bims-micpro 2022-02-13 papers

Issue of 2022‒02‒13
two papers selected by
Thomas Farid Martínez
University of California, Irvine

Plant Cell Environ. 2022 Feb 06.

Plants Utilise Ancient Conserved Peptide Upstream Open Reading Frames in Stress-Responsive Translational Regulation.

Barry Causier, Tayah Hopes, Mary McKay, Zachary Paling, Brendan Davies.

The regulation of protein synthesis plays an important role in growth and development in all organisms. Upstream open reading frames (uORFs) are commonly found in eukaryotic mRNA transcripts and typically attenuate the translation of associated downstream main ORFs (mORFs). Conserved peptide uORFs (CPuORFs) are a rare subset of uORFs, some of which have been shown to conditionally regulate translation by ribosome stalling. Here we show that Arabidopsis CPuORF19, CPuORF46 and CPuORF47, which are ancient in origin, regulate translation of any downstream ORF, in response to the agriculturally significant environmental signals, heat stress and water limitation. Consequently, these CPuORFs represent a versatile toolkit for inducible gene expression with broad applications. Finally, we note that different classes of CPuORFs may operate during distinct phases of translation, which has implications for the bioengineering of these regulatory factors. This article is protected by copyright. All rights reserved.

Keywords: 5’-UTR; 5’-leader; Arabidopsis; CPuORF; abiotic stress; ribosome stalling; translation regulation; uORF

DOI: https://doi.org/10.1111/pce.14277

Front Cell Dev Biol. 2022 ;10 795084

LncPep: A Resource of Translational Evidences for lncRNAs.

Teng Liu, Jingni Wu, Yangjun Wu, Wei Hu, Zhixiao Fang, Zishan Wang, Chunjie Jiang, Shengli Li.

Long noncoding RNAs (lncRNAs) are a type of transcript that is >200 nucleotides long with no protein-coding capacity. Accumulating studies have suggested that lncRNAs contain open reading frames (ORFs) that encode peptides. Although several noncoding RNA-encoded peptide-related databases have been developed, most of them display only a small number of experimentally validated peptides, and resources focused on lncRNA-encoded peptides are still lacking. We used six types of evidence, coding potential assessment tool (CPAT), coding potential calculator v2.0 (CPC2), N6-methyladenosine modification of RNA sites (m6A), Pfam, ribosome profiling (Ribo-seq), and translation initiation sites (TISs), to evaluate the coding potential of 883,804 lncRNAs across 39 species. We constructed a comprehensive database of lncRNA-encoded peptides, LncPep (http://www.shenglilabs.com/LncPep/). LncPep provides three major functional modules: 1) user-friendly searching/browsing interface, 2) prediction and BLAST modules for exploring novel lncRNAs and peptides, and 3) annotations for lncRNAs, peptides and supporting evidence. Taken together, LncPep is a user-friendly and convenient platform for discovering and investigating peptides encoded by lncRNAs.

Keywords: cancer; lncRNA; m6A; peptide; ribo-seq; translation

DOI: https://doi.org/10.3389/fcell.2022.795084