Status of genes encoding the mitochondrial S1 ribosomal protein in closely-related legumes

The rps1 gene, which encodes ribosomal protein S1 of the mitochondrial ribosome in flowering plants, is located in the mitochondrion of some but not all species, and this is assumed to reflect multiple gene transfers to the nucleus. We investigated its status in legumes and found that in alfalfa, sweet clover and fenugreek, the mitochondrial-located rps1 is a pseudogene, in contrast to intact, transcribed and edited rps1 genes in the mitochondria of rest harrow, pea, soybean and bean. Among these lineages, the genomic environment upstream of rps1 differs, and this contrasts with a stable downstream linkage with the first two exons of the trans-split nad5 gene. Consequently, the rps1 transcript profiles differ for each of these closely-related species, and typically do not include monocistronic rps1 or nad5 mRNAs. In alfalfa, sweet clover and fenugreek, the functional rps1 gene is located in the nucleus and it is still flanked by residual non-coding mitochondrial sequences. Notably, the upstream ones provide part of the 5′ UTR as well as the 3′ splice site of an intron preceding rps1. This exploitation of non-coding mitochondrial sequences in nuclear gene activation adds to a growing list of mechanisms by which successful transfer of mitochondrial genes is achieved.