bims-plasge 2023-03-19 papers

New Phytol. 2023 Mar 15.

MSP1 encodes an essential RNA-binding PPR factor required for nad1 maturation and complex I biogenesis in Arabidopsis mitochondria.

Corinne Best, Ron Mizrahi, Rana Edris, Hui Tang, Hagit Zer, Catherine Colas des Francs-Small, Omri M Finkel, Hongliang Zhu, Ian D Small, Oren Ostersetzer-Biran.

Mitochondrial biogenesis relies on nuclearly-encoded factors, which regulate the expression of the organellar-encoded genes. Pentatricopeptide repeat (PPR) proteins constitute a major gene-family in angiosperms that is pivotal in many aspects of mitochondrial (mt)RNA metabolism (e.g., trimming, splicing or stability). Here, we report the analysis of MITOCHONDRIA STABILITY/PROCESSING PPR FACTOR1 (MSP1, At4g20090), a canonical PPR protein that is necessary for mitochondrial functions and embryo-development. Loss-of-function allele of MSP1 leads to seed-abortion. Here, we employed an embryo-rescue method for the molecular characterization of msp1 mutants. Our analyses reveal that msp1 embryogenesis fails to proceed beyond the heart/torpedo stage as a consequence of a nad1 pre-RNA processing defect, resulting in the loss of respiratory complex I activity. Functional complementation confirmed that msp1 phenotypes result from a disruption of the MSP1 gene. In Arabidopsis, the maturation of nad1 involves the processing of three RNA-fragments, nad1.1, nad1.2 and nad1.3. Based on biochemical analyses and mtRNA profiles of wild-type and msp1 plants, we concluded that MSP1 facilitates the generation of the 3' terminus of nad1.1 transcript, a prerequisite for nad1 exons a-b splicing. Our data substantiate the importance of mtRNA metabolism for the biogenesis of the respiratory system during early plant life.

Keywords: 3’-end processing; Arabidopsis; MITOCHONDRIA STABILITY/PROCESSING PPR FACTOR1 (MSP1); Pentatricopeptide (PPR) proteins; RNA metabolism; group II; introns; mitochondria; splicing

DOI: https://doi.org/10.1111/nph.18880

Mol Phylogenet Evol. 2023 Mar 13. pii: S1055-7903(23)00060-X. [Epub ahead of print] 107760

Rate accelerations in plastid and mitochondrial genomes of Cyperaceae occur in the same clades.

Chaehee Lee, Tracey A Ruhlman, Robert K Jansen.

Cyperaceae, the second largest family in the monocot order Poales, comprises more than 5,500 species and includes the genus Eleocharis with ∼ 250 species. A previous study of complete plastomes of two Eleocharis species documented extensive structural heteroplasmy, gene order changes, high frequency of dispersed repeats along with gene losses and duplications. To better understand the phylogenetic distribution of gene and intron content as well as rates and patterns of sequence evolution within and between mitochondrial and plastid genomes of Eleocharis and Cyperaceae, an additional 29 Eleocharis organelle genomes were sequenced and analyzed. Eleocharis experienced extensive gene loss in both genomes while loss of introns was mitochondria-specific. Eleocharis has higher rates of synonymous (dS) and nonsynonymous (dN) substitutions in the plastid and mitochondrion than most sampled angiosperms, and the pattern was distinct from other eudicot lineages with accelerated rates. Several clades showed higher dS and dN in mitochondrial genes than in plastid genes. Furthermore, nucleotide substitution rates of mitochondrial genes were significantly accelerated on the branch leading to Cyperaceae compared to most angiosperms. Mitochondrial genes of Cyperaceae exhibited dramatic loss of RNA editing sites and a negative correlation between RNA editing and dS values was detected among angiosperms. Mutagenic retroprocessing and dysfunction of DNA replication, repair and recombination genes are the most likely cause of striking rate accelerations and loss of edit sites and introns in Eleocharis and Cyperaceae organelle genomes.

Keywords: Cyperaceae; Eleocharis; mitogenome; plastome; substitution rate

DOI: https://doi.org/10.1016/j.ympev.2023.107760

Theor Appl Genet. 2023 Mar 13. 136(3): 56

A novel 7-base pair deletion at a splice site in MS-2 impairs male fertility via premature tapetum degradation in common bean (Phaseolis vulgaris L.).

Kun Xu, Jinlong Zhu, Ning Guo, Jinyu Liu, Hong Zhai, Xiaobin Zhu, Yi Gao, Hongyan Wu, Zhengjun Xia.

KEY MESSAGE: A novel splice-site mutation in the P. vulgarisgene for TETRAKETIDE α-PYRONE REDUCTASE 2 impairs male fertility, and parthenocarpic pod development can be improved by external application of IAA. Snap bean (Phaseolus vulgaris L.) is an important vegetable crop in many parts of the world, and the main edible part is the fresh pod. Here, we report the characterization of the genic male sterility (ms-2) mutant in common bean. Loss of function of MS-2 accelerates degradation of the tapetum, resulting in a complete male sterility. Through fine-mapping, co-segregation, and re-sequencing analysis, we identified Phvul.003G032100, which encodes the TETRAKETIDE α-PYRONE REDUCTASE 2 (PvTKPR2) protein in common bean, as the causal gene for MS-2. PvTKPR2 is predominantly expressed at the early stages of flower development. A novel 7-bp (+ 6028 bp to + 6034 bp) deletion mutation spans the splice site between the fourth intron and fifth exon, leading to a 9-bp deletion in transcribed mRNA and a 3-amino acid (G210M211V212) deletion in the protein coding sequence of the PvTKPR2ms-2 gene. The 3-D structural changes in the protein due to the mutation may impair the activities of NAD-dependent epimerase/dehydratase and the NAD(P)-binding domains of PvTKPR2ms-2 protein. The ms-2 mutant plants produce many small parthenocarpic pods, and the size of the pods can be doubled by external application of 2 mM indole-3-acetic acid (IAA). Our results demonstrate that a novel mutation in PvTKPR2 impairs male fertility through premature degradation of the tapetum.

DOI: https://doi.org/10.1007/s00122-023-04255-8