostelium protein kinase genes represent 2.6% of the genome. Dictyostelium-specific families/sub-families shown in italics.

 There are members of 24 subfamilies not found in yeast, even though Dictyostelium is more evolutionarily divergent that fungi.  This suggests that these kinases were present in very early eukaryotes, but lost from fungi, due to their simpler lifestyle.  There are a number of Dictyostelium-specific kinases that appear to be involved in unique aspects of Dictyostelium biology (e.g. spore differentiation).

 Dictyostelium, like yeast, lacks the tyrosine kinase group. It has an expanded (66 – almost twice the proportion of the kinome compared to metazoa) TKL (tyrosine kinase-like group). The presence of TKLs in Dictyostelium (and plants) indicates that this group is ancient and has been lost in yeast.  Tyrosine phosphorylation is well documented in Dictyostelium – despite the lack of TKs. The Dictyostelium TKLs include kinases that have been shown to have tyrosine kinase activity.  The similarity between TKs and TKLs may have a functional basis (ability to phosphorylate tyrosine) and an evolutionary basis, where the TK group may have evolved from the ancient TKL group. The proportion of the kinome devoted to the major groups in Dictyostelium (Dd), yeast (Sc), worm (Ce), flies (Dm), and humans (Hs).

Comparison of Dictyostelium with four other kinomes suggests that 75 distinct subfamilies existed in their common ancestor, and that new subfamilies were born (positive numbers) and lost (negative numbers) in most lineages. Numbers in parenthesis indicate “unique” kinases within each lineage. Most notably, S. cerevisiae has lost 24 subfamilies present in the common ancestor, while metazoans invented an additional 80 conserved subfamilies.

Human kinases implicated in disease that are conserved in Dictyostelium. The ability to easily disrupt genes in Dictyostelium make it useful for understanding the functions of disease-associated kinases. Dictyostelium may also prove to be useful for kinase drug screening.

The sea urchin kinome  The sea urchin belongs to the phylum Echinodermata (Echinoderms), which are the closest invertebrates to the chordate phylum, and so a starting point to understanding chordate- and vertebrate- specific features.  Comparison of human, insect, and nematode kinases suggested that 13 kinase subfamilies were vertebrate-specific. However, there are homologs of 9 of these families in urchin, showing that they developed earlier than expected, and that there was much less invention of new classes of kinases within vertebrates.

The sea urchin kinome.

 Unlike both Drosophila and C. elegans, which have both lost many kinase classes found in their common ancestor, urchins appear to have lost none, making it a simple non-redundant model for vertebrate kinases.  The other major feature of the Urchin kinome is its simplicity. Despite having 183 of the 187 human subfamilies, it has only 353 kinases, compared with the 518 found in human. Most subfamilies have just one urchin member, but have several in vertebrates.  As with other kinomes, urchin does have its own idiosyncratic expansions. The largest family, called 'Urch' has 29 members and is remote from any other family, while other unique families are found in the TK and TKL groups.  Several 'Other-Unique' singleton kinases in human are now seen to have urchin orthologues, showing that they have conserved and relatively ancient functions.

The Tetrahymena kinome  Tetrahymena is a eukaryote, but only very remotely related to humans (Tetrahymena and other ciliates are members of the kingdom Alveolata, distinct from both animals/fungi and plants), so genes are accordingly very divergent.  It is single-celled but large (up to 50  m long) and complex (some 27,000 protein coding genes, similar to that of the human genome).

 There are 1069 predicted protein kinases, the largest number, and the largest fraction of the proteome (3.9%) for any kinome to date.  This number is very preliminary, as many encode only fragments of kinase domains.  Only 416 kinases (39%) can be classified into previously- known classes, leaving a record 653 kinases that fall into 41 new tentative families (a few have homologues in plants or other distant organisms, but most are ciliate-specific for now).

 By comparing kinase subfamilies between organisms, we see that:  As we go deeper in time, we lose more common kinases: Tetrahymena lacks 24 kinases that were likely present in the common ancestor of the other species. 7 of these are found in all other kinomes analyzed.  The other 17 are found in Dictyostelium and metazoans but not in yeast, suggesting that they are less core to basic cellular function, being absent both from the primitiveTetrahymena and the more evolved yeast.  7 of the 24 kinases found in Dictyostelium, but not yeast, are also found in Tetrahymena, further suggesting that they are ancient kinases that were secondarily lost from yeast.  Another 3 kinases are found in Tetrahymena and metazoans but not in Dictyostelium or yeast, suggesting that these may be primordial kinases that were then lost from both these later branches, though they may also be derived from horizontal transfer events.

 As well as the 61% of kinases that are currently unique to ciliates, Tetrahymena also has extensive expansions of several well-known kinase classes.  The expansions of mitotic kinase classes correlates with the complex two-nucleus biology.  The NEK family is also expanded (39 members) and has roles both in chromosomal segregation and in control of the many distinct cilia found throughout the body).  The enormous expansions of 52 ULK members and 83 histidine kinases remain functionally obscure.

Summary  Phylogenetic comparison confirms that most kinase families are shared among metazoans and reveals classes that are expanded in each lineage.  The function of human kinases can be inferred from family members in model organisms.  In Dictyostelium, there are protein kinases present that are not found in yeast, even though it is more evolutionarily divergent that fungi. These kinases were presumably present in very early eukaryotes, but lost from fungi, due to their simpler lifestyle.  There are homologues of 9 ‘vertebrate-specific’ families of kinases in sea urchin, showing that they developed earlier than expected, and that there was much less invention of new classes of kinases within vertebrates.

References Manning, G. et al. (2002) Trends in Biochem. Sci. 27, Evolution of protein kinase signalling from yeast to man. Goldberg, J. M. et al., (2006) PLoS Genetics 2, e38. Dictyostelium kinome.