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
D. Vernon et al., 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, MOL BIOL EV, 18(9), 2001, pp. 1810-1822
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.