Site-directed mutations reveal long-range compensatory interactions in the Adh gene of Drosophila melanogaster

Abstract

Long-range interactions between the 5 and 3 ends of mRNA molecules have been suggested to play a role in the initiation of translation and the regulation of gene expression. To identify such interactions and to study their molecular evolution, we used phylogenetic analysis to generate a model of mRNA higher-order structure in the Adh transcript of Drosophila melanogaster. This model predicts long-range, tertiary contacts between a region of the protein-encoding sequence just downstream of the start codon and a conserved sequence in the 3 untranslated region (UTR). To further examine the proposed structure, site-directed mutations were generated in vitro in a cloned D. melanogaster Adh gene, and the mutant constructs were introduced into the Drosophila germ line through P-element mediated transformation. Transformants were spectrophotometrically assayed for alcohol dehydrogenase activity. Our results indicate that transformants containing a silent mutation near the start of the proteinencoding sequence show an Ϸ15% reduction in alcohol dehydrogenase activity relative to wild-type transformants. This activity can be restored to wild-type levels by a second, compensatory mutation in the 3 UTR. These observations are consistent with a higher-order structure model that includes long-range interactions between the 5 and 3 ends of the Adh mRNA. However, our results do not fit the classical compensatory substitution model because the second mutation by itself (in the 3 UTR) did not show a measurable reduction in gene expression.There is a growing body of evidence for functional, long-range interactions between the 5Ј and 3Ј ends of eukaryotic mRNA molecules. Tarun and Sachs (1) have shown that a protein which binds to the 3Ј end of yeast mRNA is involved in the initiation of translation which occurs at the 5Ј end. Similarly, in Drosophila, proteins that bind to an mRNA's 3Ј untranslated region (UTR) have been shown to affect levels of translation (2, 3). In addition to these studies of protein-protein interactions, several sources have suggested direct RNA-RNA pairings between the two ends of mRNA molecules. Konings et al. (4) used a free-energy minimization algorithm to predict folding patterns for 38 eukaryotic mRNAs. Their results indicate a common pattern of mRNA folding, where the 3Ј UTR forms contacts with the coding region just downstream of the start codon. Stephan and Kirby (5) used a phylogenetic comparison method to predict mRNA secondary structures in Drosophila and found evidence for long-range pairings between the 3Ј UTR and the protein-encoding region. These findings raise a number of important questions. For instance, which nucleotides are involved in RNA-RNA interactions and how are they arranged into secondary and tertiary pairing regions? Do the currently available models describe the evolution of compensatory mutations adequately? To begin to address these questions, we have focused on identifying elements of the Adh mRNA higher-order structure in Drosophila melanogaster.Adh produces two deve...

‘Escaping’ the X chromosome leads to increased gene expression in the male germline of Drosophila melanogaster

“…Indeed, we find that the mini-white gene, which is present in all of our transformation vectors, shows expression patterns consistent with dosage compensation in the somatic (eye) tissue (Table 3). This is in agreement with previous studies reporting that, in males, X-linked alcohol dehydrogenase (Adh) transgenes show higher expression than those inserted on autosomes (Laurie-Ahlberg and Stam, 1987;Parsch et al, 1997). These findings indicate that the reduced X-linked expression seen for our testis-expressed transgenes is not an artifact of the P-element vector used for transformation, as this pattern is not observed for somatically expressed transgenes.…”

Experimentally Increased Codon Bias in the DrosophilaAdhGene Leads to an Increase in Larval, But Not Adult, Alcohol Dehydrogenase Activity

“…None of these minor differences in local structures appear to be sufficient to differentially inhibit the helicase activity of the ribosome, which has been experimentally demonstrated to be capable of melting a highly stable 27-bp helix (À52.1 kcal/mol) without dissociation from the mRNA (Takyar et al 2005). Furthermore, the 7up mutations did not alter any of the putative secondary structural elements identified by previous covariation analysis of multiple Drosophila species or by previous experimental manipulation (Kirby et al 1995;Parsch et al 1997;Carlini et al 2001;Chen and Stephan 2003;Baines et al 2004). We also determined a consensus mRNA secondary structure for Adh coding sequences of 12 Drosophila species from the recent 12 genomes project, using RNAalifold (Gruber et al 2008).…”

Dobzhansky–Muller incompatibilities in protein evolution

“…Known cases of epistatic selection in rRNAs and mRNAs are due to one obvious mechanism, Watson-Crick pairing of nucleotides that maintains secondary structure (28)(29)(30). In contrast, studies of second-site intragenic suppression of missense mutations revealed a variety of mechanisms of molecular compensation in proteins (15)(16)(17)(18)(19).…”

“…Such differences may involve mild DM incompatibilities, with some combinations of states having reduced but nonzero fitness. For selection acting on RNAs, such DM incompatibilities can occur even between polymorphic sites within a population (30). However, here we considered mostly lethal DM incompatibilities, because almost all pathogenic mutations causing Mendelian diseases would be lethal to a human under natural conditions, at least when homozygous.…”