The stringency of start codon selection in the filamentous fungus Neurospora crassa

J Biol Chem. 2013 Mar 29;288(13):9549-62. doi: 10.1074/jbc.M112.447177. Epub 2013 Feb 8.


In eukaryotic cells initiation may occur from near-cognate codons that differ from AUG by a single nucleotide. The stringency of start codon selection impacts the efficiency of initiation at near-cognate codons and the efficiency of initiation at AUG codons in different contexts. We used a codon-optimized firefly luciferase reporter initiated with AUG or each of the nine near-cognate codons in preferred context to examine the stringency of start codon selection in the model filamentous fungus Neurospora crassa. In vivo results indicated that the hierarchy of initiation at start codons in N. crassa (AUG ≫ CUG > GUG > ACG > AUA ≈ UUG > AUU > AUC) is similar to that in human cells. Similar results were obtained by translating mRNAs in a homologous N. crassa in vitro translation system or in rabbit reticulocyte lysate. We next examined the efficiency of initiation at AUG, CUG, and UUG codons in different contexts in vitro. The preferred context was more important for efficient initiation from near-cognate codons than from AUG. These studies demonstrated that near-cognate codons are used for initiation in N. crassa. Such events could provide additional coding capacity or have regulatory functions. Analyses of the 5'-leader regions in the N. crassa transcriptome revealed examples of highly conserved near-cognate codons in preferred contexts that could extend the N termini of the predicted polypeptides.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acid Sequence
  • Cell-Free System
  • Codon
  • Codon, Initiator*
  • Computational Biology / methods
  • DNA, Complementary / metabolism
  • Gene Expression Regulation, Fungal
  • Genes, Fungal
  • Humans
  • Models, Biological
  • Molecular Sequence Data
  • Neurospora crassa / genetics*
  • Neurospora crassa / metabolism*
  • Peptides / chemistry
  • Plasmids / metabolism
  • Prevalence
  • Protein Biosynthesis
  • Protein Structure, Tertiary
  • RNA, Messenger / metabolism
  • Sequence Homology, Amino Acid


  • Codon
  • Codon, Initiator
  • DNA, Complementary
  • Peptides
  • RNA, Messenger