bims-plasge 2025-02-23 papers

Issue of 2025–02–23
five papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Sci Rep. 2025 Feb 21. 15(1): 6288

Fine-tuning of the PPR protein directs the RNA editing activity toward C-to-U or U-to-C conversion.

Mizuho Ichinose, Takamasa Teramoto, Izumi Nakamura, Yasuka Shimajiri, Yusuke Yagi, Bernard Gutmann.

A subfamily of pentatricopeptide repeat (PPR) proteins, known as PPR-DYW:PG, catalyzes the cytidine to uridine (C-to-U) RNA editing in plant organelles. A related PPR subfamily, PPR-DYW:KP, catalyzes the uridine to cytidine (U-to-C) reaction, via a crosslinking mechanism involving a lysine residue. We demonstrate that Lys88 in the DYW:KP domain is essential for the U-to-C editing activity of PPR-DYW:KP proteins. Substituting Lys88 with other amino acids in designer proteins switches the protein activity to C-to-U and prevents crosslinking with the edited RNA. However, this mutation leads to C-to-U off-target editing downstream the targeted site. Finally, other modifications can modulate the catalytic activity and alter the type of reaction catalyzed by the DYW domain. Altogether, our results suggest that subtle modifications in the DYW domain can influence the position of the edited nucleotide and the type of RNA editing reaction.

Keywords: C-to-U editing; DYW; PPR; Pentatricopeptide repeat; U-to-C editing

DOI: https://doi.org/10.1038/s41598-025-90722-9

bioRxiv. 2025 Feb 05. pii: 2025.02.03.636310. [Epub ahead of print]

Loss of an uncharacterized mitochondrial methionine tRNA-synthetase induces mitochondrial unfolded protein response in Caenorhabditis elegans.

Bharat Vivan Thapa, Mohit Das, James P Held, Maulik R Patel.

Aminoacyl-tRNA synthetases (aaRSs) are essential for translation, as they charge tRNA molecules with their corresponding amino acids. Alterations in aaRSs can significantly disrupt both cytosolic and mitochondrial translation. Through a forward genetic screen for mitochondrial unfolded protein response (UPR mt ) activators in C. elegans , we identified a missense mutation (P447V) in the previously uncharacterized gene Y105E8A.20, which encodes a dually localized methionine tRNA synthetase (MetRS). Here, we characterize the UPR mt induction by Y105E8A.20, which we call mars-2 , and demonstrate that the P447V allele is a loss-of-function mutation. Furthermore, we show impaired mars-2 activity in the mitochondria triggers UPR mt . This strain provides a valuable tool for studying mitochondrial translation and understanding how aaRSs are involved in mitochondrial homeostasis.

DOI: https://doi.org/10.1101/2025.02.03.636310

Plant Commun. 2025 Feb 14. pii: S2590-3462(25)00047-1. [Epub ahead of print] 101285

Mitochondrial support of high rates of photosynthesis.

Guillaume Decros, Youjun Zhang, Alisdair R Fernie.

Keywords: carbon metabolism; mitochondria; organelle movement; photosynthesis

DOI: https://doi.org/10.1016/j.xplc.2025.101285

BMC Genom Data. 2025 Feb 20. 26(1): 13

Transcriptome profiling across 11 different tissues in Pisum sativum.

Ru-Zhi Li, Guan Li, Xiao-Yan Zhang, Lei-Lei Li, Zhi-Wei Wang, Feng-Jing Song, Kai-Hua Jia, Na-Na Li, Peng-Fei Chu.

OBJECTIVES: Peas (Pisum sativum) are vital for human nutrition and have significantly contributed to the understanding of Mendelian inheritance laws. In this study, we performed transcriptome sequencing on 11 distinct pea tissues, offering an extensive gene expression dataset. This study not only provides valuable insights into the gene expression patterns across various pea tissues but also lays the foundation for future research aimed at understanding the molecular mechanisms underlying pea growth, development, and response to environmental stimuli.
DATA DESCRIPTION: In this study, we conducted transcriptome sequencing on tissue samples from 11 distinct pea plants, each with three biological replicates. This approach yielded a comprehensive RNA-seq dataset, abundant in transcriptomic information. Through principal component analysis (PCA) and gene ontology (GO) enrichment analysis, we identified significant variations in gene expression across different samples. This valuable transcriptomic resource enhances our understanding of gene expression in diverse pea tissues and provides new strategies, along with potential candidate genes, for the genetic improvement of peas.

Keywords: Pisum sativum ; Gene expression; Pea tissues; Transcriptomics

DOI: https://doi.org/10.1186/s12863-024-01287-x

Exp Cell Res. 2025 Feb 18. pii: S0014-4827(25)00062-X. [Epub ahead of print] 114466

Exploring mitonuclear interactions in the regulation of cell physiology: insights from interspecies cybrids.

Kateryna Gaertner, Riikka Tapanainen, Sina Saari, Zsófia Fekete, Steffi Goffart, Jaakko L O Pohjoismäki, Eric Dufour.

Brown hares (Lepus europaeus) and mountain hares (Lepus timidus) frequently hybridize in regions where their range overlaps, producing fertile offspring and enabling gene flow between the species. Despite this, no hybrid species has emerged, suggesting that hybrid backcrosses may incur fitness costs. One potential mechanism for such costs involves the interactions between mitochondrial and nuclear gene products, where incompatibilities between species-specific alleles may reinforce species barriers and lead to hybrid breakdown. However, direct experimental evidence for this hypothesis remains limited. In this study, we used fibroblasts derived from skin biopsies of wild-caught hares to generate cytoplasmic hybrid (cybrid) cell lines, wherein mitochondria and mtDNA from one species were transferred to mitochondria-depleted cells of the other species, creating novel mitonuclear gene combinations while preserving the original diploid nuclear background. Employing a range of techniques - including transcriptomics, metabolomics, microscopy, and respirometry - we explored the consequences of mitochondrial transfer between these hare species. Our results reveal that in the studied species mitonuclear incompatibilities exhibit strong effects on cellular fitness but are limited to specific genotypes. We propose mechanisms of cellular-level incompatibility and their potential consequences for interspecific hybrids, offering new insights into the complexity of mitonuclear interactions.

Keywords: cytoplasmic hybrid; hares; metabolism; mitochondrial transfer; mitonuclear interactions; speciation

DOI: https://doi.org/10.1016/j.yexcr.2025.114466