bims-plasge 2022-11-13 papers

Issue of 2022–11–13
three papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Plant Cell. 2022 Nov 07. pii: koac318. [Epub ahead of print]

Structural insight into the activation of an Arabidopsis organellar C-to-U RNA editing enzyme by active site complementation.

Sachiko Toma-Fukai, Yuto Sawada, Ayako Maeda, Hikaru Shimizu, Toshiharu Shikanai, Mizuki Takenaka, Toshiyuki Shimizu.

RNA-binding pentatricopeptide repeat (PPR) proteins catalyze hundreds of cytidine to uridine (C-to-U) RNA editing events in plant organelles; these editing events are essential for proper gene expression. More than half of the PPR-type RNA editing factors, however, lack the DYW cytidine deaminase domain. Genetic analyses have suggested their cytidine deaminase activity arises by association with a family of DYW1-like proteins that contain an N-terminally truncated DYW domain, but their molecular mechanism has been unclear. Here, we report the crystal structure of the Arabidopsis thaliana DYW1 deaminase domain at 1.8 Å resolution. DYW1 has a cytidine deaminase fold lacking the PG box. The internal insertion within the deaminase fold shows an α-helical fold instead of the β-finger reported for the gating domain of the Arabidopsis thaliana ORGANELLE TRANSCRIPT PROCESSING 86. The substrate binding pocket is incompletely formed and appears to be complemented in the complex by the E2 domain and the PG box of the interacting PPR protein. In vivo RNA editing assays corroborate the activation model for DYW1 deaminase. Our study demonstrates the common activation mechanism of the DYW1-like proteins by molecular complementation of the DYW domain and reconstitution of the substrate-binding pocket.

Keywords: DYW deaminase; PPR protein; RNA editing enzyme; crystal structure

DOI: https://doi.org/10.1093/plcell/koac318

Int J Mol Sci. 2022 Nov 07. pii: 13659. [Epub ahead of print]23(21):

Fine Mapping and Candidate Gene Analysis of Pm36, a Wild Emmer-Derived Powdery Mildew Resistance Locus in Durum Wheat.

Domenica Nigro, Antonio Blanco, Luciana Piarulli, Massimo Antonio Signorile, Pasqualina Colasuonno, Emanuela Blanco, Rosanna Simeone.

Powdery mildew (PM) is an economically important foliar disease of cultivated cereals worldwide. The cultivation of disease-resistant varieties is considered the most efficient, sustainable and economical strategy for disease management. The objectives of the current study were to fine map the chromosomal region harboring the wild emmer PM resistance locus Pm36 and to identify candidate genes by exploiting the improved tetraploid wheat genomic resources. A set of backcross inbred lines (BILs) of durum wheat were genotyped with the SNP 25K chip array and comparison of the PM-resistant and susceptible lines defined a 1.5 cM region (physical interval of 1.08 Mb) harboring Pm36. The genetic map constructed with F2:3 progenies derived by crossing the PM resistant line 5BIL-42 and the durum parent Latino, restricted to 0.3 cM the genetic distance between Pm36 and the SNP marker IWB22904 (physical distance 0.515 Mb). The distribution of the marker interval including Pm36 in a tetraploid wheat collection indicated that the positive allele was largely present in the domesticated and wild emmer Triticum turgidum spp. dicoccum and ssp. dicoccoides. Ten high-confidence protein coding genes were identified in the Pm36 region of the emmer, durum and bread wheat reference genomes, while three added genes showed no homologous in the emmer genome. The tightly linked markers can be used for marker-assisted selection in wheat breeding programs, and as starting point for the Pm36 map-based cloning.

Keywords: Blumeria graminis; Triticum turgidum ssp. dicoccoides; backcross inbred lines; disease resistance; powdery mildew; powdery mildew candidate genes; wheat; wild emmer wheat

DOI: https://doi.org/10.3390/ijms232113659

Genome Res. 2022 Nov 09. pii: gr.276885.122. [Epub ahead of print]

Hybridization drives mitochondrial DNA degeneration and metabolic shift in a species with biparental mitochondrial inheritance.

Mathieu Hénault, Souhir Marsit, Guillaume Charron, Christian R Landry.

Mitochondrial DNA (mtDNA) is a cytoplasmic genome that is essential for respiratory metabolism. While uniparental mtDNA inheritance is most common in animals and plants, distinct mtDNA haplotypes can coexist in a state of heteroplasmy, either because of paternal leakage or de novo mutations. mtDNA integrity and the resolution of heteroplasmy have important implications, notably for mitochondrial genetic disorders, speciation, and genome evolution in hybrids. However, the impact of genetic variation on the transition to homoplasmy from initially heteroplasmic backgrounds remains largely unknown. Here, we use Saccharomyces yeasts, fungi with constitutive biparental mtDNA inheritance, to investigate the resolution of mtDNA heteroplasmy in a variety of hybrid genotypes. We previously designed 11 crosses along a gradient of parental evolutionary divergence using undomesticated isolates of Saccharomyces paradoxus and Saccharomyces cerevisiae Each cross was independently replicated 48 to 96 times, and the resulting 864 hybrids were evolved under relaxed selection for mitochondrial function. Genome sequencing of 446 MA lines revealed extensive mtDNA recombination, but recombination rate was not predicted by parental divergence level. We found a strong positive relationship between parental divergence and the rate of large-scale mtDNA deletions, which lead to the loss of respiratory metabolism. We also uncovered associations between mtDNA recombination, mtDNA deletion, and genome instability that were genotype-specific. Our results show that hybridization in yeast induces mtDNA degeneration through large-scale deletion and loss of function, with deep consequences for mtDNA evolution, metabolism and the emergence of reproductive isolation.

DOI: https://doi.org/10.1101/gr.276885.122