Translation regulation by 5′ transcript leader cis-elements

Gene expression is tightly controlled at many different stages. Alterations in translation of mRNA into proteins rapidly modulates the proteome without changing upstream steps such as transcription, pre-mRNA splicing, and nuclear export.{{Cite journal|last1=Akirtava|first1=Christina|last2=McManus|first2=Charles Joel|title=Control of translation by eukaryotic mRNA transcript leaders—Insights from high-throughput assays and computational modeling|url= |journal=WIREs RNA|year=2021|language=en|volume=12|issue=3|pages=e1623|doi=10.1002/wrna.1623|pmc=7914273|pmid=32869519}} The strict regulation of translation in both space and time is in part governed by cis-regulatory elements located in 5′ mRNA transcript leaders (TLs) and 3′ untranslated regions (UTRs).

Due to their role in translation initiation, mRNA 5′ transcript leaders (TLs) strongly influence protein expression.{{Cite journal|last1=Li|first1=Jingyi Jessica|author-link1= Jingyi Jessica Li|last2=Chew|first2=Guo-Liang|last3=Biggin|first3=Mark Douglas|date=2019-08-09|title=Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes|journal=Genome Biology|volume=20|issue=1|pages=162|doi=10.1186/s13059-019-1761-9|pmc=6689182|pmid=31399036 |doi-access=free }}{{Cite journal|last1=Li|first1=Jingyi Jessica|last2=Chew|first2=Guo-Liang|last3=Biggin|first3=Mark D.|date=2017-11-16|title=Quantitating translational control: mRNA abundance-dependent and independent contributions and the mRNA sequences that specify them|journal=Nucleic Acids Research|volume=45|issue=20|pages=11821–11836|doi=10.1093/nar/gkx898|pmc=5714229|pmid=29040683}}{{Cite journal|date=2016-02-23|title=Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation|journal=Cell Reports|language=en|volume=14|issue=7|pages=1787–1799|doi=10.1016/j.celrep.2016.01.043|doi-access=free|last1=Weinberg|first1=David E.|last2=Shah|first2=Premal|last3=Eichhorn|first3=Stephen W.|last4=Hussmann|first4=Jeffrey A.|last5=Plotkin|first5=Joshua B.|last6=Bartel|first6=David P.|pmid=26876183|pmc=4767672}} Eukaryotic translation consists of three stages: initiation elongation, and termination. Translation is primary regulated at the initiation stage where the small ribosomal subunit and initiation factors are recruited to the mRNA; directionally scanning along the 5′ TL to select the first “best” start codon to begin protein synthesis.{{Cite journal|last=Hinnebusch|first=Alan G.|date=September 2011|title=Molecular Mechanism of Scanning and Start Codon Selection in Eukaryotes|journal=Microbiology and Molecular Biology Reviews |volume=75|issue=3|pages=434–467|doi=10.1128/MMBR.00008-11|pmc=3165540|pmid=21885680}} Cap-dependent ribosomal scanning accounts for 95-97% of all translation in eukaryotes under normal conditions.{{Cite journal|last=Merrick|first=William C.|date=2004-05-12|title=Cap-dependent and cap-independent translation in eukaryotic systems|journal=Gene|volume=332|pages=1–11|doi=10.1016/j.gene.2004.02.051|pmid=15145049}} Therefore, the cis-regulatory elements in TLs greatly influence translation initiation and ultimately protein expression.

