Translation initiation from conserved non-AUG codons provides additional layers of regulation and coding capacity

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dc.contributor.authorIvanov, Ivaylo P.
dc.contributor.authorWei, Jiajie
dc.contributor.authorCaster, Stephen Z.
dc.contributor.authorSmith, Kristina M.
dc.contributor.authorMichel, Audrey M.
dc.contributor.authorZhang, Ying
dc.contributor.authorFirth, Andrew E.
dc.contributor.authorFreitag, Michael
dc.contributor.authorDunlap, Jay C.
dc.contributor.authorBell-Pedersen, Deborah
dc.contributor.authorAtkins, John F.
dc.contributor.authorSachs, Matthew S.
dc.contributor.funderTexas A and M University
dc.contributor.funderWellcome Trust
dc.contributor.funderScience Foundation Ireland
dc.contributor.funderNational Institutes of Health
dc.date.accessioned2017-09-26T11:39:19Z
dc.date.available2017-09-26T11:39:19Z
dc.date.issued2017
dc.description.abstractNeurospora crassa cpc-1 and Saccharomyces cerevisiae GCN4 are homologs specifying transcription activators that drive the transcriptional response to amino acid limitation. The cpc-1 mRNA contains two upstream open reading frames (uORFs) in its >700-nucleotide (nt) 5' leader, and its expression is controlled at the level of translation in response to amino acid starvation. We used N. crassa cell extracts and obtained data indicating that cpc-1 uORF1 and uORF2 are functionally analogous to GCN4 uORF1 and uORF4, respectively, in controlling translation. We also found that the 5' region upstream of the main coding sequence of the cpc-1 mRNA extends for more than 700 nucleotides without any in-frame stop codon. For 100 cpc-1 homologs from Pezizomycotina and from selected Basidiomycota, 5' conserved extensions of the CPC1 reading frame are also observed. Multiple non-AUG near-cognate codons (NCCs) in the CPC1 reading frame upstream of uORF2, some deeply conserved, could potentially initiate translation. At least four NCCs initiated translation in vitro. In vivo data were consistent with initiation at NCCs to produce N-terminally extended N. crassa CPC1 isoforms. The pivotal role played by CPC1, combined with its translational regulation by uORFs and NCC utilization, underscores the emerging significance of noncanonical initiation events in controlling gene expression. IMPORTANCE There is a deepening and widening appreciation of the diverse roles of translation in controlling gene expression. A central fungal transcription factor, the best-studied example of which is Saccharomyces cerevisiae GCN4, is crucial for the response to amino acid limitation. Two upstream open reading frames (uORFs) in the GCN4 mRNA are critical for controlling GCN4 synthesis. We observed that two uORFs in the corresponding Neurospora crassa cpc-1 mRNA appear functionally analogous to the GCN4 uORFs. We also discovered that, surprisingly, unlike GCN4, the CPC1 coding sequence extends far upstream from the presumed AUG start codon with no other in-frame AUG codons. Similar extensions were seen in homologs from many filamentous fungi. We observed that multiple non-AUG near-cognate codons (NCCs) in this extended reading frame, some conserved, initiated translation to produce longer forms of CPC1, underscoring the significance of noncanonical initiation in controlling gene expression.en
dc.description.sponsorshipNational Institutes of Health (GM068087, GM47498) Wellcome Trust (106207)en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.articleide00844-17
dc.identifier.citationIvanov, I. P., Wei, J., Caster, S. Z., Smith, K. M., Michel, A. M., Zhang, Y., Firth, A. E., Freitag, M., Dunlap, J. C., Bell-Pedersen, D., Atkins, J. F. and Sachs, M. S. (2017) 'Translation initiation from conserved non-AUG codons provides additional layers of regulation and coding capacity', mBio, 8(3). e00844-17 (17pp). doi: 10.1128/mBio.00844-17en
dc.identifier.doi10.1128/mBio.00844-17
dc.identifier.issn2150-7511
dc.identifier.issued3
dc.identifier.journaltitlemBioen
dc.identifier.urihttps://hdl.handle.net/10468/4788
dc.identifier.volume8
dc.language.isoenen
dc.publisherAmerican Society for Microbiologyen
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Principal Investigator Programme (PI)/08/IN.1/B1889/IE/Altered Genetic Code Readout/
dc.relation.urihttp://mbio.asm.org/content/8/3/e00844-17
dc.rights© 2017, Ivanov et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectNeurosporaen
dc.subjectFilamentous fungien
dc.subjectGene regulationen
dc.subjectMolecular geneticsen
dc.subjectTranslational controlen
dc.subjectMessengerrna translationen
dc.subjectAminoacid biosynthesisen
dc.subjectFactor 1 eIF1en
dc.subjectNeurosporacrassaen
dc.subjectMammaliancellsen
dc.subjectIn vivoen
dc.subjectModulates autoregulationen
dc.subjectNucleotide resolutionen
dc.subjectFunctional elementsen
dc.subjectRibosome bindingen
dc.titleTranslation initiation from conserved non-AUG codons provides additional layers of regulation and coding capacityen
dc.typeArticle (peer-reviewed)en
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