Characterization of nuclear 18S rRNA gene sequence diversity and expression in an individual lake sturgeon (Acipenser fulvescens)

Abstract

The unexpected discovery of extensive intraindividual variation of the 18S rRNA gene in nine North American species of sturgeon (and its absence in the North American paddlefish) was described in a previous paper by Krieger and Fuerst (2002b). As part of the study, genomic 18S rRNA genes from a lake sturgeon (Acipenser fulvescens) individual were amplified by polymerase chain reaction (PCR), cloned and sequenced, resulting in the identification of at least 17 different sequence variants. Because of the number of variants detected and the improbability that such a large number of different alleles are required for survival, these sequence variants were subjected to further analyses (sequence comparison, phylogenetic and relative rate) to examine the possibility that some variants may be pseudogenes. The cDNA produced by reverse transcriptase (RT)-PCR amplification of 18S rRNA isolated from lake sturgeon liver tissue was also sequenced. The topology of the phylogenetic tree produced suggests a split of the sequence variants into two groups: paddlefish-like (PL) alleles and non-paddlefish-like (NPL) alleles. Relative rate comparisons of these two groups indicate that the alleles within the NPL allele group are evolving more quickly than those in the paddlefish-like (PL) group, and so are likely under relaxed functional constraints. Less than one-third of nucleotide changes in the non-paddlefish-like (NPL) alleles occur at positions that are considered to be highly conserved in a universal eukaryotic model of rRNA structure. No substitutions at eukaryotic universally conserved sites occur in the PL alleles. Analysis of the sequence of the RT-PCR product shows that a single lake sturgeon 18S rDNA sequence variant is expressed in major quantities in the liver, and that this single product is identical to the allele most similar in sequence to the paddlefish. These results provide support for the idea that many variants are unimportant for proper cellular function or are pseudogenes. Although concerted evolution has apparently failed to homogenize the many rDNA sequence variants found within sturgeon, the detection of a single major expressed sequence variant in lake sturgeon indicates that the expression of the variants is in fact under the control of selective factors.