The first step in initiation is formation of the pre-initiation complex, 48S PIC. The small ribosomal subunit and various eukaryotic initiation factors are recruited to the mRNA 5′ TL and to form the 48S PIC complex, which scans 5′ to 3′ along the mRNA transcript, inspecting each successive triplet for a functional start codon.{{Cite journal|last1=Sonenberg|first1=Nahum|last2=Dever|first2=Thomas E.|date=February 2003|title=Eukaryotic translation initiation factors and regulators|journal=Current Opinion in Structural Biology|volume=13|issue=1|pages=56–63|doi=10.1016/s0959-440x(03)00009-5|pmid=12581660|url=https://escholarship.mcgill.ca/concern/articles/br86b842d |url-access=subscription}}{{Cite journal|last1=Richter|first1=Joel D.|last2=Sonenberg|first2=Nahum|date=February 2005|title=Regulation of cap-dependent translation by eIF4E inhibitory proteins|journal=Nature|language=en|volume=433|issue=7025|pages=477–480|doi=10.1038/nature03205|pmid=15690031|bibcode=2005Natur.433..477R|s2cid=4347657|url=https://escholarship.mcgill.ca/concern/articles/k930c3532 }} Translation initiation is most successful at an AUG codon surrounded upstream and downstream by a favorable sequence known as the “Kozak consensus sequence” or “Kozak context”.{{Cite journal|last=Kozak|first=M|date=1987-10-26|title=An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs.|journal=Nucleic Acids Research|volume=15|issue=20|pages=8125–8148|doi=10.1093/nar/15.20.8125|pmid=3313277|pmc=306349}} (See A) Weak or absent Kozak context surrounding the AUG leads to “leaky” scanning where the start codon is skipped, whereas a strong Kozak context leads to start codon recognition by the 48S PIC and binding of Met-tRNAi in the “closed” state. Recent studies suggest that initiation occurs surprisingly often in eukaryotes at Near Cognate Codons (NCCs), which differ from AUG by one nucleotide.{{Cite journal|date=2020-08-26|title=Translation Initiation Site Profiling Reveals Widespread Synthesis of Non-AUG-Initiated Protein Isoforms in Yeast|journal=Cell Systems|language=en|volume=11|issue=2|pages=145–160.e5|doi=10.1016/j.cels.2020.06.011|doi-access=free|last1=Eisenberg|first1=Amy R.|last2=Higdon|first2=Andrea L.|last3=Hollerer|first3=Ina|last4=Fields|first4=Alexander P.|last5=Jungreis|first5=Irwin|last6=Diamond|first6=Paige D.|last7=Kellis|first7=Manolis|last8=Jovanovic|first8=Marko|last9=Brar|first9=Gloria A.|pmid=32710835|pmc=7508262}}{{Cite journal|last=Ingolia|first=Nicholas T.|date=March 2014|title=Ribosome profiling: new views of translation, from single codons to genome scale|journal=Nature Reviews Genetics|language=en|volume=15|issue=3|pages=205–213|doi=10.1038/nrg3645|pmid=24468696|s2cid=13069682}} Eukaryotic initiation factors rearrange the 48S PIC and permit the large subunit to join, thus forming the complete translation competent 80S ribosome.{{Cite journal|last=Hinnebusch|first=Alan G.|date=August 2017|title=Structural Insights into the Mechanism of Scanning and Start Codon Recognition in Eukaryotic Translation Initiation|journal=Trends in Biochemical Sciences|volume=42|issue=8|pages=589–611|doi=10.1016/j.tibs.2017.03.004|pmid=28442192}}

Upstream open reading frames (uORFs) in the 5′ TLs typically inhibit translation of the downstream main protein coding region (CDS).{{Cite journal|last=Wethmar|first=Klaus|date=November 2014|title=The regulatory potential of upstream open reading frames in eukaryotic gene expression|journal=Wiley Interdisciplinary Reviews. RNA|volume=5|issue=6|pages=765–778|doi=10.1002/wrna.1245|pmid=24995549|s2cid=37819848}}{{Cite journal|last1=Young|first1=Sara K.|last2=Wek|first2=Ronald C.|date=2016-08-12|title=Upstream Open Reading Frames Differentially Regulate Gene-specific Translation in the Integrated Stress Response|journal=The Journal of Biological Chemistry|volume=291|issue=33|pages=16927–16935|doi=10.1074/jbc.R116.733899|pmc=5016099|pmid=27358398|doi-access=free}} (See B) Translation suppression of the CDS is attributable to the 5′ to 3′ directional nature of 48S PIC scanning. After successfully translating the uORF, the ribosome dissociates from the mRNA as part of termination before it can reach and translate the CDS. This destabilization of the translational machinery can trigger nonsense mediated decay of the mRNA transcript. However, in some cases uORFs will actually enhance the translation of the downstream CDS. For example, in S. cerevisiae, the gene GCN4 has a 5′ TL with multiple uORFs. The uORFs closest to the 5′ cap protect the CDS from the inhibitory activities of the downstream uORFs located closer to the CDS.{{Cite journal|last=Hinnebusch|first=Alan G.|title=Translational Regulation Ofgcn4And the General Amino Acid Control of Yeast|date=October 2005|journal=Annual Review of Microbiology|language=en|volume=59|issue=1|pages=407–450|doi=10.1146/annurev.micro.59.031805.133833|pmid=16153175}} In summary, uORFs generally decease translation of the main ORF, but they are also capable of increasing protein synthesis under certain circumstances.

