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Conservation of Nonsense-Mediated mRNA Decay Complex Components Throughout Eukaryotic Evolution

Authors
  • Causier, Barry1
  • Li, Zhen2, 3
  • De Smet, Riet2, 3
  • Lloyd, James P. B.1
  • Van de Peer, Yves2, 3, 4
  • Davies, Brendan1
  • 1 Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK , Leeds (United Kingdom)
  • 2 Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, Gent, B-9052, Belgium , Gent (Belgium)
  • 3 VIB Center for Plant Systems Biology, Technologiepark 927, Gent, B-9052, Belgium , Gent (Belgium)
  • 4 Genomics Research Institute, University of Pretoria, Department of Genetics, Private Bag X20, Pretoria, 0028, South Africa , Pretoria (South Africa)
Type
Published Article
Journal
Scientific Reports
Publisher
Springer Nature
Publication Date
Nov 30, 2017
Volume
7
Issue
1
Identifiers
DOI: 10.1038/s41598-017-16942-w
Source
Springer Nature
License
Green

Abstract

Nonsense-mediated mRNA decay (NMD) is an essential eukaryotic process regulating transcript quality and abundance, and is involved in diverse processes including brain development and plant defenses. Although some of the NMD machinery is conserved between kingdoms, little is known about its evolution. Phosphorylation of the core NMD component UPF1 is critical for NMD and is regulated in mammals by the SURF complex (UPF1, SMG1 kinase, SMG8, SMG9 and eukaryotic release factors). However, since SMG1 is reportedly missing from the genomes of fungi and the plant Arabidopsis thaliana, it remains unclear how UPF1 is activated outside the metazoa. We used comparative genomics to determine the conservation of the NMD pathway across eukaryotic evolution. We show that SURF components are present in all major eukaryotic lineages, including fungi, suggesting that in addition to UPF1 and SMG1, SMG8 and SMG9 also existed in the last eukaryotic common ancestor, 1.8 billion years ago. However, despite the ancient origins of the SURF complex, we also found that SURF factors have been independently lost across the Eukarya, pointing to genetic buffering within the essential NMD pathway. We infer an ancient role for SURF in regulating UPF1, and the intriguing possibility of undiscovered NMD regulatory pathways.

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