Keywords

CDPK, Evolution, CRK, Intron, Gene fusion, Protists, Phylogeny, Calmodulin, Kinase evolution

Reference

DOI: 10.1007/s002390010211

Abstract

This study explores the molecular evolution of calmodulin-like domain protein kinases (CDPKs) across plants and Alveolate protists using intron/exon structural analysis combined with phylogenetic trees based on kinase catalytic domains. The results strongly support a monophyletic origin of plant and protist CDPKs along with CDPK-related kinases (CRKs) and provide intriguing insights into how ancient intron-mediated gene fusion may have shaped the emergence of CDPKs. This work suggests that CDPK genes may have originated via fusion of protein kinase and calmodulin genes, facilitated by shared introns.

Notes

1. CDPKs and CRKs Share a Monophyletic Origin

  • Both CDPKs and CRKs are grouped in a single evolutionary lineage based on:
    • Conserved intron positions (e.g., introns 11, 16, 18, 21 shared across all subgroups).
    • Phylogenetic trees built on kinase domains.
  • Plant CDPKs divide into two major branches, but protist CDPKs are much more divergent.

Key point: Plant and protist CDPKs are evolutionarily linked despite functional divergence.

2. Intron Analysis as a Phylogenetic Tool

  • Introns were numbered (1–29) from N-terminal to C-terminal along aligned CDPK sequences:
    • 1–16: located in the kinase domain (KD).
    • 17: junction domain (JD).
    • 18: border between JD and CaM-like domain (CaM-LD).
    • 19–29: within CaM-LD.
  • Conserved introns mirror phylogenetic trees, supporting evolutionary relatedness.

Intron position analysis can serve as an independent line of evidence for evolutionary relationships, beyond sequence similarity.

3. Ancestral Gene Fusion Hypothesis for CDPK Evolution

  • The presence of a phase zero intron at the start of CaM-LD (shared with animal/fungal CaM genes) suggests that CDPK originated from a recombination between a kinase gene and a CaM gene.
  • No CDPK-like fusions found in animals or fungi, and no CaMK-like genes in plants.
  • Likely, CDPK represents a unique evolutionary innovation in plants and protists.

Ancient exon shuffling via introns may have produced the unique multi-domain architecture of CDPKs.

4. Evolutionary Diversification Reflected in Domain Conservation

  • Kinase domain (KD) is the most conserved (52% similarity).
  • Junction domain (JD): ~42% similarity.
  • CaM-like domain (CaM-LD): ~36% similarity.
  • N-terminal regions are highly variable—likely connected to substrate specificity and localization.

Pattern of conservation suggests core kinase activity is preserved, while regulation and substrate recognition are diversified.

5. Introns as Evolutionary Markers

  • Introns shared across plants and protists precede their divergence, marking an ancient common ancestor.
  • Intron loss and gain observed:
    • Likely through reverse transcription and reintegration (intron loss).
    • De novo insertion (intron gain).
  • Combination of ancient and new introns, supporting both introns-early and introns-late theories.

CDPKs embody a rich evolutionary history of intron dynamics, reflecting both deep ancestry and lineage-specific changes.

6. Shared Evolutionary Relationship with PEPCK?

  • Plant phosphoenolpyruvate carboxylase kinases (PEPCKs) have kinase domains similar to CDPKs but lack JD and CaM-LD.
  • Intron comparison hints at shared ancestry or parallel evolution—yet the lack of CaM-LD in PEPCKs raises questions about domain gain/loss events.

Possible evolutionary “cousins” of CDPKs, though with domain simplifications.

7. Protist CDPK Diversity & Divergence

  • Protist CDPK genes are highly diverged in both sequence and intron positions.
  • Hypotheses:
    1. Frame shifting/sliding of introns.
    2. Nonhomologous introns insertion/loss.

Protist CDPKs exhibit greater diversity, possibly linked to their unique ecological and parasitic adaptations.

8. Final Insights: Unique Evolutionary Niche of CDPKs

  • Why are CDPKs absent from animals and fungi?
  • Why do plants lack CaMK-like genes?
  • Possibly, CDPK evolution filled a niche for direct Ca2+-regulated kinases in plants and protists, replacing the need for CaMKs or PKCs found in animals.

CDPKs may represent an evolutionary “solution” to calcium signaling, tailored to plant and protist lifeforms.

🌿🌼🌼 Final Thought

“What if the ancient fusion of kinase and calmodulin-like domains was not a one-time event? Could similar recombination events be engineered today to create synthetic signaling molecules with novel regulatory capacities?"