Lynch, 2000). Alternatively, the progressive accumulation of detrimental mutations in asexual mt genomes by Muller's ratchet may favor transfer of genes to the nucleus. Evidence for Muller's ratchet has been found in tRNA genes of animal mitochondria (Lynch, 1996) and in the genomes of endosymbiotic bacteria (Moran, 1996). However, the rate of nucleotide substitutions is very low in plant mitochondria (about 10-fold lower than in the nucleus), which should counterbalance the effects of Muller's ratchet (Martin and Herrman, 1998; Race et al., 1999) and negate (for plants) the hypothesis (Allen and Raven, 1996) that a nuclear location is favored because it provides relief from the effects of oxygen free radical damage incurred by organellar genes. Selection for a small, compact genome, although perhaps operating in other eukaryotes, is unlikely to be a factor favoring continued gene transfer in plants, because plant mt genomes readily incorporate and retain foreign DNA (Nugent and Palmer, 1988; Palmer, 1992; Unseld et al., 1997; Cho et al., 1998; Marienfeld et al., 1999) and are very large and mostly noncoding (Ward et al., 1981; Palmer, 1990, 1992; Unseld et al., 1997; Marienfeld et al., 1999). Finally, there is the possibility that genes for some organellar proteins may be better regulated in the nucleus (Thorsness and Weber, 1996). Although this possibility is intriguing, we are unaware of any evidence to support or refute it.
Why are a few protein genes preferentially retained by mt genomes across all or most eukaryotes? One view is that the products of these genes, all of which function in respiration, are highly hydrophobic and difficult to both import into mitochondria and properly insert (post-translationally) into the inner mt membrane (see, e.g., Popot and de Vitry, 1990; Thorsness and Weber, 1996; Palmer, 1997). Evidence for this includes experiments in which cytoplasmically synthesized cytochrome b, a highly hydrophobic protein with eight transmembrane helices, could not be imported in its entirety, with successful import limited to regions comprising only three to four transmembrane domains (Claros et al., 1995). In general, genes whose products have many hydrophobic transmembrane domains are usually located in the mitochondrion whereas genes whose products have few such domains are more often transferred to the nucleus (Popot and de Vitry, 1990; Gray et al., 1998). Indeed, the only two protein genes contained in all of the many completely sequenced mt genomes encode what are by some criteria (Claros et al., 1995) the two most hydrophobic proteins present in the mitochondrion, cytochrome b and subunit 1 of cytochrome oxidase (Gray et al., 1998; Gray, 1999). Although the hydrophobicity hypothesis cannot account for the distribution of every mt gene in every eukaryote, it seems likely to be a factor favoring the retention of certain respiratory genes. A second hypothesis for retention of certain genes in organelles is that their products are toxic when present in the cytosol or in some other, inappropriate cellular compartment to