bims-micpro 2022-10-16 papers

Issue of 2022‒10‒16
three papers selected by
Thomas Farid Martínez
University of California, Irvine

Cell Res. 2022 Oct 14.

A novel protein RASON encoded by a lncRNA controls oncogenic RAS signaling in KRAS mutant cancers.

Rongjie Cheng, Fanying Li, Maolei Zhang, Xin Xia, Jianzhuang Wu, Xinya Gao, Huangkai Zhou, Zhi Zhang, Nunu Huang, Xuesong Yang, Yaliang Zhang, Shunli Shen, Tiebang Kang, Zexian Liu, Feizhe Xiao, Hongwei Yao, Jianbo Xu, Chao Yan, Nu Zhang.

Mutations of the RAS oncogene are found in around 30% of all human cancers yet direct targeting of RAS is still considered clinically impractical except for the KRASG12C mutant. Here we report that RAS-ON (RASON), a novel protein encoded by the long intergenic non-protein coding RNA 00673 (LINC00673), is a positive regulator of oncogenic RAS signaling. RASON is aberrantly overexpressed in pancreatic ductal adenocarcinoma (PDAC) patients, and it promotes proliferation of human PDAC cell lines in vitro and tumor growth in vivo. CRISPR/Cas9-mediated knockout of Rason in mouse embryonic fibroblasts inhibits KRAS-mediated tumor transformation. Genetic deletion of Rason abolishes oncogenic KRAS-driven pancreatic and lung cancer tumorigenesis in LSL-KrasG12D; Trp53R172H/+ mice. Mechanistically, RASON directly binds to KRASG12D/V and inhibits both intrinsic and GTPase activating protein (GAP)-mediated GTP hydrolysis, thus sustaining KRASG12D/V in the GTP-bound hyperactive state. Therapeutically, deprivation of RASON sensitizes KRAS mutant pancreatic cancer cells and patient-derived organoids to EGFR inhibitors. Our findings identify RASON as a critical regulator of oncogenic KRAS signaling and a promising therapeutic target for KRAS mutant cancers.

DOI: https://doi.org/10.1038/s41422-022-00726-7

Mol Cell Proteomics. 2022 Oct 06. pii: S1535-9476(22)00231-6. [Epub ahead of print] 100423

Probing the sORF-encoded peptides of Deinococcus radiodurans in response to extreme stress.

Congli Zhou, Qianqian Wang, Yin Huang, Zijing Chen, Shuo Chen, Ye Zhao, Chenxi Jia.

Organisms have developed different mechanisms to respond to stresses. However, the roles of sORF-encoded peptides (SEPs) in these regulatory systems remain elusive, which is partially due to the lack of comprehensive knowledge regarding these biomolecules. We chose the extremophile Deinococcus radiodurans R1 as a model species and conducted large-scale profiling of the SEPs related to the stress response. The integrated workflow consisting of multiple omics approaches for SEP identification was streamlined, and an SEPome of D. radiodurans containing 109 novel and high-confidence SEPs was drafted. Forty-four percent of these SEPs were predicted to function as antimicrobial peptides. Quantitative peptidomics analysis indicated that the expression of SEP068184 was upregulated upon oxidative treatment and gamma irradiation of the bacteria. SEP068184 was conserved in Deinococcus and exhibited negative regulation of oxidative stress resistance in a comparative phenotypic assay of its mutants. Further quantitative and interactive proteomics analyses suggested that SEP068184 might function through metabolic pathways and interact with cytoplasmic proteins. Collectively, our findings demonstrate that SEPs are involved in the regulation of oxidative resistance, and the SEPome dataset provides a rich resource for research on the molecular mechanisms of the response to extreme stress in organisms.

Keywords: Deinococcus radiodurans; oxidative stress; peptidomics; sORF-encoded peptides (SEPs); small open reading frames (sORFs)

DOI: https://doi.org/10.1016/j.mcpro.2022.100423

Front Plant Sci. 2022 ;13 971400

Analysis of herbivore-responsive long noncoding ribonucleic acids reveals a subset of small peptide-coding transcripts in Nicotiana tabacum.

Jingjing Jin, Lijun Meng, Kai Chen, Yalong Xu, Peng Lu, Zhaowu Li, Jiemeng Tao, Zefeng Li, Chen Wang, Xiaonian Yang, Shizhou Yu, Zhixiao Yang, Linggai Cao, Peijian Cao.

Long non-coding RNAs (lncRNAs) regulate many biological processes in plants, including defense against pathogens and herbivores. Recently, many small ORFs embedded in lncRNAs have been identified to encode biologically functional peptides (small ORF-encoded peptides [SEPs]) in many species. However, it is unknown whether lncRNAs mediate defense against herbivore attack and whether there are novel functional SEPs for these lncRNAs. By sequencing Spodoptera litura-treated leaves at six time-points in Nicotiana tabacum, 22,436 lncRNAs were identified, of which 787 were differentially expressed. Using a comprehensive mass spectrometry (MS) pipeline, 302 novel SEPs derived from 115 tobacco lncRNAs were identified. Moreover, 61 SEPs showed differential expression after S. litura attack. Importantly, several of these peptides were characterized through 3D structure prediction, subcellular localization validation by laser confocal microscopy, and western blotting. Subsequent bioinformatic analysis revealed some specific chemical and physical properties of these novel SEPs, which probably represent the largest number of SEPs identified in plants to date. Our study not only identifies potential lncRNA regulators of plant response to herbivore attack but also serves as a valuable resource for the functional characterization of SEP-encoding lncRNAs.

Keywords: herbivore defense; lncRNAs; mass spectrometry; small ORF-encoded peptide; tobacco

DOI: https://doi.org/10.3389/fpls.2022.971400