Ancient mechanisms for the evolution of the bicoid homeodomain's function in fly development

Abstract

The ancient mechanisms that caused developmental gene regulatory networks to diversify among distantly related taxa are not well understood. Here we use ancestral protein reconstruction, biochemical experiments, and developmental assays of transgenic animals carrying reconstructed ancestral genes to investigate how the transcription factor Bicoid (Bcd) evolved its central role in anterior-posterior patterning in flies. We show that most of Bcd’s derived functions are attributable to evolutionary changes within its homeodomain (HD) during a phylogenetic interval >140 million years ago. A single substitution from this period (Q50K) accounts almost entirely for the evolution of Bcd’s derived DNA specificity in vitro. In transgenic embryos expressing the reconstructed ancestral HD, however, Q50K confers activation of only a few of Bcd’s transcriptional targets and yields a very partial rescue of anterior development. Adding a second historical substitution (M54R) confers regulation of additional Bcd targets and further rescues anterior development. These results indicate that two epistatically interacting mutations played a major role in the evolution of Bcd’s controlling regulatory role in early development. They also show how ancestral sequence reconstruction can be combined with in vivo characterization of transgenic animals to illuminate the historical mechanisms of developmental evolution.

Arthropod segmentation

“…Spatial information is usually provided by a novel anterior patterning centre (i.e. a morphogen gradient such as Bicoid; Liu et al, 2018;McGregor, 2005), which regulates gap gene expression. Gap genes pass this information to the primary pair-rule genes, through newly evolved regulatory elements (SSEs).…”

Evolutionary Dynamics of the SKN-1 → MED → END-1,3 Regulatory Gene Cascade inCaenorhabditisEndoderm Specification

“…Bcd specifies anterior fates in early cyclorrhaphan embryos, while outside of this group bcd is not found, and other factors play an analogous role (Lynch et al 2006;McGregor 2005). Bcd arose as a duplicate of the Hox gene Zen, and likely acquired derived DNA-binding characteristics primarily through two missense mutations in the DNA-binding domain (Liu et al 2018;McGregor 2005). From studies in the flour beetle Tribolium, which lacks bcd, it is hypothesized that Bcd took over functions of some of its downstream gap gene targets, which it then became an activator of (McGregor 2005).…”

Structural studies of geranylgeranylglyceryl phosphate synthase, a prenyltransferase found in thermophilic Euryarchaeota

“…Ecological parameters affect protein function, and thus also affect the evolution of the amino-acid sequences. Therefore, the use of phylogenetic analyses in assessing protein function potentiates the broader understanding of protein function (see, for example, Liu et al, 2018).…”

“…ASR is a method by which ancestral character states can be extrapolated from those in living taxa (Cunningham et al, 1998). The ASR methodology has been applied to questions exploring the evolution of discrete and continuous character states (see, for example, Reyes et al, 2018) as well as the evolution of amino-acid sequences (Liu et al, 2018;Cai et al, 2004). Furthermore, ASR strategies have also targeted the ancestral reconstruction of niche habitability, using temperature as an ecological character (see, for example, Vieites et al, 2009).…”