Convergent Evolution of RFX Transcription Factors and Ciliary Genes Predated the Origin of Metazoans

Background: Intraflagellar transport (IFT) genes, which are critical for the development and function of cilia andflagella in metazoans, are tightly regulated by the Regulatory Factor X (RFX) transcription factors (TFs). However, howand when their evolutionary relationship was established remains unknown.Results: We have identified evidence suggesting that RFX TFs and IFT genes evolved independently and theirevolution converged before the first appearance of metazoans. Both ciliary genes and RFX TFs exist in all metazoans aswell as some unicellular eukaryotes. However, while RFX TFs and IFT genes are found simultaneously in all sequencedmetazoan genomes, RFX TFs do not co-exist with IFT genes in most pre-metazoans and thus do not regulate them inthese organisms. For example, neither the budding yeast nor the fission yeast possesses cilia although both have welldefinedRFX TFs. Conversely, most unicellular eukaryotes, including the green alga Chlamydomonas reinhardtii, havetypical cilia and well conserved IFT genes but lack RFX TFs. Outside of metazoans, RFX TFs and IFT genes co-exist onlyin choanoflagellates including M. brevicollis, and only one fungus Allomyces macrogynus of the 51 sequenced fungusgenomes. M. brevicollis has two putative RFX genes and a full complement of ciliary genes.Conclusions: The evolution of RFX TFs and IFT genes were independent in pre-metazoans. We propose that theirconvergence in evolution, or the acquired transcriptional regulation of IFT genes by RFX TFs, played a pivotal role in theestablishment of metazoan.