bims-micpro 2022-08-14 papers

Issue of 2022‒08‒14
six papers selected by
Thomas Farid Martínez
University of California, Irvine

Genomics. 2022 Aug 03. pii: S0888-7543(22)00189-6. [Epub ahead of print] 110444

Identification and analysis of smORFs in Chlamydomonas reinhardtii.

Zhao Peng, Sheng Yao, Baolong Zhang, Kaiyao Huang, Cuihong Wan.

Small open reading frames (smORFs) have been acknowledged as an important partner in organism functions ranging from bacteria to higher eukaryotes. However, lack of investigation of smORFs in green algae, despite their importance in ecology and evolution. We applied bioinformatic analysis, ribosome profiling, and small peptide proteomics to provide a genome-wide and high-confident smORF database in the model green alga Chlamydomonas reinhardtii. The whole genome was screened first to mine potential coding smORFs. Then conservative analysis, ribosome profiling, and proteomics data were processed to identify conserved smORFs and generate translation evidence. The combination of procedures resulted in 2014 smORFs that might exist in the C. reinhardtii genome. The expression of smORFs in Cd treatment suggested that two smORFs might participate in redox reaction, three in inorganic phosphate transport, and one in DNA repair under stress. Our study built a genome-widely database in C. reinhardtii, providing target smORFs for further research.

Keywords: Green algae; Ribosome profiling; SEP; Small peptide proteomics; smORF

DOI: https://doi.org/10.1016/j.ygeno.2022.110444

RNA. 2022 Aug 12. pii: rna.079194.122. [Epub ahead of print]

DAP5 drives translation of specific mRNA targets with upstream ORFs in human embryonic stem cells.

Maya David, Tsviya Olender, Orel Mizrahi, Shira Weingarten-Gabbay, Gilgi Friedlander, Sara Meril, Nadav Goldberg, Alon Savidor, Yishai Levin, Vered Salomon, Noam Stern-Ginossar, Shani Bialik, Adi Kimchi.

Death Associated Protein 5 (DAP5/eIF4G2/NAT1) is a member of the eIF4G translation initiation factors that has been shown to mediate non-canonical and/or cap-independent translation. It is essential for embryonic development and for differentiation of embryonic stem cells (ESCs), specifically its ability to drive translation of specific target mRNAs. In order to expand the repertoire of DAP5 target mRNAs, we compared ribosome profiles in control and DAP5 knock-down (KD) human ESCs (hESCs) to identify mRNAs with decreased ribosomal occupancy upon DAP5 silencing. A cohort of 68 genes showed decreased translation efficiency in DAP5 KD cells. Mass spectrometry confirmed decreased protein abundance of a significant portion of these targets. Among these was Kmt2d, a histone methylase previously shown to be essential for ESC differentiation and embryonic development. We found that nearly half of the cohort of DAP5 target mRNAs displaying reduced translation efficiency of their main coding sequences upon DAP5 KD contained upstream open reading frames (uORFs) that are actively translated independently of DAP5. This is consistent with previously suggested mechanisms by which DAP5 mediates leaky scanning through uORFs and/or re-initiation at the main coding sequence. Crosslinking protein-RNA immunoprecipitation experiments indicated that a significant subset of DAP5 mRNA targets bound DAP5, indicating that direct binding between DAP5 protein and its target mRNAs is a frequent but not absolute requirement for DAP5-dependent translation of the main coding sequence. Thus, we have extended DAP5's function in translation of specific mRNAs in hESCs by a mechanism allowing translation of the main coding sequence following upstream translation of short ORFs.

Keywords: DAP5/eIF4G2; RNA-seq; non-canonical protein translation; pluripotent embryonic stem cells; ribosome profiling

DOI: https://doi.org/10.1261/rna.079194.122

Front Genet. 2022 ;13 935351

Profiling a Community-Specific Function Landscape for Bacterial Peptides Through Protein-Level Meta-Assembly and Machine Learning.

Mitra Vajjala, Brady Johnson, Lauren Kasparek, Michael Leuze, Qiuming Yao.

Small proteins, encoded by small open reading frames, are only beginning to emerge with the current advancement of omics technology and bioinformatics. There is increasing evidence that small proteins play roles in diverse critical biological functions, such as adjusting cellular metabolism, regulating other protein activities, controlling cell cycles, and affecting disease physiology. In prokaryotes such as bacteria, the small proteins are largely unexplored for their sequence space and functional groups. For most bacterial species from a natural community, the sample cannot be easily isolated or cultured, and the bacterial peptides must be better characterized in a metagenomic manner. The bacterial peptides identified from metagenomic samples can not only enrich the pool of small proteins but can also reveal the community-specific microbe ecology information from a small protein perspective. In this study, metaBP (Bacterial Peptides for metagenomic sample) has been developed as a comprehensive toolkit to explore the small protein universe from metagenomic samples. It takes raw sequencing reads as input, performs protein-level meta-assembly, and computes bacterial peptide homolog groups with sample-specific mutations. The metaBP also integrates general protein annotation tools as well as our small protein-specific machine learning module metaBP-ML to construct a full landscape for bacterial peptides. The metaBP-ML shows advantages for discovering functions of bacterial peptides in a microbial community and increases the yields of annotations by up to five folds. The metaBP toolkit demonstrates its novelty in adopting the protein-level assembly to discover small proteins, integrating protein-clustering tool in a new and flexible environment of RBiotools, and presenting the first-time small protein landscape by metaBP-ML. Taken together, metaBP (and metaBP-ML) can profile functional bacterial peptides from metagenomic samples with potential diverse mutations, in order to depict a unique landscape of small proteins from a microbial community.

