bims-plasge 2025-01-19 papers

Issue of 2025–01–19
three papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

J Genet Genomics. 2025 Jan 09. pii: S1673-8527(25)00003-7. [Epub ahead of print]

The maize mTERF18 regulates transcriptional termination of the mitochondrial nad6 gene and is essential for kernel development.

Zhengwei Guan, Yong Wang, Jun Yang.

Mitochondria are semi-autonomous organelle present in eukaryotic cells, containing their own genome and transcriptional machinery. However, their functions are intricately linked to proteins encoded by the nuclear genome. Mitochondrial transcription termination factors (mTERFs) are nucleic acid-binding proteins involved in RNA splicing and transcription termination within plant mitochondria and chloroplasts. Despite their recognized importance, the specific roles of mTERF proteins in maize remain largely unexplored. Here, we clone and functionally characterize maize mTERF18 gene. Our findings reveal that mTERF18 mutations lead to severely undifferentiated embryos, resulting in abortive phenotypes. Early kernel exhibits abnormal basal endosperm transfer layer and a significant reduction in both starch and protein accumulation in mterf18. We identify the mTERF18 gene through mapping-based cloning and validate this gene through allelic tests. mTERF18 is widely expressed across various maize tissues and encodes a highly conserved mitochondrial protein. Transcriptome data reveal that mTERF18 mutations disrupt transcriptional termination of the nad6 gene, leading to undetectable levels of Nad6 protein and reduced complex I assembly and activity. Furthermore, transmission electron microscopy observation of mterf18 endosperm uncover severe mitochondrial defects. Collectively, these findings highlight the critical role of mTERF18 in mitochondrial gene transcription termination and its pivotal impact on maize kernel development.

Keywords: Kernel development; Mitochondria; Nad6; Transcriptional termination; Zea mays; mTERF18

DOI: https://doi.org/10.1016/j.jgg.2025.01.001

BMC Genomics. 2025 Jan 10. 26(1): 28

Mitochondrial genome structural variants and candidate cytoplasmic male sterility-related gene in sugarcane.

Yihan Li, Shuangyu Li, Xiuting Hua, Yi Xu, Shuqi Chen, Zehuai Yu, Gui Zhuang, Yuhong Lan, Wei Yao, Baoshan Chen, Muqing Zhang, Jisen Zhang.

BACKGROUND: Sugarcane is a crucial crop for both sugar and bioethanol production. The nobilization breeding and utilization of wild germplasm have significantly enhanced its productivity. However, the pollen sterility in Saccharum officinarum restricts its role to being a female parent in crosses with Saccharum spontaneum during nobilization breeding, resulting in a narrow genetic basis for modern sugarcane cultivars. Mitochondria, often referred to as the intracellular "energy factories", provide energy for plant life activities, and are also implicated in cytoplasmic male sterility (CMS).
RESULTS: We performed mitochondrial genome assembly and structural analysis of two Saccharum founding species. We discovered that the proportions of repeat sequences are the primary factor contributing to the variations in mitochondrial genome structure and size between the two Saccharum species. Heterologous expression of the mitochondrial chimeric gene ORF113, which is highly expressed in male-sterile S. officinarum flowers, significantly inhibits growth and ATP synthesis in yeast cells, making it a key candidate CMS-related gene in sugarcane. Furthermore, we developed two co-dominant simple sequence repeat (SSR) markers based on the mitochondrial genome, which can effectively distinguish the cytoplasmic types of the two Saccharum species.
CONCLUSION: In this study, we identified structural variants and developed SSR molecular markers in the mitochondrial genomes of both S. officinarum and S. spontaneum. We also identified a novel mitochondrial chimeric ORF as a key candidate CMS-related gene. These findings offer valuable insights into variety identification, genetic resource development, and cross-breeding strategies in sugarcane.

Keywords: Cytoplasmic male sterility (CMS); Mitochondrial genome; Repeat sequences; Simple sequence repeat (SSR); Sugarcane

DOI: https://doi.org/10.1186/s12864-025-11210-y

PLoS Genet. 2025 Jan 13. 21(1): e1011451

Identification of novel genes responsible for a pollen killer present in local natural populations of Arabidopsis thaliana.

Anthony Ricou, Matthieu Simon, Rémi Duflos, Marianne Azzopardi, Fabrice Roux, Françoise Budar, Christine Camilleri.

Gamete killers are genetic loci that distort segregation in the progeny of hybrids because the killer allele promotes the elimination of the gametes that carry the sensitive allele. They are widely distributed in eukaryotes and are important for understanding genome evolution and speciation. We had previously identified a pollen killer in hybrids between two distant natural accessions of Arabidopsis thaliana. This pollen killer involves three genetically linked genes, and we previously reported the identification of the gene encoding the antidote that protects pollen grains from the killer activity. In this study, we identified the two other genes of the pollen killer by using CRISPR-Cas9 induced mutants. These two genes are necessary for the killer activity that we demonstrated to be specific to pollen. The cellular localization of the pollen killer encoded proteins suggests that the pollen killer activity involves the mitochondria. Sequence analyses reveal predicted domains from the same families in the killer proteins. In addition, the C-terminal half of one of the killer proteins is identical to the antidote, and one amino acid, crucial for the antidote activity, is also essential for the killer function. Investigating more than 700 worldwide accessions of A. thaliana, we confirmed that the locus is subject to important structural rearrangements and copy number variation. By exploiting available de novo genomic sequences, we propose a scenario for the emergence of this pollen killer in A. thaliana. Furthermore, we report the co-occurrence and behavior of killer and sensitive genotypes in several local populations, a prerequisite for studying gamete killer evolution in the wild. This highlights the potential of the Arabidopsis model not only for functional studies of gamete killers but also for investigating their evolutionary trajectories at complementary geographical scales.

DOI: https://doi.org/10.1371/journal.pgen.1011451