bims-micpro 2023-06-04 papers

Issue of 2023‒06‒04
two papers selected by
Thomas Farid Martínez
University of California, Irvine

Curr Opin Immunol. 2023 May 27. pii: S0952-7915(23)00061-4. [Epub ahead of print]83 102342

Game of Omes: ribosome profiling expands the MHC-I immunopeptidome.

Peptide ligands presented by cell-surface MHC class-I molecules enable T cells to eradicate intracellular pathogens and cancers. The presented peptide repertoire, the class-I immunopeptidome, is generated from each cell's translatome in a highly biased manner to avoid overrepresenting highly abundant translation products. The immunopeptidome can only be defined by mass spectrometry (MS). Here, we review recent advances in immunopeptidomics, focusing on using ribosome profiling as the optimal MS database to optimize the false- and failed-discovery rates and relate these findings to the contribution of defective ribosomal products and cellular quality control mechanisms to MHC class-I antigen processing and presentation.

DOI: https://doi.org/10.1016/j.coi.2023.102342

Int J Biol Macromol. 2023 May 29. pii: S0141-8130(23)01846-9. [Epub ahead of print] 124952

Unveiling the secrets of non-coding RNA-encoded peptides in plants: A comprehensive review of mining methods and research progress.

Zhengjie Wang, Qi Cui, Chenglin Su, Siyuan Zhao, Ruiming Wang, Zhicheng Wang, Jun Meng, Yushi Luan.

Non-coding RNAs (ncRNAs) are not conventionally involved in protein encoding. However, recent findings indicate that ncRNAs possess the capacity to code for proteins or peptides. These ncRNA-encoded peptides (ncPEPs) are vital for diverse plant life processes and exhibit significant potential value. Despite their importance, research on plant ncPEPs is limited, with only a few studies conducted and less information on the underlying mechanisms, and the field remains in its nascent stage. This manuscript provides a comprehensive overview of ncPEPs mining methods in plants, focusing on prediction, identification, and functional analysis. We discuss the strengths and weaknesses of various techniques, identify future research directions in the ncPEPs domain, and elucidate the biological functions and agricultural application prospects of plant ncPEPs. By highlighting the immense potential and research value of ncPEPs, we aim to lay a solid foundation for more in-depth studies in plant science.

Keywords: Non-coding RNA; Small peptide; ncPEP; sORF

DOI: https://doi.org/10.1016/j.ijbiomac.2023.124952