Keywords: bacterial peptide; machine learning; metagenomics; protein annotation; protein clustering

DOI: https://doi.org/10.3389/fgene.2022.935351

Front Oncol. 2022 ;12 944159

CircRNA-Encoded Peptides or Proteins as New Players in Digestive System Neoplasms.

Enqing Meng, Jie Deng, Rongqi Jiang, Hao Wu.

Circular RNAs (circRNAs) were considered non-coding RNAs. Nowadays, a large number of studies have found that these RNAs contain open reading frames that can be translated in a cap-independent manner, such as internal ribosome entry site (IRES) and N6-methyladenosine (m6A). The encoded peptides or proteins affect the occurrence and development of tumors by regulating the Yap-hippo and the Wnt/β-catenin signaling pathways, as well as the malignant progression of tumors through phosphorylation and ubiquitination of specific molecules. This review will summarize the regulation of circRNA translation and the functional roles and underlying mechanisms of circRNA-derived peptides or proteins in digestive tract tumors. Some circRNA-encoded peptides or proteins may be used as tumor biomarkers and prognostic factors for early screening and treatment of clinical gastrointestinal tumors.

Keywords: circular RNAs; digestive cancers; peptides; signaling pathways; translation

DOI: https://doi.org/10.3389/fonc.2022.944159

J Mol Evol. 2022 Aug 13.

uORF-Mediated Translational Regulation of ATF4 Serves as an Evolutionarily Conserved Mechanism Contributing to Non-Small-Cell Lung Cancer (NSCLC) and Stress Response.

Wenjing Xiao, Yang Sun, Jinpeng Xu, Na Zhang, Lina Dong.

Diseases and environmental stresses are two distinct challenges for virtually all living organisms. In light of evolution, cellular responses to diseases and stresses might share similar molecular mechanisms, but the detailed regulation pathway is not reported yet.We obtained the transcriptomes and translatomes from several NSCLC (non-small-cell lung cancer) patients as well as from different species under normal or stress conditions. We found that the translation level of gene ATF4 is remarkably enhanced in NSCLC due to the reduced number of ribosomes binding to its upstream open reading frames (uORFs). We also showed the evolutionary conservation of this uORF-ATF4 regulation in the stress response of other species. Molecular experiments showed that knockdown of ATF4 reduced the cell growth rate while overexpression of ATF4 enhanced cell growth, especially for the ATF4 allele with mutated uORFs. Population genetics analyses in multiple species verified that the mutations that abolish uATGs (start codon of uORFs) are highly deleterious, suggesting the functional importance of uORFs.Our study proposes an evolutionarily conserved pattern that enhances the ATF4 translation by uORFs upon stress or disease. We generalized the concept of cellular response to diseases and stresses. These two biological processes may share similar molecular mechanisms.

Keywords: ATF4; Evolutionarily conserved; Non-small-cell lung cancer (NSCLC); Stress response; Translation regulation; Upstream open reading frame (uORF)

DOI: https://doi.org/10.1007/s00239-022-10068-y

J Biochem. 2022 Aug 12. pii: mvac064. [Epub ahead of print]

Identification of unannotated coding sequences and their physiological functions.

Kazuya Ichihara, Keiichi I Nakayama, Akinobu Matsumoto.

Most protein-coding sequences (CDSs) are predicted sequences based on criteria such as a size sufficient to encode a product of at least 100 amino acids and with translation starting at an AUG initiation codon. However, recent studies based on ribosome profiling and mass spectrometry have shown that several RNAs annotated as long noncoding RNAs (lncRNAs) are actually translated to generate polypeptides of fewer than 100 amino acids, and that many proteins are translated from near-cognate initiation codons such as CUG and GUG. Furthermore, studies of genetically engineered mouse models have revealed that such polypeptides and proteins contribute to diverse physiological processes. In this review, we describe the latest methods for the identification of unannotated CDSs and provide examples of their physiological functions.

Keywords: long noncoding RNA (lncRNA); near-cognate initiation codon; polypeptide; ribosome profiling; translation

DOI: https://doi.org/10.1093/jb/mvac064