Coevolution in bicoid‐dependent promoters and the inception of regulatory incompatibilities among species of higher Diptera

Abstract

To what extent and in what way do gene promoters and their transacting regulatory proteins coevolve? In this and in earlier publications we show that the Bicoid-dependent promoters of the segmentation genes hunchback and tailless in species of higher Diptera (Drosophila, Musca, Calliphora, and Lucilia) are different with respect to the copy number, spacing, sequence, and orientation of Bicoid binding sites. At the same time there are significant amino acid differences in the Bicoid homeodomain. To test these interspecific differences, we used a series of functional assays, starting with the analysis of Bicoid binding affinities of individual sites, through to transgene rescue experiments, to compare within-species with between-species mixtures of Bicoid homeodomains and hunchback or tailless promoters. We observed that components taken from different species interact with less efficiency compared with those taken from within the same species. Our interpretation is that such interspecific incompatibilities are a consequence of interactive genetic elements coevolving one with another, hence maintaining functional compatibility within each species. At the same time such a process allows differences to accumulate between species regarding the precise molecular basis whereby the common function is effected.

Compensatory cis-trans Evolution and the Dysregulation of Gene Expression in Interspecific Hybrids of Drosophila

“…We can show whether, for individual genes, the interaction of the trans-regulatory elements from one species with the cis-regulatory elements of the other is responsible for the dysregulation in the hybrid. This model might be most appropriate for genes whose cis-and trans-regulatory elements have evolved since the time that the parental species became reproductively isolated (e.g., Shaw et al 2002). It is this hypothesis that we set out to examine for a sample of genes.…”

“…Direct experimental confirmation that cis-and trans-regulatory elements have coevolved by compensatory changes would require (1) characterization of the genetic regulatory elements and (2) measurements of gene expression of each parental allele in the genetic background of the other species. The key variables of the model, such as binding affinity and number of binding sites in the promoter, can be assayed (e.g., Oda et al 1998;Stormo and Fields 1998;Shaw et al 2002). Furthermore, the requisite technology exists to transfer individual Drosophila genes and their promoters between species (e.g., Laurie et al 1990;Wittkopp et al 2002).…”

“…One of the few examples of cis-trans-regulatory incompatibilities that have been identified is between bicoid and its binding sites in the tailless and hunchback promoters in D. melanogaster and Musca domestica. In most interactions, the bicoid protein from one species has a higher affinity for binding sites from the same species, but in the case of the Musca Bicoid protein, incompatibility is manifested through its higher affinity for the tailless promoter of both species (Shaw et al 2002). Compensatory evolution can therefore occur at the cis-cis-, transtrans-, and cis-trans-regulatory levels.…”

“…This can be achieved in many ways, but we concentrate on cases in which regulatory compensation is brought about by differences in the number of binding sites (n, a cis effect) balanced against differences in the expression level or binding affinity of the transcription factor (A, a trans effect). Other scenarios can be readily imagined (e.g., Shaw et al 2002), but we focus on this mechanism because it can evidently lead to a rapid increase in genetic variation (Stone and Wray 2001).…”

Evolution of cis-regulatory sequence and function in Diptera

“…Despite this conservation, hb cisregulatory elements have undergone changes in primary sequence that affect the number and organization of binding sites, especially for Bicoid (Hancock et al, 1999;McGregor et al, 2001b). Biochemical and transgenic experiments demonstrate that the DNA binding domain of the Bicoid protein coevolved with the binding sites in the hb promoter to maintain their regulatory interaction (Shaw et al, 2002). Similar coevolution of transcription factor specificity and cis-regulatory binding sites has been invoked to explain divergent bristle locations between D. melanogaster and D. simulans and as a possible cause for the divergence of the D. erecta eve stripe 2 enhancer (Ludwig et al, 2005).…”