In Arabidopsis thaliana mitochondria 5′ end polymorphisms of nad4L-atp4 and nad3-rps12 transcripts are linked to RNA PROCESSING FACTORs 1 and 8

KEY MESSAGE: RNA 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. ABSTRACT: 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. SUPPLEMENTARY INFORMATION: The online version of this article contains supplementary material available (10.1007/s11103-021-01153-9).