Accelerated evolution of functional plastid rRNA and elongation factor genes due to reduced protein synthetic load after the loss of photosynthesis in the chlorophyte alga Polytoma

Polytoma obtusum and Polytoma uvella are members of a clade of nonphotosynt hetic chlorophyte algae closely related to Chlamydomonas humicola and other photosynthetic members of the Chlamydomonadaceae. Descended from a nonphot osynthetic mutant, these obligate heterotrophs retain a plastid (leucoplast ) with a functional protein synthetic system, and a plastid genome (1pDNA) with functional genes encoding proteins required for transcription and tran slation. Comparative studies of the evolution of genes in chloroplasts and leucoplasts can identify modes of selection acting on the plastid genome. T wo plastid genes-rrn16, encoding the plastid small-subunit rRNA, and tufA, encoding elongation factor Tu-retain their functions in protein synthesis a fter the loss of photosynthesis in two nonphotosynthetic Polytoma clades bu t show a substantially accelerated rate of base substitution in the P. uvel la clade. The accelerated evolution of tufA is due, at least partly, to rel axed codon bias favoring codons that can be read without wobble, mainly in three amino acids. Selection for these codons may be relaxed because leucop lasts are required to synthesize fewer protein molecules per unit time than are chloroplasts (reduced protein synthetic load) and thus require a lower rate of synthesis of elongation factor Tu. Relaxed selection due to a lowe r protein synthetic load is also a plausible explanation for the accelerate d rate of evolution or rrn16, but the available data are insufficient to te st the hypothesis for this gene. The tufA and rrn16 genes in Polytoma ovifo rme, the sole member of a second nonphotosynthetic clade, are also function al but show no sign of relaxed selection.