A Case of Gene Fragmentation in Plant Mitochondria Fixed by the Selection of a Compensatory Restorer of Fertility-Like PPR Gene

Abstract

The high mutational load of mitochondrial genomes combined with their uniparental inheritance and high polyploidy favor the maintenance of deleterious mutations within populations. How cells compose and adapt to the accumulation of disadvantageous mitochondrial alleles remains unclear. Most harmful changes are likely corrected by purifying selection, however, the intimate collaboration between mitochondria- and nuclear-encoded gene products offers theoretical potential for compensatory adaptive changes. In plants, cytoplasmic male sterilities are known examples of nucleo-mitochondrial co-adaptation situations in which nuclear-encoded restorer of fertility (Rf) genes evolve to counteract the effect of mitochondria-encoded cytoplasmic male sterility (CMS) genes and restore fertility. Most cloned Rfs belong to a small monophyletic group, comprising 26 pentatricopeptide repeat (PPR) genes in Arabidopsis, called Rf-like (RFL). In this analysis, we explored the functional diversity of RFL genes in Arabidopsis and found that the RFL8 gene is not related to CMS suppression but essential for plant embryo development. In vitro-rescued rfl8 plantlets are deficient in the production of the mitochondrial heme-lyase complex. A complete ensemble of molecular and genetic analyses allowed us to demonstrate that the RFL8 gene has been selected to permit the translation of the mitochondrial ccmFN2 gene encoding a heme-lyase complex subunit which derives from the split of the ccmFN gene, specifically in Brassicaceae plants. This study represents thus a clear case of nuclear compensation to a lineage-specific mitochondrial genomic rearrangement in plants and demonstrates that RFL genes can be selected in response to other mitochondrial deviancies than CMS suppression.

MISF2 Encodes an Essential Mitochondrial Splicing Cofactor Required for nad2 mRNA Processing and Embryo Development in Arabidopsis thaliana

“…Embryo rescue by in vitro culture allows to establish certain Arabidopsis mutants showing germination-defective phenotypes [ 58 ]. Among these are a few mutants affected in mitochondria biogenesis and function, such as the cod1 [ 59 ], ndufv1 [ 60 ] cal1 / cal2 [ 61 , 62 ], nmat3 [ 63 ], or rfl8 [ 33 ] mutants. Therefore, white seeds contained in young siliques of heterozygous misf2 plants (i.e., 10~12 days post-anthesis, DPA), were sown on MS-agar plates supplemented with 1% sucrose and various vitamins (see Section 4 , Materials and Methods) and then transferred to a controlled growth chamber.…”

“…PPR proteins are recognized by a degenerate 35 amino-acid motif folding into two antiparallel helices connected by a short loop/turn [ 28 , 29 ]. In association with the complexity of plant mitochondria gene expression, PPR proteins have been shown to play multifarious functions in organellar RNA metabolism, such as RNA stability and protection [ 12 , 30 ], C-to-U RNA editing [ 13 ], mRNA translation [ 31 , 32 , 33 ], and group II intron splicing [ 11 , 12 , 34 , 35 , 36 ]. Members of the PPR family are also linked to fertility restoration, where they regulate the expression of mitochondrial CMS-associated ORFs [ 37 , 38 ].…”

The pentatricopeptide repeat protein MTSF3 is required fornad2mRNA stability and embryogenesis in Arabidopsis

“…If we exclude the ones showing no growth alterations, most mutants fall into two major phenotypical classes corresponding either to slow growing plants or to germination defective/embryo-lethal (EL) mutants (Colas des Francs- Small and Small, 2014). The first mutant class concerns almost exclusively complex I deficient plants whose loss was found to be non-lethal to plants, whereas EL mutants tend to be affected in latter stages of the respiratory chain, like in complex III or IV, or in cytochrome c biogenesis (Dahan et al, 2014;Nguyen et al, 2021). Nevertheless, very few examples of mutants affected in these late stages of the plant respiratory chain were characterized up to now and the embryo-lethality associated with the emb2794 (mtsf3) mutation led us to consider that it could reveal a new interesting case.…”

A unique C-terminal domain contributes to the molecular function of restorer-of-fertility proteins in plant mitochondria

“…Binding of RsRfo causes blockage of ribosome progression rather than induction of RNA cleavage (Wang et al 2021a) and Rf1b, unlike Rf1a, appears to trigger RNA degradation without causing a specific cleavage event (Wang et al 2006). Moreover, AtRFL8 that also lacks a C-terminal extension was shown not to induce RNA cleavage but rather act as a translational activator of the mitochondrial ccmFN2 transcript (Nguyen et al 2021). This apparent correlation between the C-terminal extensions and protein function triggered our interest to investigate these sequences in more detail.…”