bims-plasge 2023-03-12 papers

Issue of 2023–03–12
three papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

J Integr Plant Biol. 2023 Mar 10.

Young Leaf White Stripe encodes a P-Type PPR protein required for chloroplast development.

Jie Lan, Qibing Lin, Chunlei Zhou, Xi Liu, Rong Miao, Tengfei Ma, Yaping Chen, Changling Mou, Ruonan Jing, Miao Feng, Thanhliem Nguyen, Yulong Ren, Zhijun Cheng, Xin Zhang, Shijia Liu, Ling Jiang, Jianmin Wan.

Pentatricopeptide repeat (PPR) proteins function in post-transcriptional regulation of organellar gene expression. Although several PPR proteins are known to function in chloroplast development in rice (Oryza sativa) the detailed molecular functions of many PPR proteins remain unclear. Here, we characterized a rice young leaf white stripe (ylws) mutant, which has defective chloroplast development during early seedling growth. Map-based cloning revealed that YLWS encodes a novel P-type chloroplast-targeted PPR protein with 11 PPR motifs. Further expression analyses showed that many nuclear- and plastid-encoded genes in the ylws mutant were significantly changed at the RNA and protein levels. The ylws mutant was impaired in chloroplast ribosome biogenesis and chloroplast development under low temperature conditions. The ylws mutation causes defects in splicing of atpF, ndhA, rpl2, and rps12, and editing of ndhA, ndhB and rps14 transcripts. YLWS directly binds to specific sites in the atpF, ndhA, and rpl2 pre-mRNAs. Our results suggest that YLWS participates in chloroplast RNA group II intron splicing and plays an important role in chloroplast development during early leaf development. This article is protected by copyright. All rights reserved.

Keywords: Chloroplast development; PPR protein; RNA splicing; ribosome biogenesis

DOI: https://doi.org/10.1111/jipb.13477

Plant Physiol. 2023 Mar 11. pii: kiad153. [Epub ahead of print]

The transcribed centromeric gene OsMRPL15 is essential for pollen development in rice.

En Xie, Jiawei Chen, Bingxin Wang, Yi Shen, Ding Tang, Guijie Du, Yafei Li, Zhukuan Cheng.

Centromeres consist of highly repetitive sequences that are challenging to map, clone, and sequence. Active genes exist in centromeric regions, but their biological functions are difficult to explore owing to extreme suppression of recombination in these regions. In this study, we used the CRISPR/Cas9 system to knock out the transcribed gene Mitochondrial Ribosomal Protein L15 (OsMRPL15), located in the centromeric region of rice (Oryza sativa) chromosome 8, resulting in gametophyte sterility. Osmrpl15 pollen was completely sterile, with abnormalities appearing at the tricellular stage including the absence of starch granules and disrupted mitochondrial structure. Loss of OsMRPL15 caused abnormal accumulation of mitoribosomal proteins and large subunit rRNA in pollen mitochondria. Moreover, the biosynthesis of several proteins in mitochondria was defective, and expression of mitochondrial genes was upregulated at the mRNA level. Osmrpl15 pollen contained smaller amounts of intermediates related to starch metabolism than wild-type pollen, while biosynthesis of several amino acids was upregulated, possibly to compensate for defective mitochondrial protein biosynthesis and initiate consumption of carbohydrates necessary for starch biosynthesis. These results provide further insight into how defects in mitoribosome development cause gametophyte male sterility.

Keywords: CRISPR/Cas9; centromere; gametophyte male sterility; mitochondrial ribosome; pollen; rice

DOI: https://doi.org/10.1093/plphys/kiad153

Mol Ecol. 2023 Mar 07.

Differential gene expression and mitonuclear incompatibilities in fast- and slow-developing inter-population Tigriopus californicus hybrids.

Timothy M Healy, Ronald S Burton.

Mitochondrial functions are intimately reliant on proteins and RNAs encoded in both the nuclear and mitochondrial genomes, leading to inter-genomic coevolution within taxa. Hybridization can break apart coevolved mitonuclear genotypes, resulting in decreased mitochondrial performance and reduced fitness. This hybrid breakdown is an important component of outbreeding depression and early-stage reproductive isolation. However, the mechanisms contributing to mitonuclear interactions remain poorly resolved. Here we scored variation in developmental rate (a proxy for fitness) among reciprocal F2 inter-population hybrids of the intertidal copepod Tigriopus californicus, and used RNA sequencing to assess differences in gene expression between fast- and slow-developing hybrids. In total, differences in expression associated with developmental rate were detected for 2,925 genes, whereas only 135 genes were differentially expressed as a result of differences in mitochondrial genotype. Up-regulated expression in fast developers was enriched for genes involved in chitin-based cuticle development, oxidation-reduction processes, hydrogen peroxide catabolic processes and mitochondrial respiratory chain complex I. In contrast, up-regulation in slow developers was enriched for DNA replication, cell division, DNA damage and DNA repair. Eighty-four nuclear-encoded mitochondrial genes were differentially expressed between fast- and slow-developing copepods, including twelve subunits of the electron transport system (ETS) which all had higher expression in fast developers than in slow developers. Nine of these genes were subunits of ETS complex I. Our results emphasize the major roles that mitonuclear interactions within the ETS, particularly in complex I, play in hybrid breakdown, and resolve strong candidate genes for involvement in mitonuclear interactions.

Keywords: RNA-seq; coevolution; copepod; cytonuclear; developmental rate; mitochondria

DOI: https://doi.org/10.1111/mec.16917