Unexpected ancient paralogs and an evolutionary model for the COPII coat complex

Genome Biology and Evolution
Alexander Schlacht, Joel B Dacks

Abstract

The coat protein complex II (COPII) is responsible for the transport of protein cargoes from the Endoplasmic Reticulum (ER) to the Golgi apparatus. COPII has been functionally characterized extensively in vivo in humans and yeast. This complex shares components with the nuclear pore complex and the Seh1-Associated (SEA) complex, inextricably linking its evolution with that of the nuclear pore and other protocoatomer domain-containing complexes. Importantly, this is one of the last coat complexes to be examined from a comparative genomic and phylogenetic perspective. We use homology searching of eight components across 74 eukaryotic genomes, followed by phylogenetic analyses, to assess both the distribution of the COPII components across eukaryote diversity and to assess its evolutionary history. We report that Sec12, but not Sed4 was present in the Last Eukaryotic Common Ancestor along with Sec16, Sar1, Sec13, Sec31, Sec23, and Sec24. We identify a previously undetected paralog of Sec23 that, at least, predates the archaeplastid clade. We also describe three Sec24 paralogs likely present in the Last Eukaryotic Common Ancestor, including one newly detected that was anciently present but lost from both opisthokonts and excavates....Continue Reading

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Citations

Jun 18, 2017·Current Opinion in Cell Biology·Joel B Dacks, Margaret S Robinson
Mar 8, 2018·BMC Biology·Lael D BarlowJoel B Dacks
Sep 28, 2016·Journal of Cell Science·Joel B DacksDamien P Devos
Feb 11, 2018·Nature Communications·Paloma Navarro NegredoMargaret S Robinson
Jan 13, 2017·Nature·Katarzyna Zaremba-NiedzwiedzkaThijs J G Ettema
May 30, 2019·Molecular Biology of the Cell·Shweta V PipaliyaJoel Dacks
May 28, 2019·Proceedings of the National Academy of Sciences of the United States of America·Eelco C TromerBerend Snel
Jun 20, 2018·Histochemistry and Cell Biology·Janine McCaughey, David J Stephens
Mar 10, 2020·FEMS Microbiology Reviews·Morgan BeebyDavid R Mitchell
May 16, 2020·Frontiers in Immunology·Stephanie Kim, Pavan Reddy
Sep 6, 2019·Biochimica Et Biophysica Acta. Molecular Cell Research·Ignacio Bravo-PlazaMiguel A Peñalva
Jan 20, 2021·The Journal of Clinical Investigation·Stephanie KimPavan Reddy
Oct 22, 2019·Trends in Cell Biology·Janine McCaughey, David J Stephens
Jan 30, 2021·Frontiers in Cell and Developmental Biology·Brittany J BisnettMichael Boyce
May 20, 2020·Current Biology : CB·Kira MoreJoel B Dacks
May 18, 2021·Parasitology International·Coh-Ichi Nihei, Masayuki Nakanishi
Jan 28, 2021·Annual Review of Biochemistry·I Raote, V Malhotra
Jul 24, 2021·Trends in Genetics : TIG·Elena KuzminCharles Boone
Jul 12, 2021·Genome Biology and Evolution·Romana VargováMarek Eliáš

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Methods Mentioned

BETA
nucleotide
GTPase
GTPases

Software Mentioned

HMMsearch
MacPyMOL
RAxML
Phylip package
HMMer
Basic Local Alignment Search Tool ( BLAST )
BLAST
MUSCLE
FigTree
Adobe Illustrator

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