Metabolite Control of Translation by Conserved Peptide uORFs: The Ribosome as a Metabolite Multisensor

Horst, Sjors van der; Filipovska, Teodora; Hanson, Johannes; Smeekens, Sjef

doi:10.1104/pp.19.00940

Cited by 43 publications

(70 citation statements)

References 91 publications

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“…Here the choice of start codon determines the amino-terminal targeting sequence of the protein (Kasaras & Kunze, 2017;Wamboldt et al, 2009). Initiation at non-AUG start codons is non-negligible, occurs routinely on specific mRNAs, influences the inhibitory potential of upstream ORFs (uORFs), and generally diversifies the spectrum of translated ORFs, especially on 5' leader sequences (Hsu et al, 2016;Laing et al, 2015;van der Horst, Filipovska, Hanson, & Smeekens, 2020;Vaughn, Ellingson, Mignone, & von Arnim, 2012;von Arnim, Jia, & Vaughn, 2014). The regulatory potential of Kozak context was brought into focus in the context of the eIF5 mimic proteins, which assist eIF1A in enforcing the Kozak rule by counteracting eIF5.…”

Section: Initiationmentioning

confidence: 99%

“…In the case of one subclass of basic leucine zipper (bZIP) transcription factors, a long CPuORF in the 5' leader represses translation in response to sucrose, the abundant transport form of photoassimilated carbohydrates. Given that translational arrest can be recapitulated in vitro, it was hypothesized that the ribosome exit tunnel in the 60S subunit and the CPuORF-encoded peptide create a specific metabolite binding pocket for sucrose, which is proposed to allosterically affect the peptidyl transfer reaction and/or peptide release (peptoswitch model) (van der Horst et al, 2020;Yamashita et al, 2017).…”

Section: Translational Control Of Bzip Transcription Factor Mrnas Bmentioning

confidence: 99%

“…In principle, the binding of a specific metabolite to a translating ribosome is a eukaryotic analog to the bacterial riboswitch (van der Horst et al, 2020). However, instead of a metabolite binding to an RNA tertiary structure, according to the sucrose "peptoswitch" model, the metabolite binds to a translating ribosome harboring a characteristic nascent peptide as its specificity determinant.…”

Section: Translational Control Of Bzip Transcription Factor Mrnas Bmentioning

confidence: 99%

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Translational gene regulation in plants: A green new deal

2020

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The molecular machinery for protein synthesis is profoundly similar between plants and other eukaryotes. Mechanisms of translational gene regulation are embedded into the broader network of RNA-level processes including RNA quality control and RNA turnover. However, over eons of their separate history, plants acquired new components, dropped others, and generally evolved an alternate way of making the parts list of protein synthesis work. Research over the past 5 years has unveiled how plants utilize translational control to defend themselves against viruses, regulate translation in response to metabolites, and reversibly adjust translation to a wide variety of environmental parameters. Moreover, during seed and pollen development plants make use of RNA granules and other translational controls to underpin developmental transitions between quiescent and metabolically active stages. The economics of resource allocation over the daily light-dark cycle also include controls over cellular protein synthesis. Important new insights into translational control on cytosolic ribosomes continue to emerge from studies of translational control mechanisms in viruses. Finally, sketches of coherent signaling pathways that connect external stimuli with a translational response are emerging, anchored in part around TOR and GCN2 kinase signaling networks. These again reveal some mechanisms that are familiar and others that are different from other eukaryotes, motivating deeper studies on translational control in plants.

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Section: Initiationmentioning

confidence: 99%

Section: Translational Control Of Bzip Transcription Factor Mrnas Bmentioning

confidence: 99%

Section: Translational Control Of Bzip Transcription Factor Mrnas Bmentioning

confidence: 99%

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Translational gene regulation in plants: A green new deal

2020

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“…The translation of many mRNAs is conditionally modulated by the presence of one or more upstream open reading frame (uORF) in the 59 leader of an mRNA that precedes the main open reading frame (mORF;von Arnim et al, 2014). uORFs generally repress the translation of the mORF, but this regulation can be conditionally or developmentally reversed (van der Horst et al, 2020). Gene transcript isoforms can also vary in the presence versus absence of uORFs due to alternative splicing.…”

