Evolutionary proteomics uncovers ciliary signaling components

Monika Abedin Sigg; Tabea Menchen; Jeffery Johnson; Chanjae Lee; Semil P. Choksi; Galo Garcia; Henriette Busengdal; Gerard Dougherty; Petra Pennekamp; Claudius Werner; Fabian Rentzsch; Nevan Krogan; John B. Wallingford; Heymut Omran; Jeremy F. Reiter

Conversely, a small subset of proteins detected in the early gastrula whole cilia fraction were not 188 detected in the ciliary fraction, likely due to enrichment by hydrophilic interaction 189 chromatography. All other sea urchin samples were analyzed exclusively by reverse phase 190 chromatography. As expected, previously identified axonemal proteins (e.g., IFTs, motor 191 proteins, Tektins) were enriched in the axonemal fraction ( Figure 2C ). Also as expected, 192 previously identified ciliary membrane-associated proteins (e.g., PKD1, BBS3, RAB8A) were 193 enriched in the membrane plus matrix fraction ( Figure 2C From the isolated cilia of three organisms, we identified peptides corresponding to over 200 3,000 proteins in total (Table 1 and S1). As we are most interested in the evolution of ciliary 201 signaling in the progression from the unicellular ancestors of animals to humans, we focused on 202 those proteins with a homolog in mammals. BLAST identified 1,266 ciliome proteins with a 203 homolog in mouse (Table 1 and S1), a set we termed the 'conserved ciliome'. As expected based 204 on their evolutionary distances to mammals, the sea urchin ciliome contains the greatest number 205 of mammalian homologs (1, 012) , followed by the sea anemone (511) and choanoflagellate 206 ciliomes (311), respectively (Table 1, Figure 3A ). 207