Conserved upstream open reading frames in higher plants

Tran, Michaël; Schultz, Carolyn J.; Baumann, Ute

doi:10.1186/1471-2164-9-361

Cited by 64 publications

(63 citation statements)

References 67 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…After application of the induced mutations, an increase in translation efficiency was observed (Barrett et al 2012). Introduction of the uORF into the construct destabilizes it by disconnecting the 5′ cap, or by ribosome subunits disintegration after termination of incorrect transcript (Tran et al 2008). In consequence, reinitiation is blocked and translation efficiency significantly decreases.…”

Section: ′Utr Sequencementioning

confidence: 98%

Cis-regulatory elements used to control gene expression in plants

Biłas

Szafran

Hnatuszko-Konka

et al. 2016

Plant Cell Tiss Organ Cult

203

113

View full text Add to dashboard Cite

Section: ′Utr Sequencementioning

confidence: 98%

Cis-regulatory elements used to control gene expression in plants

Biłas

Szafran

Hnatuszko-Konka

et al. 2016

Plant Cell Tiss Organ Cult

203

113

View full text Add to dashboard Cite

“…In either case, uORFs can drastically reduce protein expression (Calvo et al 2009;Zhou et al 2010). In some cases, uORFs are conserved at the peptide-level (Franceschetti et al 2001;Hayden and Jorgensen 2007;Tran et al 2008;Rahmani et al 2009)-referred to as ''conserved peptide uORFs'' (CPuORFs). CPuORFs shared by Arabidopsis thaliana and rice fall into 19 homologous groups (Hayden and Jorgensen 2007).…”

Section: Introductionmentioning

confidence: 99%

Known and novel post-transcriptional regulatory sequences are conserved across plant families

Vaughn¹,

Ellingson²,

Mignone³

et al. 2012

RNA

View full text Add to dashboard Cite

The sequence elements that mediate post-transcriptional gene regulation often reside in the 59 and 39 untranslated regions (UTRs) of mRNAs. Using six different families of dicotyledonous plants, we developed a comparative transcriptomics pipeline for the identification and annotation of deeply conserved regulatory sequences in the 59 and 39 UTRs. Our approach was robust to confounding effects of poor UTR alignability and rampant paralogy in plants. In the 39 UTR, motifs resembling PUMILIObinding sites form a prominent group of conserved motifs. Additionally, Expansins, one of the few plant mRNA families known to be localized to specific subcellular sites, possess a core conserved RCCCGC motif. In the 59 UTR, one major subset of motifs consists of purine-rich repeats. A distinct and substantial fraction possesses upstream AUG start codons. Half of the AUG containing motifs reveal hidden protein-coding potential in the 59 UTR, while the other half point to a peptideindependent function related to translation. Among the former, we added four novel peptides to the small catalog of conserved-peptide uORFs. Among the latter, our case studies document patterns of uORF evolution that include gain and loss of uORFs, switches in uORF reading frame, and switches in uORF length and position. In summary, nearly three hundred posttranscriptional elements show evidence of purifying selection across the eudicot branch of flowering plants, indicating a regulatory function spanning at least 70 million years. Some of these sequences have experimental precedent, but many are novel and encourage further exploration.

show abstract

“…More than 30% of eukaryotic mRNAs are loaded with uORFs within their 59-UTRs, and there is mounting evidence that uORFs are major repressors of translation and thus play a key role in growth and development (Tran et al, 2008;Calvo et al, 2009). uORF-mRNAs, which are common in Arabidopsis (Hanada et al, 2007;Hayden and Jorgensen, 2007;Kim et al, 2007), encode many regulatory proteins, including transcriptional factors (e.g.…”

Section: Role Of Tor In Regulation Of Translation Of Specific Mrnas Mmentioning

confidence: 99%

Recent Discoveries on the Role of TOR (Target of Rapamycin) Signaling in Translation in Plants

2017

View full text Add to dashboard Cite

Protein synthesis is an intricate, energy-demanding, and tightly controlled process that plays a fundamental role in cell growth, proliferation, and differentiation. The target of rapamycin (TOR) protein kinase integrates stress-, nutrient-, and energy-related signals to optimize protein synthesis outputs. In mammals, TOR is a main controller of capped mRNA translation; how TOR participates in translation initiation in plants is unclear, but active TOR is required for regulation of translation of mRNA with 59-untranslated region (59-UTR) upstream open reading frames (uORFs)-known translation regulatory elements in eukaryotes. Recent data implicates diverse signals such as stress, hormones, and metabolites in regulation of TOR signal transduction pathways and, thus, in response to environmental stress. Here, we review current knowledge of plant TOR complex composition and activation, and its function in translation, compiling data on downstream processes that are under stringent control of TOR in mammals but not yet investigated in plants.Plants have evolved various adaptation mechanisms to ensure their optimal growth, with plant development and behavior being strongly responsive to various external and internal stimuli. By monitoring their environment, plants trigger signal transduction cascades in order to regulate downstream cellular processes, mainly via protein synthesis-a major energy-consuming process (Buttgereit and Brand, 1995). The TOR protein kinase integrates extracellular signals (hormones, biotic and abiotic stresses, growth factors) together with intracellular nutrient availability and energy status to control protein synthesis and other anabolic processes if conditions are favorable, and represses catabolic processes such as autophagy (Albert and Hall, 2015). The past 10 years has boosted research on plant TOR complex composition, highlighted TOR upstream signals and downstream targets, and revealed an interplay between TOR signaling and hormonal, stress, and other pathways in photosynthetic organisms. We are beginning to understand how TOR is activated, and how it controls many cellular processes, such as transcription, translation, and autophagy. Here, we give an overview of recent results on the role of TOR in plant translation control and draw the reader's attention to future questions to address. In plants, inactivation of TOR correlates with a decrease in total polysomal levels (Deprost et al., 2007;Schepetilnikov et al., 2011Schepetilnikov et al., , 2013, strongly suggesting a role for TOR in plant translation. Although a role for TOR in global translation in plants has been documented, the players and mechanisms used to influence different steps of translation initiation -the step most controlled by TOR in mammals-are only starting to emerge. Here, we summarize the current state of knowledge of specific plant translation initiation mechanisms that are controlled by 59-UTR elements of mRNAs and discuss regulation of these mechanisms by TOR/S6 kinase 1 (S6K1) signaling. Examples where TOR re...

show abstract

Conserved upstream open reading frames in higher plants

Cited by 64 publications

References 67 publications

Cis-regulatory elements used to control gene expression in plants

Cis-regulatory elements used to control gene expression in plants

Known and novel post-transcriptional regulatory sequences are conserved across plant families

Recent Discoveries on the Role of TOR (Target of Rapamycin) Signaling in Translation in Plants

Contact Info

Product

Resources

About