The 3-dimensional structure of the 5′ TL may also impact translation. (See C) Stem-loops have been demonstrated to both inhibit and enhance translation. Stem-loops can prevent cap binding and efficient 48S PIC scanning. Conversely, downstream stem-loops may increase the probability of translation initiation at start codons with a weak Kozak context, possibly by blocking scanning.{{Cite journal|last1=Cigan|first1=A M|last2=Pabich|first2=E K|last3=Donahue|first3=T F|date=July 1988|title=Mutational analysis of the HIS4 translational initiator region in Saccharomyces cerevisiae.|journal=Molecular and Cellular Biology|volume=8|issue=7|pages=2964–2975|doi=10.1128/mcb.8.7.2964|pmid=3043201|pmc=363516}}{{Cite journal|last=Kozak|first=M|date=November 1989|title=Circumstances and mechanisms of inhibition of translation by secondary structure in eucaryotic mRNAs.|journal=Molecular and Cellular Biology|volume=9|issue=11|pages=5134–5142|doi=10.1128/mcb.9.11.5134|pmid=2601712|pmc=363665}}{{Cite journal|last=Kozak|first=M.|date=November 1990|title=Downstream secondary structure facilitates recognition of initiator codons by eukaryotic ribosomes|journal=Proceedings of the National Academy of Sciences of the United States of America|volume=87|issue=21|pages=8301–8305|doi=10.1073/pnas.87.21.8301|pmid=2236042|pmc=54943|bibcode=1990PNAS...87.8301K|doi-access=free}} Besides stem-loops, other higher order structures such as G-quadraplexes and pseudoknots also impede eukaryotic translation.{{Cite journal|last1=Leppek|first1=Kathrin|last2=Das|first2=Rhiju|last3=Barna|first3=Maria|date=March 2018|title=Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them|journal=Nature Reviews Molecular Cell Biology|language=en|volume=19|issue=3|pages=158–174|doi=10.1038/nrm.2017.103|pmid=29165424|pmc=5820134}} To overcome translati on suppression by structures, DEAD-box RNA helicases unwind RNA structures, promoting scanning through the 5′ TL.{{Cite journal|last1=Hilliker|first1=Angela|last2=Gao|first2=Zhaofeng|last3=Jankowsky|first3=Eckhard|last4=Parker|first4=Roy|date=2011-09-16|title=The DEAD-box protein Ded1 modulates translation by the formation and resolution of an eIF4F-mRNA complex|journal=Molecular Cell|volume=43|issue=6|pages=962–972|doi=10.1016/j.molcel.2011.08.008|pmc=3268518|pmid=21925384}}

Multiple transcription start sites may be used for the same gene generating alternative 5′ TLs with varied length and regulatory features. (See D)This is especially common in organisms with relatively compact genomes such as yeasts. In S. cerevisiae, alternative transcription start sites generate long alternative mRNA TLs with substantially lower translation efficiencies.{{Cite journal|last1=Cheng|first1=Ze|last2=Otto|first2=George Maxwell|last3=Powers|first3=Emily Nicole|last4=Keskin|first4=Abdurrahman|last5=Mertins|first5=Philipp|last6=Carr|first6=Steven Alfred|last7=Jovanovic|first7=Marko|last8=Brar|first8=Gloria Ann|date=2018-02-22|title=Pervasive, Coordinated Protein-Level Changes Driven by Transcript Isoform Switching during Meiosis|journal=Cell|volume=172|issue=5|pages=910–923.e16|doi=10.1016/j.cell.2018.01.035|pmc=5826577|pmid=29474919}} Counterintuitively, upstream transcriptional induction of these genes actually silences their expression during meiosis by blocking translation.{{Cite journal|last1=Rojas-Duran|first1=Maria F.|last2=Gilbert|first2=Wendy V.|date=December 2012|title=Alternative transcription start site selection leads to large differences in translation activity in yeast|journal=RNA|volume=18|issue=12|pages=2299–2305|doi=10.1261/rna.035865.112|pmc=3504680|pmid=23105001}}{{Cite journal|last1=Arribere|first1=Joshua A.|last2=Gilbert|first2=Wendy V.|date=June 2013|title=Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing|journal=Genome Research|volume=23|issue=6|pages=977–987|doi=10.1101/gr.150342.112|pmc=3668365|pmid=23580730}} Furthermore, alternative transcription initiation within the CDS may generate protein isoforms with varied functions in S. cerevisiae.{{Cite journal|last1=Wei|first1=Wu|last2=Hennig|first2=Bianca P.|last3=Wang|first3=Jingwen|last4=Zhang|first4=Yujie|last5=Piazza|first5=Ilaria|last6=Sanchez|first6=Yerma Pareja|last7=Chabbert|first7=Christophe D.|last8=Adjalley|first8=Sophie H.|last9=Steinmetz|first9=Lars M.|last10=Pelechano|first10=Vicent|date=2019-11-18|title=Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast|journal=Genome Research|volume=29|issue=12|pages=1974–1984|language=en|doi=10.1101/gr.243378.118|pmid=31740578|pmc=6886497|doi-access=free}} These examples from the model organism S. cerevisiae suggest that mRNA transcripts with alternative 5′ TLs may have a regulatory function in eukaryotes especially during events requiring proteome remodeling such as meiosis and stress responses.

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{{DEFAULTSORT:Translation regulation by 5' transcript leader cis-elements}}

Category:Eukaryote genetics

Category:Cell biology

Category:Protein biosynthesis

Category:Cellular processes