Competition between translation initiation factor eIF5 and its mimic protein 5MP determines non-AUG initiation rate genome-wide

  • Nucleic Acids Res. 2017 Nov 16;45(20):11941-11953. doi: 10.1093/nar/gkx808.
Leiming Tang  1 ,  Jacob Morris  1 ,  Ji Wan  2 ,  Chelsea Moore  1 ,  Yoshihiko Fujita  3 ,  Sarah Gillaspie  1 ,  Eric Aube  1 ,  Jagpreet Nanda  4 ,  Maud Marques  5 ,  Maika Jangal  5 ,  Abbey Anderson  1 ,  Christian Cox  1 ,  Hiroyuki Hiraishi  1 ,  Leiming Dong  2 ,  Hirohide Saito  3 ,  Chingakham Ranjit Singh  1 ,  Michael Witcher  5 ,  Ivan Topisirovic  5 ,  Shu-Bing Qian  2 ,  Katsura Asano  1
Affiliations
  • 1. Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA.
  • 2. Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA.
  • 3. Center for iPS Cell Research and Application, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan.
  • 4. NIGMS, NIH, Bethesda, MD 20892, USA.
  • 5. Lady Davis Institute, and the Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 2B4, Canada.
PMID: 28981728 DOI: 10.1093/nar/gkx808
Abstract

In the human genome, translation initiation from non-AUG codons plays an important role in various gene regulation programs. However, mechanisms regulating the non-AUG initiation rate remain poorly understood. Here, we show that the non-AUG initiation rate is nearly consistent under a fixed nucleotide context in various human and insect cells. Yet, it ranges from <1% to nearly 100% compared to AUG translation, depending on surrounding sequences, including Kozak, and possibly additional nucleotide contexts. Mechanistically, this range of non-AUG initiation is controlled in part, by the eIF5-mimic protein (5MP). 5MP represses non-AUG translation by competing with eIF5 for the Met-tRNAi-binding factor eIF2. Consistently, eIF5 increases, whereas 5MP decreases translation of NAT1/EIF4G2/DAP5, whose sole start codon is GUG. By modulating eIF5 and 5MP1 expression in combination with ribosome profiling we identified a handful of previously unknown non-AUG initiation sites, some of which serve as the exclusive start codons. If the initiation rate for these codons is low, then an AUG-initiated downstream ORF prevents the generation of shorter, AUG-initiated isoforms. We propose that the homeostasis of the non-AUG translatome is maintained through balanced expression of eIF5 and 5MP.