bims-plasge 2024-08-04 papers

Issue of 2024–08–04
two papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Plant Cell Physiol. 2024 Aug 02. pii: pcae086. [Epub ahead of print]

PCIS1, encoded by a pentatricopeptide protein co-expressed gene, is required for splicing of three mitochondrial nad transcripts in angiosperms.

Brody Frink, Matthias Burger, Maya Yarkoni, Sofi Shevtsov-Tal, Hagit Zer, Shohei Yamaoka, Oren Ostersetzer-Biran, Mizuki Takenaka.

Group II introns are large catalytic RNAs, which reside mainly within genes encoding respiratory complex I (CI) subunits in angiosperms' mitochondria. Genetic and biochemical analyses led to the identification of many nuclear-encoded factors that facilitate the splicing of the degenerated organellar introns in plants. Here, we describe the analysis of the PPR Co-expressed Intron Splicing1 (PCIS1) factor, which was identified in-silico by its co-expression pattern with many PPR proteins. PCIS1 is well conserved in land plants but has no sequence similarity with any known protein motifs. PCIS1 mutant lines are arrested in embryogenesis and can be maintained by the temporal expression of the gene under the embryo-specific ABI3 promoter. The pABI3::PCIS1 mutant plants display low germination and stunted growth phenotypes. RNA-seq and RT-qPCR analyses of wild type and mutant plants indicated that PCIS1 is a novel splicing cofactor that is pivotal for the maturation of several nad transcripts in Arabidopsis mitochondria. These phenotypes are tightly associated with respiratory complex I defects and altered plant growth. Our data further emphasizes the key roles of nuclear-encoded cofactors that regulate the maturation and expression of mitochondrial transcripts for the biogenesis of the oxidative phosphorylation (OXPHOS) system, and hence for plant physiology. The discovery of novel splicing factors other than typical RNA-binding proteins suggests further complexity of splicing mechanisms in plant mitochondria.

Keywords: Arabidopsis thaliana ; PCIS1 ; PPR protein; RNA splicing; mitochondria; nad genes

DOI: https://doi.org/10.1093/pcp/pcae086

Plant Genome. 2024 Jul 31. e20485

Association study of crude seed protein and fat concentration in a USDA pea diversity panel.

Renan Uhdre, Clarice J Coyne, Britton Bourland, Julia Piaskowski, Ping Zheng, Girish M Ganjyal, Zhiwu Zhang, Rebecca J McGee, Dorrie Main, Nonoy Bandillo, Mario Morales, Yu Ma, Chengci Chen, William Franck, Adam Thrash, Marilyn L Warburton.

Pea (Pisum sativum L.) is a key rotational crop and is increasingly important in the food processing sector for its protein. This study focused on identifying diverse high seed protein concentration (SPC) lines in pea plant genetic resources. Objectives included identifying high-protein pea lines, exploring genetic architecture across environments, pinpointing genes and metabolic pathways associated with high protein, and documenting information for single nucleotide polymorphism (SNP)-based marker-assisted selection. From 2019 to 2021, a 487-accession pea diversity panel, More protein, More pea, More profit, was evaluated in a randomized complete block design. DNA was extracted for genomic analysis via genotype-by-sequencing. Phenotypic analysis included protein and fat measurements in seeds and flower color. Genome-wide association study (GWAS) used multiple models, and the Pathways Association Study Tool was used for metabolic pathway analysis. Significant associations were found between SNPs and pea seed protein and fat concentration. Gene Psat7g216440 on chromosome 7, which targets proteins to cellular destinations, including seed storage proteins, was identified as associated with SPC. Genes Psat4g009200, Psat1g199800, Psat1g199960, and Psat1g033960, all involved in lipid metabolism, were associated with fat concentration. GWAS also identified genes annotated for storage proteins associated with fat concentration, indicating a complex relationship between fat and protein. Metabolic pathway analysis identified 20 pathways related to fat and seven to protein concentration, involving fatty acids, amino acid and protein metabolism, and the tricarboxylic acid cycle. These findings will assist in breeding of high-protein, diverse pea cultivars, and SNPs that can be converted to breeder-friendly molecular marker assays are identified for genes associated with high protein.

DOI: https://doi.org/10.1002/tpg2.20485