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Before It Gets Started: Regulating Translation at the 5' UTR.

Araujo PR, Yoon K, Ko D, Smith AD, Qiao M, Suresh U, Burns SC, Penalva LO - Comp. Funct. Genomics (2012)

Bottom Line: Translation regulation plays important roles in both normal physiological conditions and diseases states.This regulation requires cis-regulatory elements located mostly in 5' and 3' UTRs and trans-regulatory factors (e.g., RNA binding proteins (RBPs)) which recognize specific RNA features and interact with the translation machinery to modulate its activity.In this paper, we discuss important aspects of 5' UTR-mediated regulation by providing an overview of the characteristics and the function of the main elements present in this region, like uORF (upstream open reading frame), secondary structures, and RBPs binding motifs and different mechanisms of translation regulation and the impact they have on gene expression and human health when deregulated.

View Article: PubMed Central - PubMed

Affiliation: Greehey Children's Cancer Research Institute, UTHSCSA, San Antonio, TX 78229-3900, USA.

ABSTRACT
Translation regulation plays important roles in both normal physiological conditions and diseases states. This regulation requires cis-regulatory elements located mostly in 5' and 3' UTRs and trans-regulatory factors (e.g., RNA binding proteins (RBPs)) which recognize specific RNA features and interact with the translation machinery to modulate its activity. In this paper, we discuss important aspects of 5' UTR-mediated regulation by providing an overview of the characteristics and the function of the main elements present in this region, like uORF (upstream open reading frame), secondary structures, and RBPs binding motifs and different mechanisms of translation regulation and the impact they have on gene expression and human health when deregulated.

No MeSH data available.


Related in: MedlinePlus

Impact of uAUG sequences on translation regulation. (a) Comparison of luciferase levels obtained for constructs having the 5′ UTR of the gene ACT (control) and genes containing uAUG: WBSCR16, MFSD5, and BCL2L13. (b) Deletion or mutation of uAUG sequence present in genes WBSCR16, MFSD5 and BCL2L13 reverts translation repression as seen as an increase in luciferase activity.
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fig3: Impact of uAUG sequences on translation regulation. (a) Comparison of luciferase levels obtained for constructs having the 5′ UTR of the gene ACT (control) and genes containing uAUG: WBSCR16, MFSD5, and BCL2L13. (b) Deletion or mutation of uAUG sequence present in genes WBSCR16, MFSD5 and BCL2L13 reverts translation repression as seen as an increase in luciferase activity.

Mentions: Although, overall it has been suggested that uORFs are negatively correlated with protein production [1, 38, 41] until now, functional activity has been demonstrated for only a limited number of uORFs and uAUGs. In Figure 3, we show examples of the impact uAUGs can have on translation efficiency. Among the most relevant features that can contribute to functionality are long 5′ cap-to-uORF distance, sequence conservation, context in which the AUG is located, strength of the initiation site for the ORF, length of the uORF, and number of AUGs in the 5′ UTR [38, 42]. Different outcomes have been observed when a ribosome encounters a uAUG or uORF [43]. Since the number of characterized events is still small, it is hard to define general mechanisms; we describe then a few well-characterized and relevant events. Leaky scanning is defined when a proportion of the scanning complexes bypass the uAUG or uORF and continue scanning for the next AUG. In this case, the upstream AUG acts as a “decoy” from the ORF AUG, functioning as a negative regulator of translation at least for some fraction of ribosomes. The production of cis-acting peptides by uORFs can reduce the initiation of translation of the downstream ORF by stalling the ribosome at the end of the uORF [44]. A classical example is provided by the evolutionarily conserved eukaryotic arginine attenuator peptide (AAP), that negatively controls the translation of proteins involved in the de novo fungal arginine biosynthesis in high arginine concentration [45]. In this scenario, arginine changes AAP conformation and/or P site environment causing ribosomal stalling at the termination codon of AAP uORF [46, 47]. AAP also reduces translation elongation by ribosome stalling when the uORF is inserted within an encoding sequence [48]. Another classical example of uORF-mediated regulation comes from yeast. Four uORFs are present in the 5′ UTR of the transcription factor GCN4. The first of the four uORFs is always efficiently translated regardless of the nutritional conditions. In unperturbed cells, rapid reloading of ribosomes and initiation cofactors allow translation of uORFs 2–4 while inhibiting the translation of the main ORF. In situations of amino acid starvation, initiation factors are scarce, resulting in a decelerated reloading of ribosomes and scanning across the sequences containing the uORFs. A functional initiation complex is reassembled only at the main coding sequence and GCN4 expressed. This mechanism allows a fast response to nutritional stress [49, 50]. Another similar example of regulated expression via uORF is the Carnitine Palmitoyltransferase 1C (CPT1C) gene. CPT1C regulates metabolism in the brain in situations of energy surplus. The presence of uORF in the 5′ UTR represses the expression of the ORF. However, this repression is relieved in response to specific stress stimuli like glucose depravation and palmitate-BSA treatment [51]. It has been suggested that uORFs can also induce mRNA degradation. A series of 5′ UTR constructs containing as a reporter the cat gene from the bacterial transposon Tn9 was tested in yeast. A single nucleotide substitution was used to create a 7-codon ORF upstream of the cat gene. The uORF was translated efficiently and caused translation inhibition of the cat ORF and destabilization of the cat mRNA [52]. A connection between uORFs and mRNA decay was also suggested based on a comparison between average levels of expression of uORF-containing and non-uORF-containing transcripts [41].


