Department of Biosciences and Nutrition, Center for Biosciences at NOVUM, Karolinska Institute, S-141 83 Huddinge, Sweden.
Proc Natl Acad Sci U S A. 2010 Jul 20;107(29):12969-74. doi: 10.1073/pnas.0914241107. Epub 2010 Jul 6.
Cilia were present in the last eukaryotic common ancestor (LECA) and were retained by most organisms spanning all extant eukaryotic lineages, including organisms in the Unikonta (Amoebozoa, fungi, choanoflagellates, and animals), Archaeplastida, Excavata, Chromalveolata, and Rhizaria. In certain animals, including humans, ciliary gene regulation is mediated by Regulatory Factor X (RFX) transcription factors (TFs). RFX TFs bind X-box promoter motifs and thereby positively regulate >50 ciliary genes. Though RFX-mediated ciliary gene regulation has been studied in several bilaterian animals, little is known about the evolutionary conservation of ciliary gene regulation. Here, we explore the evolutionary relationships between RFX TFs and cilia. By sampling the genome sequences of >120 eukaryotic organisms, we show that RFX TFs are exclusively found in unikont organisms (whether ciliated or not), but are completely absent from the genome sequences of all nonunikont organisms (again, whether ciliated or not). Sampling the promoter sequences of 12 highly conserved ciliary genes from 23 diverse unikont and nonunikont organisms further revealed that phylogenetic footprints of X-box promoter motif sequences are found exclusively in ciliary genes of certain animals. Thus, there is no correlation between cilia/ciliary genes and the presence or absence of RFX TFs and X-box promoter motifs in nonanimal unikont and in nonunikont organisms. These data suggest that RFX TFs originated early in the unikont lineage, distinctly after cilia evolved. The evolutionary model that best explains these observations indicates that the transcriptional rewiring of many ciliary genes by RFX TFs occurred early in the animal lineage.
纤毛存在于最后的真核生物共同祖先（LECA）中，并被包括原生动物界（变形虫、真菌、领鞭毛虫和动物）、古植物界、吞噬体、色素体和根足动物在内的所有现存真核生物谱系中的大多数生物保留下来。在某些动物中，包括人类，纤毛基因的调控是由调节因子 X（RFX）转录因子（TF）介导的。RFX TF 结合 X 盒启动子基序，从而正向调节 >50 个纤毛基因。尽管在几种两侧对称动物中研究了 RFX 介导的纤毛基因调控，但对于纤毛基因调控的进化保守性知之甚少。在这里，我们探索了 RFX TF 和纤毛之间的进化关系。通过对>120 种真核生物的基因组序列进行采样，我们发现 RFX TF 仅存在于原生动物界生物（无论是否有纤毛）中，但完全不存在于所有非原生动物界生物（无论是否有纤毛）的基因组序列中。从 23 种不同的原生动物和非原生动物中 12 个高度保守的纤毛基因的启动子序列中采样，进一步表明 X 盒启动子基序序列的系统发育足迹仅存在于某些动物的纤毛基因中。因此，在非动物原生动物界和非原生动物界生物中，纤毛/纤毛基因与 RFX TF 和 X 盒启动子基序的存在与否之间没有相关性。这些数据表明，RFX TF 起源于原生动物谱系的早期，明显晚于纤毛的进化。能够最好地解释这些观察结果的进化模型表明，RFX TF 对许多纤毛基因的转录重布线发生在动物谱系的早期。
