Mitochondrial S1 ribosomal protein genes in legumes: Expression and transfer to the nucleus during evolution

The gene encoding the mitochondrial S1 ribosomal protein (rps1 ) is regarded as being among the most dynamic with respect to gene transfer from the mitochondrion to the nucleus during flowering plant evolution. To provide a detailed characterization of the rps1 gene, including transcriptional status and transcript editing, as well as to address issues surrounding its transfer to the nucleus, I examined mitochondrial- and nuclear-located rps1 sequences in closely-related legume species. I found that this gene is nuclear-located in alfalfa and its very close relatives, and is a pseudogene in their mitochondria. In contrast, the functional rps1 is mitochondrial-located in legume species that are slightly more distantly-related. The nuclear-located copies have retained mitochondrial-type upstream sequences and these provide part of the rps1 5' UTR, and the 3' splice site of an upstream intron. This is the first such documented case and illustrates that sequences of mitochondrial origin can be used as nuclear-specific expression elements. From comparative sequence analysis, I inferred that this single transfer event occurred recently in legume evolution. As such, the conservation among rps1-associated sequences permitted the evaluation of adaptive changes that occurred following integration into the nuclear genome.;By sequencing rps1 (and psirps1) flanking regions in the mitochondria of these legumes, I found that rps1 is linked downstream to the first two exons of nad5 , yet in each lineage, the genomic environment greater than ∼60 nt upstream of rps1 differs. Northern analyses suggest that the lineage-specific upstream sequences contribute to the variation in transcript profiles, which are complex in part due to the cis- and trans-arrangement of the five exons of nad5. Variation among homologous sequences immediately preceding mitochondrial-located rps1 in legumes was observed, and using a bioinformatics approach, a broad range of sequence conservation (including non-homology) was seen upstream of protein-coding genes located in the seven completely-sequenced flowering plant mitochondrial genomes. This along with the absence of an RNA-binding domain from the mitochondrial S1 ribosomal protein, and the divergence of the 3' end of the SSU rRNA from that in bacteria point to the use of a non-classical-bacterial type of ribosome binding in initiator codon recognition. The duplication and recruitment of mitochondrial upstream sequences by multiple genes, as well as the available copies of such sequences that are dispersed in intergenic regions may be an indication of how plant mitochondrial gene expression systems tolerate (or exploit) the highly-recombinogenic genome.