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Genetic Engineering of Dictyostelium discoideum Cells Based on Selection and Growth on Bacteria

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Published on: January 25, 2019

Evolution of patchily distributed proteins shared between eukaryotes and prokaryotes: Dictyostelium as a case study.

Jan O Andersson¹

¹Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University, Uppsala, Sweden. jan.andersson @ ebc.uu.se

Journal of Molecular Microbiology and Biotechnology

|March 25, 2011

Summary

Gene transfer, not gene loss, likely explains patchy protein distribution across life. This study reveals widespread horizontal gene transfer shaping eukaryotic evolution and diversification.

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Area of Science:

Evolutionary biology
Genomics
Molecular evolution

Background:

Protein families exhibit patchy distribution across the tree of life, present in distant yet absent in close relatives.
This distribution pattern suggests either lateral gene transfer or gene loss as primary evolutionary mechanisms.
Understanding these patterns is crucial for deciphering the origin and evolution of genes, particularly in eukaryotes.

Purpose of the Study:

To investigate the evolutionary dynamics of patchily distributed proteins shared between prokaryotes and eukaryotes.
To develop a novel approach for analyzing the phylogenetic distribution of these proteins.
To determine the relative contributions of lateral gene transfer and gene loss in shaping protein family evolution.

Main Methods:

Identification of proteins encoded in the Dictyostelium discoideum genome and other select lineages, including prokaryotes.
Phylogenetic analysis of 49 patchily distributed protein families to assess their distribution patterns.
Examination of phylogenetic tree topologies to detect conflicts with established organismal phylogenies.

Main Results:

Phylogenetic analyses revealed conflicts between protein family distribution and organismal phylogenies.
25 protein families were shared with distantly related Naegleria (Excavata) but only two with the more closely related Entamoeba.
Eukaryotic polyphyly was observed in 85% of the phylogenetic trees, indicating extensive gene transfer.

Conclusions:

Gene transfer, specifically horizontal gene transfer, appears to be a significant mechanism driving the distribution of patchily distributed proteins across all domains of life.
The findings challenge traditional views of vertical inheritance and highlight the importance of gene exchange in shaping genomes.
Further research into this exchangeable gene fraction is essential for a comprehensive understanding of eukaryotic gene origins and diversification.