Charophytic Green Algae Encode Ancestral Polymerase IV/Polymerase V Subunits and a CLSY/DRD1 Homolog

Area of Science:

• Plant molecular biology
• Evolutionary genomics
• Epigenetics

Background:

• RNA-directed DNA Methylation (RdDM) silences transposons in flowering plants via small RNAs.
• RdDM requires RNA Polymerases IV and V, featuring plant-specific subunits.
• The evolutionary history of these key RdDM components, particularly Pol IV and Pol V largest subunits, is unclear.

Purpose of the Study:

• To investigate the evolutionary origins of RNA Polymerase IV and V in land plant ancestors.
• To clarify the duplication events in the evolution of Pol IV and Pol V largest subunits.
• To reconstruct the ancestral state of the RNA-directed DNA Methylation pathway.

Main Methods:

• Comparative genomics analysis of charophytic green algae.
• Phylogenetic analysis of RNA Polymerase IV and V subunit genes.
• Identification and characterization of conserved domains in algal polymerases.

Main Results:

• Charophytic green algae possess a single-copy precursor for the largest subunits of both RNA Polymerase IV and V.
• A Polymerase V-like C-terminal domain is present in algal homologs, suggesting functional conservation.
• A single CLSY/DRD1-type chromatin remodeling protein exists in these algae.

Conclusions:

• The two duplications in the Pol IV/V largest subunit gene family occurred after the divergence of charophytic algae from land plants.
• The earliest RNA-directed DNA Methylation pathway likely involved a single, specialized polymerase.
• Charophytic algae provide insights into the ancestral machinery of epigenetic gene silencing.