Low-level ectopic expression of Fushi tarazu in Drosophila melanogaster results in ftzUal/Rpl-like phenotypes and rescues ftz phenotypes

Phenotypic Nonspecificity as the Result of Limited Specificity of Transcription Factor Function

Drosophila transcription factor (TF) function is phenotypically nonspecific. Phenotypic nonspecificity is defined as one phenotype being induced or rescued by multiple TFs. To explain this unexpected result, a hypothetical world of limited specificity is explored where all TFs have unique random distributions along the genome due to low information content of DNA sequence recognition and somewhat promiscuous cooperative interactions with other TFs. Transcription is an emergent property of these two conditions. From this model, explicit predictions are made. First, many more cases of TF nonspecificity are expected when examined. Second, the genetic analysis of regulatory sequences should uncover cis-element bypass and, third, genetic analysis of TF function should generally uncover differential pleiotropy. In addition, limited specificity provides evolutionary opportunity and explains the inefficiency of expression analysis in identifying genes required for biological processes.

Non-specificity of transcription factor function in Drosophila melanogaster

A major problem in developmental genetics is how HOX transcription factors, like Proboscipedia (PB) and Ultrabithorax (UBX), regulate distinct programs of gene expression to result in a proboscis versus a haltere, respectively, when the DNA-binding homeodomain (HD) of HOX transcription factors recognizes similar DNA-binding sequences. Indeed, the lack of DNA-binding specificity is a problem for all transcription factors (TFs), as the DNA-binding domains generally recognize small targets of five to six bases in length. Although not the initial intent of the study, I found extensive non-specificity of TF function. Multiple TFs including HOX and HD-containing and non-HD-containing TFs induced both wingless and eyeless phenotypes. The TFs Labial (LAB), Deformed (DFD), Fushi tarazu (FTZ), and Squeeze (SQZ) induced ectopic larval thoracic (T) 1 beard formation in T2 and T3. The TF Doublesex male (DSX^M) rescued the reduced maxillary palp pb phenotype. These examples of non-specificity of TF function across classes of TFs, combined with previous observations, compromise the implicit, initial assumption often made that an intrinsic mechanism of TF specificity is important for function. Interestingly, the functional complementation of the pb phenotype may suggest a larger role for regulation of expression of TFs in restriction of function as opposed to an intrinsic specificity of TF function. These observations have major ramifications for analysis of functional conservation in evolution and development.

Differential pleiotropy and HOX functional organization

Key studies led to the idea that transcription factors are composed of defined modular protein motifs or domains, each with separable, unique function. During evolution, the recombination of these modular domains could give rise to transcription factors with new properties, as has been shown using recombinant molecules. This archetypic, modular view of transcription factor organization is based on the analyses of a few transcription factors such as GAL4, which may represent extreme exemplars rather than an archetype or the norm. Recent work with a set of Homeotic selector (HOX) proteins has revealed differential pleiotropy: the observation that highly-conserved HOX protein motifs and domains make small, additive, tissue specific contributions to HOX activity. Many of these differentially pleiotropic HOX motifs may represent plastic sequence elements called short linear motifs (SLiMs). The coupling of differential pleiotropy with SLiMs, suggests that protein sequence changes in HOX transcription factors may have had a greater impact on morphological diversity during evolution than previously believed. Furthermore, differential pleiotropy may be the genetic consequence of an ensemble nature of HOX transcription factor allostery, where HOX proteins exist as an ensemble of states with the capacity to integrate an extensive array of developmental information. Given a new structural model for HOX functional domain organization, the properties of the archetypic TF may require reassessment.