bims-micpro 2020-08-09 papers

Issue of 2020‒08‒09
four papers selected by
Thomas Martinez
Salk Institute for Biological Studies

EMBO J. 2020 Aug 03. e104763

Translation of small downstream ORFs enhances translation of canonical main open reading frames.

Qiushuang Wu, Matthew Wright, Madelaine M Gogol, William D Bradford, Ning Zhang, Ariel A Bazzini.

In addition to canonical open reading frames (ORFs), thousands of translated small ORFs (containing less than 100 codons) have been identified in untranslated mRNA regions (UTRs) across eukaryotes. Small ORFs in 5' UTRs (upstream (u)ORFs) often repress translation of the canonical ORF within the same mRNA. However, the function of translated small ORFs in the 3' UTRs (downstream (d)ORFs) is unknown. Contrary to uORFs, we find that translation of dORFs enhances translation of their corresponding canonical ORFs. This translation stimulatory effect of dORFs depends on the number of dORFs, but not the length or peptide they encode. We propose that dORFs represent a new, strong, and universal translation regulatory mechanism in vertebrates.

Keywords: dORF; ribosome profiling; translation efficiency

DOI: https://doi.org/10.15252/embj.2020104763

Elife. 2020 Aug 03. pii: e58659. [Epub ahead of print]9

A human ESC-based screen identifies a role for the translated lncRNA LINC00261 in pancreatic endocrine differentiation.

Bjoern Gaertner, Sebastiaan van Heesch, Valentin Schneider-Lunitz, Jana Felicitas Schulz, Franziska Witte, Susanne Blachut, Steven Nguyen, Regina Wong, Ileana Matta, Norbert Hübner, Maike Sander.

Long noncoding RNAs (lncRNAs) are a heterogenous group of RNAs, which can encode small proteins. The extent to which developmentally regulated lncRNAs are translated and whether the produced microproteins are relevant for human development is unknown. Using a human embryonic stem cell (hESC)-based pancreatic differentiation system, we show that many lncRNAs in direct vicinity of lineage-determining transcription factors (TFs) are dynamically regulated, predominantly cytosolic, and highly translated. We genetically ablated ten such lncRNAs, most of them translated, and found that nine are dispensable for pancreatic endocrine cell development. However, deletion of LINC00261 diminishes insulin+ cells, in a manner independent of the nearby TF FOXA2. One-by-one deletion of each of LINC00261's open reading frames suggests that the RNA, rather than the produced microproteins, is required for endocrine development. Our work highlights extensive translation of lncRNAs during hESC pancreatic differentiation and provides a blueprint for dissection of their coding and noncoding roles.

Keywords: computational biology; developmental biology; human; systems biology

DOI: https://doi.org/10.7554/eLife.58659

Plant Physiol Biochem. 2020 Jul 22. pii: S0981-9428(20)30355-7. [Epub ahead of print]155 42-58

Ribosome profiling reveals the effects of nitrogen application translational regulation of yield recovery after abrupt drought-flood alternation in rice.

Qiangqiang Xiong, Lei Zhong, Jie Du, Changlan Zhu, Xiaosong Peng, Xiaopeng He, Junru Fu, Linjuan Ouyang, Jianmin Bian, Lifang Hu, Xiaotang Sun, Jie Xu, Dahu Zhou, Yicong Cai, Haihui Fu, Haohua He, Xiaorong Chen.

Abrupt drought-flood alternation is a frequent meteorological disaster during the summer in Southern China. The study of physiological and translation mechanisms of rice yield recovery after abrupt drought-flood alternation has great potential benefits in field production. Our results showed that yield recovery upon nitrogen (N) application after abrupt drought-flood alternation was due to the increase in effective panicle numbers per plant. The N application resulted in the regulation of physiological and biochemical as well as growth development processes, which led to a rapid growth recovery effect after abrupt drought-flood alternation stress in rice. Using ribosome profiling combined with RNA sequencing (RNA-seq) technology, the interactions between transcription and translation for N application after abrupt drought-flood alternation were analyzed. It was found that a small proportion of response genes were shared at the transcriptional and translational levels, that is, 14% of the expressed genes were upregulated and 6.6% downregulated. Further analysis revealed that the translation efficiency (TE) of the genes was influenced by their sequence characteristics, including their GC content, coding sequence length and normalized minimal free energy. Compared with the number of untranslated upstream open reading frames (uORFs), the increased number of translated uORFs promoted the improvement of TE. The TE of the uORFs for N application was lower than the control without N application after abrupt drought-flood alternation. This study characterizes the translational regulatory pattern in response to N application after abrupt drought-flood alternation stress.

Keywords: Abrupt drought-flood alternation; Nitrogen; RNA-seq; Ribosome profiling; Translation efficiency; uORFs

DOI: https://doi.org/10.1016/j.plaphy.2020.07.021

J Biol Chem. 2020 Aug 05. pii: jbc.RA120.014346. [Epub ahead of print]

A potential role for a novel ZC3H5 complex in regulating mRNA translation in Trypanosoma brucei.

Kathrin Bajak, Kevin Leiss, Christine Clayton, Esteban Erben.

In Trypanosoma brucei and related kinetoplastids, gene expression regulation occurs mostly post-transcriptionally. Consequently, RNA-binding proteins play a critical role in the regulation of mRNA and protein abundance. Yet, the roles of many RNA-binding proteins are not understood. Our previous research identified the RNA-binding protein ZC3H5 as possibly involved in gene repression, but its role in controlling gene expression was unknown. We here show that ZC3H5 is an essential cytoplasmic RNA-binding protein: RNAi targeting ZC3H5 causes accumulation of pre-cytokinetic cells followed by rapid cell death. Affinity purification and pair-wise yeast 2-hybrid analysis suggest that ZC3H5 forms a complex with three other proteins, encoded by genes Tb927.11.4900, Tb927.8.1500 and Tb927.7.3040. RNA immunoprecipitation revealed that ZC3H5 is preferentially associated with poorly translated, low-stability mRNAs, the 5'-untranslated regions and coding regions of which are enriched in the motif (U/A)UAG(U/A). As previously found in high-throughput analyses, artificial tethering of ZC3H5 to a reporter mRNA or other complex components repressed reporter expression. However, depletion of ZC3H5 in vivo caused only very minor decreases in a few targets, marked increases in the abundances of very stable mRNAs, an increase in monosomes at the expense of large polysomes, and appearance of "halfmer" disomes containing two 80S subunits and one 40S subunit. We speculate that the ZC3H5 complex might be implicated in quality control during the translation of sub-optimal open reading frames.

Keywords: RNA-binding proteins; RNA-protein interaction; Trypanosoma brucei; ZC3H5; halfmers; post-transcriptional regulation; translation; zinc finger

DOI: https://doi.org/10.1074/jbc.RA120.014346