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Complex evolutionary history of translation elongation factor 2 and diphthamide biosynthesis in archaea and parabasalids

Narrowe, Adrienne B. ; Spang, Anja ; Stairs, Courtney W. LU orcid ; Caceres, Eva F. ; Baker, Brett J. ; Miller, Christopher S. and Ettema, Thijs J.G. (2018) In Genome Biology and Evolution 10(9). p.2380-2393
Abstract

Diphthamide is a modified histidine residue which is uniquely present in archaeal and eukaryotic elongation factor 2 (EF-2), an essential GTPase responsible for catalyzing the coordinated translocation of tRNA andmRNA through the ribosome. In part due to the roleofdiphthamide inmaintaining translational fidelity, itwas previously assumed that diphthamide biosynthesis genes (dph) are conserved across all eukaryotes and archaea. Here, comparative analysis of new and existing genomes reveals that some archaea (i.e., members of the Asgard superphylum,Geoarchaea, andKorarchaeota) and eukaryotes (i.e., parabasalids) lack dph. In addition, while EF-2 was thought to exist as a single copy in archaea, many of these dph-lacking archaeal genomes... (More)

Diphthamide is a modified histidine residue which is uniquely present in archaeal and eukaryotic elongation factor 2 (EF-2), an essential GTPase responsible for catalyzing the coordinated translocation of tRNA andmRNA through the ribosome. In part due to the roleofdiphthamide inmaintaining translational fidelity, itwas previously assumed that diphthamide biosynthesis genes (dph) are conserved across all eukaryotes and archaea. Here, comparative analysis of new and existing genomes reveals that some archaea (i.e., members of the Asgard superphylum,Geoarchaea, andKorarchaeota) and eukaryotes (i.e., parabasalids) lack dph. In addition, while EF-2 was thought to exist as a single copy in archaea, many of these dph-lacking archaeal genomes encode a second EF-2 paralog missing key residues required for diphthamide modification and for normal translocase function, perhaps suggesting functional divergence linked to loss of diphthamide biosynthesis. Interestingly, some Heimdallarchaeota previously suggested to be most closely related to the eukaryotic ancestormaintain dph genes and a single gene encoding canonical EF-2.Our findings reveal that the ability to produce diphthamide, once thought to be a universal feature in archaea and eukaryotes, has been lost multiple times during evolution, and suggest that anticipated compensatory mechanisms evolved independently.

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author
; ; ; ; ; and
publishing date
type
Contribution to journal
publication status
published
keywords
Asgard, Diphthamide, EF-2, Korarchaeota, Metagenomics, Trichomonas
in
Genome Biology and Evolution
volume
10
issue
9
pages
2380 - 2393
publisher
Oxford University Press
external identifiers
  • scopus:85054098427
  • pmid:30060184
ISSN
1759-6653
DOI
10.1093/gbe/evy154
language
English
LU publication?
no
id
7c4d9318-9929-4371-8c7f-e46c7aa066b3
date added to LUP
2020-10-23 10:59:36
date last changed
2024-05-15 20:27:07
@article{7c4d9318-9929-4371-8c7f-e46c7aa066b3,
  abstract     = {{<p>Diphthamide is a modified histidine residue which is uniquely present in archaeal and eukaryotic elongation factor 2 (EF-2), an essential GTPase responsible for catalyzing the coordinated translocation of tRNA andmRNA through the ribosome. In part due to the roleofdiphthamide inmaintaining translational fidelity, itwas previously assumed that diphthamide biosynthesis genes (dph) are conserved across all eukaryotes and archaea. Here, comparative analysis of new and existing genomes reveals that some archaea (i.e., members of the Asgard superphylum,Geoarchaea, andKorarchaeota) and eukaryotes (i.e., parabasalids) lack dph. In addition, while EF-2 was thought to exist as a single copy in archaea, many of these dph-lacking archaeal genomes encode a second EF-2 paralog missing key residues required for diphthamide modification and for normal translocase function, perhaps suggesting functional divergence linked to loss of diphthamide biosynthesis. Interestingly, some Heimdallarchaeota previously suggested to be most closely related to the eukaryotic ancestormaintain dph genes and a single gene encoding canonical EF-2.Our findings reveal that the ability to produce diphthamide, once thought to be a universal feature in archaea and eukaryotes, has been lost multiple times during evolution, and suggest that anticipated compensatory mechanisms evolved independently.</p>}},
  author       = {{Narrowe, Adrienne B. and Spang, Anja and Stairs, Courtney W. and Caceres, Eva F. and Baker, Brett J. and Miller, Christopher S. and Ettema, Thijs J.G.}},
  issn         = {{1759-6653}},
  keywords     = {{Asgard; Diphthamide; EF-2; Korarchaeota; Metagenomics; Trichomonas}},
  language     = {{eng}},
  number       = {{9}},
  pages        = {{2380--2393}},
  publisher    = {{Oxford University Press}},
  series       = {{Genome Biology and Evolution}},
  title        = {{Complex evolutionary history of translation elongation factor 2 and diphthamide biosynthesis in archaea and parabasalids}},
  url          = {{http://dx.doi.org/10.1093/gbe/evy154}},
  doi          = {{10.1093/gbe/evy154}},
  volume       = {{10}},
  year         = {{2018}},
}