Dissection of a rice OsMac1 mRNA 5' UTR to uncover regulatory elements that are responsible for its efficient translation

Identification of a minimal strong translation enhancer within the 5'-untranslated region of OsMac3 mRNA

The long 5' untranslated region (5'UTR) exhibits enhancer activity in translation of rice OsMac3 mRNA. In this report, we describe elements of OsMac3 5'UTR that may be responsible for its enhancer activity, including a long uORF and several secondary structure elements. OsMac3 5'UTR can be dissected into three stem-loop structures SL1, small SL and SL2, where the uORF starts within SL1 and ends within SL2. As expected, uORF inhibits translation of downstream ORF since deletion of the uORF AUG or the SL1 stem-loop increases translation by approximately two-fold. Thus, the 158 nt 3' region of the 5'UTR lacking SL1 together with the AUG uORF, which has significant enhancer activity, was named dMac3. We investigated two critical regions within dMac3 mRNA that influence its translation: SL2, which destabilization potentially decreases translation activity, and another 13 nt located downstream of SL2. We further confirmed that dMac3 promotes mRNA translation initiation in an in vitro translation system and during transient expression in either cultured cells or Nicotiana benthamiana leaves. Thus, the dMac3 5'UTR is a useful tool for efficient protein production in various in vitro and in vivo translation systems.

Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes

mRNA translation relies on identifying translation initiation sites (TISs) in mRNAs. Alternative TISs are prevalent across plant transcriptomes, but the mechanisms for their recognition are unclear. Using ribosome profiling and machine learning, we developed models for predicting alternative TISs in the tomato (Solanum lycopersicum). Distinct feature sets were predictive of AUG and nonAUG TISs in 5' untranslated regions and coding sequences, including a novel CU-rich sequence that promoted plant TIS activity, a translational enhancer found across dicots and monocots, and humans and viruses. Our results elucidate the mechanistic and evolutionary basis of TIS recognition, whereby cis-regulatory RNA signatures affect start site selection. The TIS prediction model provides global estimates of TISs to discover neglected protein-coding genes across plant genomes. The prevalence of cis-regulatory signatures across plant species, humans, and viruses suggests their broad and critical roles in reprogramming the translational landscape.

Translation initiation at AUG and non-AUG triplets in plants

In plants and other eukaryotes, precise selection of translation initiation site (TIS) on mRNAs shapes the proteome in response to cellular events or environmental cues. The canonical translation of mRNAs initiates at a 5' proximal AUG codon in a favorable context. However, the coding and non-coding regions of plant genomes contain numerous unannotated alternative AUG and non-AUG TISs. Determining how and why these unexpected and prevalent TISs are activated in plants has emerged as an exciting research area. In this review, we focus on the selection of plant TISs and highlight studies that revealed previously unannotated TISs used in vivo via comparative genomics and genome-wide profiling of ribosome positioning and protein N-terminal ends. The biological signatures of non-AUG TIS-initiated open reading frames (ORFs) in plants are also discussed. We describe what is understood about cis-regulatory RNA elements and trans-acting eukaryotic initiation factors (eIFs) in the site selection for translation initiation by featuring the findings in plants along with supporting findings in non-plant species. The prevalent, unannotated TISs provide a hidden reservoir of ORFs that likely help reshape plant proteomes in response to developmental or environmental cues. These findings underscore the importance of understanding the mechanistic basis of TIS selection to functionally annotate plant genomes, especially for crops with large genomes.

Transcriptional and post-transcriptional controls for tuning gene expression in plants

Plant biotechnologists seek to modify plants through genetic reprogramming, but our ability to precisely control gene expression in plants is still limited. Here, we review transcription and translation in the model plants Arabidopsis thaliana and Nicotiana benthamiana with an eye toward control points that may be used to predictably modify gene expression. We highlight differences in gene expression requirements between these plants and other species, and discuss the ways in which our understanding of gene expression has been used to engineer plants. This review is intended to serve as a resource for plant scientists looking to achieve precise control over gene expression.