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Ancestral resurrection reveals evolutionary mechanisms of kinase plasticity.

Howard CJ, Hanson-Smith V, Kennedy KJ, Miller CJ, Lou HJ, Johnson AD, Turk BE, Holt LJ - Elife (2014)

Bottom Line: Mutant analysis revealed that a variable residue within the kinase catalytic cleft, DFGx, modulates +1 specificity.Expansion of Ime2 kinase specificity by mutation of this residue did not cause dominant deleterious effects in vivo.Tolerance of cells to new specificities likely enabled the evolutionary divergence of kinases.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.

ABSTRACT
Protein kinases have evolved diverse specificities to enable cellular information processing. To gain insight into the mechanisms underlying kinase diversification, we studied the CMGC protein kinases using ancestral reconstruction. Within this group, the cyclin dependent kinases (CDKs) and mitogen activated protein kinases (MAPKs) require proline at the +1 position of their substrates, while Ime2 prefers arginine. The resurrected common ancestor of CDKs, MAPKs, and Ime2 could phosphorylate substrates with +1 proline or arginine, with preference for proline. This specificity changed to a strong preference for +1 arginine in the lineage leading to Ime2 via an intermediate with equal specificity for proline and arginine. Mutant analysis revealed that a variable residue within the kinase catalytic cleft, DFGx, modulates +1 specificity. Expansion of Ime2 kinase specificity by mutation of this residue did not cause dominant deleterious effects in vivo. Tolerance of cells to new specificities likely enabled the evolutionary divergence of kinases.

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Raw data and selectivity values for a positional scanning peptide library array of an alternate reconstruction of AncCMGI.(A) Raw PSPL result for an alternative reconstruction of AncCMGI. (B) Averaged quantified data from (A) and a replicate analysis with AncCMGI. Data were collected and quantified as in Figure 1—figure supplements 1 and 2.DOI:http://dx.doi.org/10.7554/eLife.04126.009
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fig2s2: Raw data and selectivity values for a positional scanning peptide library array of an alternate reconstruction of AncCMGI.(A) Raw PSPL result for an alternative reconstruction of AncCMGI. (B) Averaged quantified data from (A) and a replicate analysis with AncCMGI. Data were collected and quantified as in Figure 1—figure supplements 1 and 2.DOI:http://dx.doi.org/10.7554/eLife.04126.009

Mentions: (A) Summary of current knowledge about CMGC group kinase specificity in the context of the maximum likelihood phylogeny of protein sequences. Major groups, such as IME2, MAK, ICK, etc, have been collapsed for simplicity. Branch lengths express the number of amino acid substitutions per protein sequence site. Branch support values are approximate likelihood ratios (aLRs), expressing the ratio of the likelihood of the maximum likelihood phylogeny to the next-best phylogeny lacking the indicated branch. For example, an aLR value of 10 indicates that the branch is 10 times more likely than the next-best phylogenetic hypothesis. The position of the common ancestor of CDK, MAPK, CDKL, GSK, and the IME2/LF4/RCK superfamily (AncCMGI), is indicated by a purple circle. (B) Position scanning peptide libraries were used to determine the primary specificity of the maximum likelihood resurrected AncCMGI kinase. Raw peptide data are shown in Figure 2—figure supplement 1. A complete repeat of the PSPL for a Bayesian sampled alternative reconstruction of AncCMGI (AncCMGI-B2) is shown in Figure 2—figure supplement 2. A structural model of AncCMGI is shown in Figure 2—figure supplement 3 in phylogenetic context along with structures and models for extant kinases that were derived from this ancestor.


Ancestral resurrection reveals evolutionary mechanisms of kinase plasticity.

Howard CJ, Hanson-Smith V, Kennedy KJ, Miller CJ, Lou HJ, Johnson AD, Turk BE, Holt LJ - Elife (2014)

Raw data and selectivity values for a positional scanning peptide library array of an alternate reconstruction of AncCMGI.(A) Raw PSPL result for an alternative reconstruction of AncCMGI. (B) Averaged quantified data from (A) and a replicate analysis with AncCMGI. Data were collected and quantified as in Figure 1—figure supplements 1 and 2.DOI:http://dx.doi.org/10.7554/eLife.04126.009
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4228266&req=5

fig2s2: Raw data and selectivity values for a positional scanning peptide library array of an alternate reconstruction of AncCMGI.(A) Raw PSPL result for an alternative reconstruction of AncCMGI. (B) Averaged quantified data from (A) and a replicate analysis with AncCMGI. Data were collected and quantified as in Figure 1—figure supplements 1 and 2.DOI:http://dx.doi.org/10.7554/eLife.04126.009
Mentions: (A) Summary of current knowledge about CMGC group kinase specificity in the context of the maximum likelihood phylogeny of protein sequences. Major groups, such as IME2, MAK, ICK, etc, have been collapsed for simplicity. Branch lengths express the number of amino acid substitutions per protein sequence site. Branch support values are approximate likelihood ratios (aLRs), expressing the ratio of the likelihood of the maximum likelihood phylogeny to the next-best phylogeny lacking the indicated branch. For example, an aLR value of 10 indicates that the branch is 10 times more likely than the next-best phylogenetic hypothesis. The position of the common ancestor of CDK, MAPK, CDKL, GSK, and the IME2/LF4/RCK superfamily (AncCMGI), is indicated by a purple circle. (B) Position scanning peptide libraries were used to determine the primary specificity of the maximum likelihood resurrected AncCMGI kinase. Raw peptide data are shown in Figure 2—figure supplement 1. A complete repeat of the PSPL for a Bayesian sampled alternative reconstruction of AncCMGI (AncCMGI-B2) is shown in Figure 2—figure supplement 2. A structural model of AncCMGI is shown in Figure 2—figure supplement 3 in phylogenetic context along with structures and models for extant kinases that were derived from this ancestor.

Bottom Line: Mutant analysis revealed that a variable residue within the kinase catalytic cleft, DFGx, modulates +1 specificity.Expansion of Ime2 kinase specificity by mutation of this residue did not cause dominant deleterious effects in vivo.Tolerance of cells to new specificities likely enabled the evolutionary divergence of kinases.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.

ABSTRACT
Protein kinases have evolved diverse specificities to enable cellular information processing. To gain insight into the mechanisms underlying kinase diversification, we studied the CMGC protein kinases using ancestral reconstruction. Within this group, the cyclin dependent kinases (CDKs) and mitogen activated protein kinases (MAPKs) require proline at the +1 position of their substrates, while Ime2 prefers arginine. The resurrected common ancestor of CDKs, MAPKs, and Ime2 could phosphorylate substrates with +1 proline or arginine, with preference for proline. This specificity changed to a strong preference for +1 arginine in the lineage leading to Ime2 via an intermediate with equal specificity for proline and arginine. Mutant analysis revealed that a variable residue within the kinase catalytic cleft, DFGx, modulates +1 specificity. Expansion of Ime2 kinase specificity by mutation of this residue did not cause dominant deleterious effects in vivo. Tolerance of cells to new specificities likely enabled the evolutionary divergence of kinases.

Show MeSH