Section: Upstream Open Reading Frame Control Of Translationmentioning

confidence: 99%

The Dynamic Kaleidoscope of RNA Biology in Plants

2020

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ACKNOWLEDGMENTSWe thank all of the authors, reviewers, and editors, especially Sarah M. Assmann, who contributed to this Focus Issue. We thank Thanin Chantarachot and Sarah M. Assmann for comments on this editorial. LITERATURE CITEDArribas-Hernández L, Brodersen P (2020) Occurrence and functions of m 6 A and other covalent modifications in plant mRNA. Plant Physiol 182: 79-96 Bai B, van der Horst S, Cordewener J, America T, Hanson J, Bentsink L (2020) Seed stored mRNAs that are specifically associated to monosome are translationally regulated during germination. Plant Physiol 182: 378-392 Beck J, Lohscheider JN, Albert S, Andersson U, Mendgen KW, Rojas-Stütz MC, Adamska I, Funck D (2017) Small one-helix proteins are essential for photosynthesis in Arabidopsis. Front Plant Sci 8: 7 Bentley DL (2005) Rules of engagement: Co-transcriptional recruitment of pre-mRNA processing factors. Curr Opin Cell Biol 17: 251-256 Borges F, Martienssen RA (2015) The expanding world of small RNAs in plants. Nat Rev Mol Cell Biol 16: 727-741 Browning KS, Bailey-Serres J (2015) Mechanism of cytoplasmic mRNA translation. The Arabidopsis Book 13: e0176 Cao Y, Ma L (2019) To splice or to transcribe: SKIP-mediated environmental fitness and development in plants. Front Plant Sci 10: 1222 Chantarachot T, Bailey-Serres J (2018) Polysomes, stress granules, and processing bodies: A dynamic triumvirate controlling cytoplasmic mRNA fate and function. Plant Physiol 176: 254-269 Chaudhary S, Khokhar W, Jabre I, Reddy ASN, Byrne LJ, Wilson CM, Syed NH (2019) Alternative splicing and protein diversity: Plants versus animals. Front Plant Sci 10: 708 Crisp PA, Hammond R, Zhou P, Vaillancourt B, Lipzen AM, Daum C, Barry KW, de Leon N, Buell CR, Kaeppler SM, et al (2020) Variation and inheritance of small RNAs in maize inbreds and F1 hybrids. Plant

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“…The 5′-untranslated regions (5′-UTRs) of many eukaryotic mRNAs contain upstream open reading frames (uORFs) [1][2][3][4]. Although most uORFs are not thought to encode functional proteins or peptides, certain uORFs encode regulatory peptides that have roles in post-transcriptional regulation of gene expression [5][6][7][8][9]. During translation of some of these regulatory uORFs, nascent peptides act inside the ribosomal exit tunnel to cause ribosome stalling [10].…”

Section: Introductionmentioning

confidence: 99%

Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA

et al. 2020

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Background: Upstream open reading frames (uORFs) in the 5′-untranslated regions (5′-UTRs) of certain eukaryotic mRNAs encode evolutionarily conserved functional peptides, such as cis-acting regulatory peptides that control translation of downstream main ORFs (mORFs). For genome-wide searches for uORFs with conserved peptide sequences (CPuORFs), comparative genomic studies have been conducted, in which uORF sequences were compared between selected species. To increase chances of identifying CPuORFs, we previously developed an approach in which uORF sequences were compared using BLAST between Arabidopsis and any other plant species with available transcript sequence databases. If this approach is applied to multiple plant species belonging to phylogenetically distant clades, it is expected to further comprehensively identify CPuORFs conserved in various plant lineages, including those conserved among relatively small taxonomic groups.

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Metabolite Control of Translation by Conserved Peptide uORFs: The Ribosome as a Metabolite Multisensor

Cited by 43 publications

References 91 publications

Translational gene regulation in plants: A green new deal

Translational gene regulation in plants: A green new deal

The Dynamic Kaleidoscope of RNA Biology in Plants

Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA

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