bims-plasge 2025-05-18 papers

Issue of 2025–05–18
three papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Int J Mol Sci. 2025 May 07. pii: 4459. [Epub ahead of print]26(9):

P-Type Pentatricopeptide Repeat Proteins YS1 and YS2 Function in Splicing of petB Intron to Maintain Chloroplast Homeostasis During Rice Seedling Development.

Hui Sun, Yanshen Nie, Li Yu, Xiaohong Yue, Xin Hou, Jie Zhao.

Regulating chloroplast gene expression is crucial for maintaining chloroplast function and plant development. Pentatricopeptide repeat (PPR) proteins form a vast protein family that regulates organelle genes and has multiple functions during plant development. Here, we found that two P-type PPR proteins, YS1 (yellow-green seedling 1) and YS2, jointly regulated seedling development in rice. The loss of YS1 and YS2 exhibited the collapsed chloroplast thylakoids and decreased photosynthetic activity, leading to the yellowing and death of rice seedlings. YS1 and YS2 could directly bind to the transcript of the psbH-petB intergenic region to facilitate the splicing of petB intron, thereby affecting the splicing efficiency of petD, which is located downstream of petB in the five-cistronic transcription unit psbB-psbT-psbH-petB-petD. The mutations in YS1 and YS2 led to decreased mature transcripts of petB and petD after splicing, significantly reducing the protein levels of PetB and PetD. This further led to deficiencies in the cytochrome b6/f and photosystem I complexes of the electron transport chain (ETC), ultimately resulting in decreased ETC-produced NADPH and reduced contents of carbohydrates in ys mutants. Moreover, transcriptome sequencing analysis revealed that YS1 and YS2 were vital for chloroplast organization and carbohydrate metabolism, as well as chloroplast RNA processing. In previous studies, the mechanism of petB intron splicing in the five-cistronic transcription unit psbB-psbT-psbH-petB-petD of rice is unclear. Our study revealed that the two highly conserved proteins YS1 and YS2 were functionally redundant and played critical roles in photosynthesis and seedling development through their involvement in petB intron splicing to maintain chloroplast homeostasis in rice. This work broadened the perspective on PPR-mediated chloroplast development and laid a foundation for exploring the biofunctions of duplicated genes in higher plants.

Keywords: RNA splicing; chloroplast development; pentatricopeptide repeat; photosystem protein; rice

DOI: https://doi.org/10.3390/ijms26094459

Plants (Basel). 2025 Apr 28. pii: 1335. [Epub ahead of print]14(9):

Phylogenomic Inference Suggests Differential Deep Time Phylogenetic Signals from Nuclear and Organellar Genomes in Gymnosperms.

Yu-En Lin, Chung-Shien Wu, Yu-Wei Wu, Shu-Miaw Chaw.

The living gymnosperms include about 1200 species in five major groups: cycads, ginkgo, gnetophytes, Pinaceae (conifers I), and cupressophytes (conifers II). Molecular phylogenetic studies have yet to reach a unanimously agreed-upon relationship among them. Moreover, cytonuclear phylogenetic incongruence has been repeatedly observed in gymnosperms. We collated a comprehensive dataset from available genomes of 17 gymnosperms across the five major groups and added our own high-quality assembly of a species from Podocarpaceae (the second largest conifer family) to increase sampling width. We used these data to infer reconciled nuclear species phylogenies using two separate methods to ensure the robustness of our conclusions. We also reconstructed organelle phylogenomic trees from 42 mitochondrial and 82 plastid genes from 38 and 289 gymnosperm species across the five major groups, respectively. Our nuclear phylogeny consistently recovers the Ginkgo-cycads clade as the first lineage split from other gymnosperm clades and the Pinaceae as sister to gnetophytes (the Gnepines hypothesis). In contrast, the mitochondrial tree places cycads as the earliest lineage in gymnosperms and gnetophytes as sister to cupressophytes (the Gnecup hypothesis) while the plastomic tree supports the Ginkgo-cycads clade and gnetophytes as the sister to cupressophytes. We also examined the effect of mitochondrial RNA editing sites on the gymnosperm phylogeny by manipulating the nucleotide and amino acid sequences at these sites. Only complete removal of editing sites has an effect on phylogenetic inference, leading to a closer congruence between mitogenomic and nuclear phylogenies. This suggests that RNA editing sites carry a phylogenetic signal with distinct evolutionary traits.

Keywords: Nageia; RNA editing; conifers; cycads; cytonuclear incongruence; ginkgo; gnetophytes; mitogenome; phylogenomics; plastome

DOI: https://doi.org/10.3390/plants14091335

J Proteome Res. 2025 May 16.

Comparative Omics Reveals Unanticipated Metabolic Rearrangements in a High-Oil Mutant of Plastid Acetyl-CoA Carboxylase.

Amr Kataya, Jose Roberto S Nascimento, Chunhui Xu, Matthew G Garneau, Somnath Koley, Athen Kimberlin, Thiya Mukherjee, Brian P Mooney, Dong Xu, Philip D Bates, Doug K Allen, Abraham J Koo, Jay J Thelen.

Heteromeric acetyl-CoA carboxylase (ACCase) catalyzes the ATP-dependent carboxylation of acetyl-CoA to produce malonyl-CoA, which is the committed step for de novo fatty acid synthesis. In plants, ACCase activity is controlled at multiple levels, including negative regulation by biotin attachment domain-containing (BADC) proteins, of which the badc1/3 double mutant leads to increased seed triacylglycerol accumulation. Unexpectedly, the Arabidopsis badc1/3 mutant also accumulated more protein. The metabolic consequences from both higher oil and protein were investigated in developing badc1/3 seed using global transcriptomics, translatomics, proteomics, metabolomics, and other biomass measurements. Changes included increased storage proteins and lipid droplet-packaging proteins, increased SDP1 lipase, altered organic acid metabolism, and reduced extracellular lipid synthesis perhaps offsetting the increase in TAG. We present a model of how Arabidopsis adapted to deregulated ACCase, resulting in more oil, and altered flux through pathways that partition carbon and propose targets for future bioengineering of seed storage reserves.

Keywords: acetyl-CoA carboxylase; central metabolism; fatty acid biosynthesis; seed oil

DOI: https://doi.org/10.1021/acs.jproteome.4c00947