Ending on a high note: Downstream ORFs enhance mRNA translational output

Unraveling the small proteome of the plant symbiont Sinorhizobium meliloti by ribosome profiling and proteogenomics

The soil-dwelling plant symbiont Sinorhizobium meliloti is a major model organism of Alphaproteobacteria. Despite numerous detailed OMICS studies, information about small open reading frame (sORF)-encoded proteins (SEPs) is largely missing, because sORFs are poorly annotated and SEPs are hard to detect experimentally. However, given that SEPs can fulfill important functions, identification of translated sORFs is critical for analyzing their roles in bacterial physiology. Ribosome profiling (Ribo-seq) can detect translated sORFs with high sensitivity, but is not yet routinely applied to bacteria because it must be adapted for each species. Here, we established a Ribo-seq procedure for S. meliloti 2011 based on RNase I digestion and detected translation for 60% of the annotated coding sequences during growth in minimal medium. Using ORF prediction tools based on Ribo-seq data, subsequent filtering, and manual curation, the translation of 37 non-annotated sORFs with ≤ 70 amino acids was predicted with confidence. The Ribo-seq data were supplemented by mass spectrometry (MS) analyses from three sample preparation approaches and two integrated proteogenomic search database (iPtgxDB) types. Searches against standard and 20-fold smaller Ribo-seq data-informed custom iPtgxDBs confirmed 47 annotated SEPs and identified 11 additional novel SEPs. Epitope tagging and Western blot analysis confirmed the translation of 15 out of 20 SEPs selected from the translatome map. Overall, by combining MS and Ribo-seq approaches, the small proteome of S. meliloti was substantially expanded by 48 novel SEPs. Several of them are part of predicted operons and/or are conserved from Rhizobiaceae to Bacteria, suggesting important physiological functions.

Identification of Microproteins in Hep3B Cells at Different Cell Cycle Stages

Microproteins are generated from small open reading frames and turn out to play various vital biological functions. As an essential biological event of eukaryotic cells, the cell cycle is involved in cell replication and division. For such a highly regulated event, microproteins associated with cell cycle regulation remained unclarified. Utilizing a combination of bottom-up and top-down proteomics, we analyzed microproteins at specific cell cycle stages of Hep3B cells. A total of 657 microproteins were identified under three cell cycle stages, including 151 in the G0/G1 stage, 163 in the S stage, and 132 in the G2/M stage. The annotation of these microproteins showed their cell cycle-specific functions, such as translation, nuclear assembly, chromatin organization, and the G2/M transition of the mitotic cell cycle. Meanwhile, more than 50% of identified microproteins were ncRNA-encoded. These nonannotated novel microproteins contain several function domains, such as the nucleoside diphosphate kinase domain, the high mobility group domain, and the DNA-binding domain. This suggested the potential functions of these novel microproteins in specific cell cycle stages. This study presented a large-scale profile of microproteins at different cell cycle stages from Hep3B and may provide new perspectives on the regulation mechanism of the cell cycle. Liquid chromatography-mass spectrometry data were deposited to ProteomeXchange using the identifier PXD030286.

Circular RNA circ_0001017 Sensitizes Cisplatin-Resistant Gastric Cancer Cells to Chemotherapy by the miR-543/PHLPP2 Axis

Resistance to cisplatin (CDDP) remains a major challenge for the treatment of gastric cancer (GC). Circular RNAs (circRNAs) have been implicated in the development of CDDP resistance of GC. However, the precise actions of circ_0001017 in CDDP resistance of GC remain to be elucidated. The levels of circ_0001017, microRNA (miR)-543 and PH-domain and leucine-rich repeat protein phosphatase 2 (PHLPP2) mRNA were gauged by quantitative real-time polymerase chain reaction (qRT-PCR). Western blot was used to analyze the protein levels of Vimentin, N-cadherin, E-cadherin, and PHLPP2. Ribonuclease R (RNase R) assay was applied to evaluate the stability of circ_0001017. Cell viability and proliferation, colony formation ability, cell cycle distribution and apoptosis, and migration and invasion were detected by the Cell Counting Kit-8 (CCK-8), colony formation, flow cytometry, and transwell assays, respectively. Direct relationship between miR-543 and circ_0001017 or PHLPP2 was verified by dual-luciferase reporter and RNA immunoprecipitation (RIP) assays. Xenograft model assay was used to assess the function of circ_0001017 in vivo. Low expression of circ_0001017 was associated with CDDP resistance of GC. Enforced expression of circ_0001017 impeded growth, metastasis, and enhanced apoptosis of HGC-27/R and AGS/R cells and sensitized them to CDDP in vitro. Circ_0001017 targeted miR-543, and circ_0001017 regulated CDDP-resistant cell behaviors and CDDP sensitivity by suppressing miR-543. PHLPP2 was a direct target of miR-543, and circ_0001017 controlled PHLPP2 expression through miR-543. Moreover, miR-543 knockdown-mediated promotion of PHLPP2 impacted CDDP-resistant cell behaviors and CDDP sensitivity in vitro. Additionally, elevated expression of circ_0001017 hindered growth of HGC-27/R cells and sensitized them to CDDP in vivo. Our findings demonstrated that enforced expression of circ_0001017 suppressed malignant behaviors and enhanced CDDP sensitivity of CDDP-resistant GC cells at least partially by the miR-543/PHLPP2 axis.

Ending on a high note: Downstream ORFs enhance mRNA translational output

Eukaryotic mRNAs were long thought to only translate a single protein product, but it is now recognized that many mRNAs can also encode small open reading frames (ORFs). In this issue of The EMBO Journal, Wu et al characterized small ORFs in the 3' untranslated regions (3' UTRs) of human and zebrafish mRNAs and found that many are indeed translated. The peptides encoded by these downstream ORFs (dORFs) are often poorly conserved across evolution, but many dORFs are nonetheless functional, as the act of their translation can promote translation of the canonical ORF.