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Reticulate evolution in eukaryotes: Origin and evolution of the nitrate assimilation pathway
Eduard Ocaña-Pallarès1, Sebastián R Najle1,2, Claudio Scazzocchio3,4
1Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain.
Plos Genetics
|February 22, 2019
Summary
Reticulate evolution, including horizontal gene transfer (HGT), significantly shaped the eukaryotic nitrate assimilation pathway. Gene fusion and multiple HGT events, particularly between fungi and oomycetes, reveal complex evolutionary pathways.
Area of Science:
- Evolutionary Biology
- Genomics
- Biochemistry
Background:
- Reticulate evolution, particularly horizontal gene transfer (HGT), plays a controversial role in eukaryotic evolution.
- Metabolic pathways with patchy distributions, like eukaryotic nitrate assimilation, suggest potential HGT events.
- Previous studies proposed HGT for the fungal nitrate assimilation gene cluster from Oomycota.
Purpose of the Study:
- To investigate the origin and evolution of the eukaryotic nitrate assimilation pathway.
- To clarify the role of HGT and gene fusion in this pathway's history.
- To explore the evolutionary relationship between Opisthokonta and Stramenopiles regarding nitrate assimilation.
Main Methods:
- Multi-scale bioinformatic analysis of genomic data.
- Phylogenetic analyses to trace gene origins and transfers.
- Experimental validation of pathway activity and regulation in Ichthyosporea.
Main Results:
- Nitrate assimilation is more widespread in eukaryotes than previously known, found in autotrophs and osmotrophs.
- The pathway originated from three bacterial transfers and involved at least seven eukaryotic HGT events.
- A complex HGT history between Opisthokonta and Stramenopiles, including at least two gene cluster transfers, was identified.
- Gene fusion was crucial for the evolution of nitrate reductases, including a novel chimeric form in Ichthyosporea.
- The Ichthyosporean pathway is physiologically active, transcriptionally co-regulated, and functionally analogous to independently acquired pathways in other eukaryotes.
Conclusions:
- Horizontal gene transfer and gene fusion are critical drivers of eukaryotic evolution, exemplified by the nitrate assimilation pathway.
- The study reveals a complex and pervasive role for HGT in shaping metabolic pathways across eukaryotic lineages.
- Convergent evolution of transcriptional control mechanisms facilitated the integration of HGT-acquired pathways into eukaryotic metabolism.
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