Peroxisomal lactate dehydrogenase is generated by translational readthrough in mammals

Elife. 2014 Sep 23:3:e03640. doi: 10.7554/eLife.03640.

Abstract

Translational readthrough gives rise to low abundance proteins with C-terminal extensions beyond the stop codon. To identify functional translational readthrough, we estimated the readthrough propensity (RTP) of all stop codon contexts of the human genome by a new regression model in silico, identified a nucleotide consensus motif for high RTP by using this model, and analyzed all readthrough extensions in silico with a new predictor for peroxisomal targeting signal type 1 (PTS1). Lactate dehydrogenase B (LDHB) showed the highest combined RTP and PTS1 probability. Experimentally we show that at least 1.6% of the total cellular LDHB is targeted to the peroxisome by a conserved hidden PTS1. The readthrough-extended lactate dehydrogenase subunit LDHBx can also co-import LDHA, the other LDH subunit, into peroxisomes. Peroxisomal LDH is conserved in mammals and likely contributes to redox equivalent regeneration in peroxisomes.

Keywords: cell biology; gene regulation; genome-wide in silico screen; human; human biology; lactate dehydrogenase; medicine; peroxisomal targeting signal; stop codon suppression; translational readthrough.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Cell Line
  • Codon, Terminator / genetics
  • Computer Simulation
  • Conserved Sequence
  • Genes, Reporter
  • Genome
  • Humans
  • Isoenzymes / genetics
  • Isoenzymes / metabolism
  • L-Lactate Dehydrogenase / genetics
  • L-Lactate Dehydrogenase / metabolism*
  • Mammals / metabolism*
  • Molecular Sequence Data
  • Peroxisomes / enzymology*
  • Protein Biosynthesis*
  • Protein Sorting Signals
  • Protein Transport
  • Rats

Substances

  • Codon, Terminator
  • Isoenzymes
  • Protein Sorting Signals
  • L-Lactate Dehydrogenase
  • lactate dehydrogenase 1

Associated data

  • Dryad/10.5061/dryad.J2N18

Grants and funding

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.