Before It Gets Started: Regulating Translation at the 5' UTR.

Araujo PR, Yoon K, Ko D, Smith AD, Qiao M, Suresh U, Burns SC, Penalva LO - Comp. Funct. Genomics (2012)

Impact of uAUG sequences on translation regulation. (a) Comparison of luciferase levels obtained for constructs having the 5′ UTR of the gene ACT (control) and genes containing uAUG: WBSCR16, MFSD5, and BCL2L13. (b) Deletion or mutation of uAUG sequence present in genes WBSCR16, MFSD5 and BCL2L13 reverts translation repression as seen as an increase in luciferase activity.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368165&req=5

fig3: Impact of uAUG sequences on translation regulation. (a) Comparison of luciferase levels obtained for constructs having the 5′ UTR of the gene ACT (control) and genes containing uAUG: WBSCR16, MFSD5, and BCL2L13. (b) Deletion or mutation of uAUG sequence present in genes WBSCR16, MFSD5 and BCL2L13 reverts translation repression as seen as an increase in luciferase activity.
Mentions: Although, overall it has been suggested that uORFs are negatively correlated with protein production [1, 38, 41] until now, functional activity has been demonstrated for only a limited number of uORFs and uAUGs. In Figure 3, we show examples of the impact uAUGs can have on translation efficiency. Among the most relevant features that can contribute to functionality are long 5′ cap-to-uORF distance, sequence conservation, context in which the AUG is located, strength of the initiation site for the ORF, length of the uORF, and number of AUGs in the 5′ UTR [38, 42]. Different outcomes have been observed when a ribosome encounters a uAUG or uORF [43]. Since the number of characterized events is still small, it is hard to define general mechanisms; we describe then a few well-characterized and relevant events. Leaky scanning is defined when a proportion of the scanning complexes bypass the uAUG or uORF and continue scanning for the next AUG. In this case, the upstream AUG acts as a “decoy” from the ORF AUG, functioning as a negative regulator of translation at least for some fraction of ribosomes. The production of cis-acting peptides by uORFs can reduce the initiation of translation of the downstream ORF by stalling the ribosome at the end of the uORF [44]. A classical example is provided by the evolutionarily conserved eukaryotic arginine attenuator peptide (AAP), that negatively controls the translation of proteins involved in the de novo fungal arginine biosynthesis in high arginine concentration [45]. In this scenario, arginine changes AAP conformation and/or P site environment causing ribosomal stalling at the termination codon of AAP uORF [46, 47]. AAP also reduces translation elongation by ribosome stalling when the uORF is inserted within an encoding sequence [48]. Another classical example of uORF-mediated regulation comes from yeast. Four uORFs are present in the 5′ UTR of the transcription factor GCN4. The first of the four uORFs is always efficiently translated regardless of the nutritional conditions. In unperturbed cells, rapid reloading of ribosomes and initiation cofactors allow translation of uORFs 2–4 while inhibiting the translation of the main ORF. In situations of amino acid starvation, initiation factors are scarce, resulting in a decelerated reloading of ribosomes and scanning across the sequences containing the uORFs. A functional initiation complex is reassembled only at the main coding sequence and GCN4 expressed. This mechanism allows a fast response to nutritional stress [49, 50]. Another similar example of regulated expression via uORF is the Carnitine Palmitoyltransferase 1C (CPT1C) gene. CPT1C regulates metabolism in the brain in situations of energy surplus. The presence of uORF in the 5′ UTR represses the expression of the ORF. However, this repression is relieved in response to specific stress stimuli like glucose depravation and palmitate-BSA treatment [51]. It has been suggested that uORFs can also induce mRNA degradation. A series of 5′ UTR constructs containing as a reporter the cat gene from the bacterial transposon Tn9 was tested in yeast. A single nucleotide substitution was used to create a 7-codon ORF upstream of the cat gene. The uORF was translated efficiently and caused translation inhibition of the cat ORF and destabilization of the cat mRNA [52]. A connection between uORFs and mRNA decay was also suggested based on a comparison between average levels of expression of uORF-containing and non-uORF-containing transcripts [41].

Bottom Line: Translation regulation plays important roles in both normal physiological conditions and diseases states.This regulation requires cis-regulatory elements located mostly in 5' and 3' UTRs and trans-regulatory factors (e.g., RNA binding proteins (RBPs)) which recognize specific RNA features and interact with the translation machinery to modulate its activity.In this paper, we discuss important aspects of 5' UTR-mediated regulation by providing an overview of the characteristics and the function of the main elements present in this region, like uORF (upstream open reading frame), secondary structures, and RBPs binding motifs and different mechanisms of translation regulation and the impact they have on gene expression and human health when deregulated.

View Article: PubMed Central - PubMed

Affiliation: Greehey Children's Cancer Research Institute, UTHSCSA, San Antonio, TX 78229-3900, USA.

ABSTRACT
Translation regulation plays important roles in both normal physiological conditions and diseases states. This regulation requires cis-regulatory elements located mostly in 5' and 3' UTRs and trans-regulatory factors (e.g., RNA binding proteins (RBPs)) which recognize specific RNA features and interact with the translation machinery to modulate its activity. In this paper, we discuss important aspects of 5' UTR-mediated regulation by providing an overview of the characteristics and the function of the main elements present in this region, like uORF (upstream open reading frame), secondary structures, and RBPs binding motifs and different mechanisms of translation regulation and the impact they have on gene expression and human health when deregulated.

No MeSH data available.


Related in: MedlinePlus