Abstract
Key messageRNA PROCESSING FACTORs 1 AND 8 (RPF1 and RPF8), both restorer of fertility like pentatricopeptide repeat proteins, are required for processing of dicistronic nad4L-atp4 and nad3-rps12 transcripts in Arabidopsis mitochondria. In mitochondria of Arabidopsis thaliana (Arabidopsis), the 5′ termini of many RNAs are generated on the post-transcriptional level. This process is still poorly understood in terms of both the underlying mechanism as well as proteins required. Our studies now link the generation of polymorphic 5′ extremities of the dicistronic nad3-rps12 and nad4L-atp4 transcripts to the function of the P-type pentatricopeptide repeat proteins RNA PROCESSING FACTORs 8 (RPF8) and 1 (RPF1). RPF8 is required to generate the nad3-rps12 -141 5′ end in ecotype Van-0 whereas the RPF8 allele in Col has no function in the generation of any 5′ terminus of this transcript. This observation strongly suggests the involvement of an additional factor in the generation of the -229 5′ end of nad3-rps12 transcripts in Col. RPF1, previously found to be necessary for the generation of the -228 5′ end of the major 1538 nucleotide-long nad4 mRNAs, is also important for the formation of nad4L-atp4 transcripts with a 5′ end at position -318 in Col. Many Arabidopsis ecotypes contain inactive RPF1 alleles resulting in the accumulation of various low abundant nad4L-atp4 RNAs which might represent precursor and/or degradation products. Some of these ecotypes accumulate major, but slightly smaller RNA species. The introduction of RPF1 into these lines not only establishes the formation of the major nad4L-atp4 dicistronic mRNA with the -318 5′ terminus, the presence of this gene also suppresses the accumulation of most alternative nad4L-atp4 RNAs. Beside RPF1, several other factors contribute to nad4L-atp4 transcript formation.
Highlights
Higher plant mitochondria contain DNA encoding several components essential for their crucial function in the cellular context and for plant fitness and viability (Gualberto and Newton 2017; Hammani and Giegé 2014)
In our efforts to identify and characterize proteins required for transcript maturation in plant mitochondria, we used circularized RNA (CR)-RT-PCRs to screen various Arabidopsis ecotypes for 5′ and 3′ end polymorphisms of nad4L-atp4 mRNAs (Fig. 1b)
To confirm that the distinct PCR product pattern originated from different nad4L-atp4 transcripts, a Northern blot analysis was performed with a probe amplified with primer pair Atnad4L-4/Atorf25-2 covering parts of both reading frames as well as the intergenic region and total RNA from Col, Got-7, Lov-5, Rrs-10, Rsch-4, Sap-0, and Sp-0
Summary
Higher plant mitochondria contain DNA encoding several components essential for their crucial function in the cellular context and for plant fitness and viability (Gualberto and Newton 2017; Hammani and Giegé 2014). P-class PPR proteins are characterized by a sequence of canonical P motifs, sometimes interspersed by other PPR motifs, containing more or less non-conserved amino acid sequences both at the N- and C-termini, respectively This protein class fulfills important roles in intron splicing and post-transcriptional 5′ and 3′ end processing of transcripts from chloroplasts and mitochondria (Barkan and Small 2014; Binder et al 2013; Rovira and Smith 2019; Wang et al 2017, 2018). Most of the so far identified factors belong to a group of PPR proteins, which are highly similar to restorer of fertility proteins identified in other plant species, where they restore cytoplasmic male sterility (Dahan and Mireau 2013; Fujii et al 2011) These proteins are characterized by high sequence variability and and many of them contain a conserved 25 amino acid-long C-terminus. Whether these proteins have additional molecular functions apart from RNA binding is unclear at present, as is the involvement of other proteins in 5′ transcript processing
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