Subcellular targeting of proteins and pathways during evolution.

The origin of mitochondria and chloroplasts were two of evolution’s all-time greatest hits, because both eukaryotes (including us) and plants (our food chain) owe their beginnings to those fateful endosymbiotic encounters. One of the more interesting aspects about chloroplast and mitochondrial symbioses is the process of gene transfer that relocated genes from those endosymbionts to the chromosomes of the host. Gene transfer and the reimport of encoded products is what welds endosymbionts and their host into a new evolutionary unit. Gene transfer from endosymbionts is hardly a new concept, as the introductory quote from Wallin (1925), who was writing about mitochondria, points out. Ninety years later, we are still in the process of more fully understanding how the transfer of genes from organelles to the nucleus and the subsequent (re-)routing of those gene products to various possible destinations within the cytosol impacts cell evolution. In this issue of New Phytologist, Baudisch et al. (pp. 80–90) deliver an important contribution on the topic. Baudisch et al. investigated the targeting of Arabidopsis thaliana mitochondrial and plastidal proteins encoded by nuclear genes that stem from cyanobacteria (plastids) and a-proteobacteria (mitochondria) and that are predicted by current targeting prediction software to be specifically imported into the respective organelles. Among 16 well-chosen proteins tested, 10 are targeted to both organelles simultaneously, as localization studies in transformed plants and in vitro organelle import assays show. Although dual targeting has been known for some time (Peeters & Small, 2001), systematic studies to assess its prevalence have been lacking. The new findings indicate that dual targeting is much more widespread than previously assumed. But the converse formulation, namely that targeting is ostensibly much less specific than most of us currently think, might turn out to be more significant. Why should we think that proteins should be specifically targeted to plastids and mitochondria in the first place? Theory on the topic probably takes root in a paper byWeeden (1981) whowas considering nuclear encoded chloroplast-cytosol isoenzymes involved in sugar phosphate metabolism, like phosphoglucoisomerase. The gene for the cytosolic enzyme should reflect the evolution of the host lineage that acquired the chloroplast, while the gene for the chloroplast isoenzyme should be an acquisition from cyanobacteria, with the product being specifically targeted back to the organelle in which it originally operated. This reasoning, often implicit in evolutionary studies, is called the ‘product specificity corollary’ to endosymbiotic theory. Work on a variety of chloroplast cytosol isoenzymes later showed that there is no strict correlation between gene origin and protein targeting (Martin & Schnarrenberger, 1997): once a copy of an organelle gene becomes established in the nucleus, its product is, over evolutionary time, free to explore various targeting possibilities within the cell and thus contribute to natural variation. A gene for an organelle-encoded protein, if copied to the nucleus (Allen, 1993) in such a way as to generate a useful promoter, will first tend to encode a cytosolic protein, for lack of the N-terminal targeting sequences that are typically thought to direct proteins to the TIC/ TOC translocon of the plastid (Strittmatter et al., 2010) or the TIM/TOM translocon of the mitochondrion (Dolezal et al., 2006). However, as many as 30% of yeast mitochondrial proteins now seem to have other targeting signals than the canonical N-terminal presequences (Chacinska et al., 2009), so we are still a far cry from understanding which signals, exactly, direct the sub-cellular compartmentation of proteins. The work by Baudisch et al. points the way towards large-scale, perhaps genome-wide, investigations that would provide the needed data.