Figure 7

Architectural conservation of cyclic nucleotide signaling genes. Deduced sequences of D. discoideum (Ddis) and D. purpureum (Dpur) proteins were analyzed by SMART [105] for the presence of functional domains, signal peptides and transmembrane helices. To build protein phylogenies, conserved shared functional domains were aligned using CLUSTAL-W [106] and edited when necessary in BioEdit [107] to juxtapose functionally essential amino acid residues. Regions that did not align unambiguously were deleted. For proteins with two similar domains (cyclases and cyclic nucleotide (cNMP) binding proteins), a tandem alignment of both domains was used, with the single domains of ACB and ACG used twice. Phylogenetic relationships between aligned sequences were determined by Bayesian inference [108] using a mixed amino acid model. Rate variation between sites was estimated by a gamma distribution with a proportion of invariable sites. Analyses were run for 100,000 generations or until the standard deviation of split frequences was <0.01. The phylogenetic trees are decorated with the domain architectures of the proteins, except for the D. mucoroides (Dmuc) and D. rosarium (Dros) cAMP receptor (cAR) sequences, which were derived from genes that were only partially amplified by PCR [79]. All trees are unrooted, except for the cAR tree, which is rooted on the single cAR of the group 3 taxon Dictyostelium minutum (Dmin). The posterior probabilities (BIPP) of nodes are represented by line thickness. (a) Cyclases; (b) cAMP receptors; (c) cNMP binding domains; (d) cNMP phosphodiesterases. Dpur protein IDs and, if available, dictyBase IDs: SGC, 153022 (DPU_G0054494); ACB, 154751 (DPU_G0058520); GCA, 151484 (DPU_G0075774); ACA, 51614 (DPU_G0071214); ACG, 38950 (DPU_G0061484); GbpC, 168746; GbpD, 88426 (DPU_G0055716); PdeD, 98774 (DPU_G0059600); PdeE, 56777 (DPU_G0059268); PkaR, 157660 (DPU_G0065616); cAR1, 99295 (DPU_G0064058); cAR2, 92050 (DPU_G0053090); Pde3, 34050 (DPU_G0053756); Pde4, 150656 (DPU_G0073898); PdsA, 98685 (DPU_G0058978); PdsB, 168741 (DPU_G0056384); PdsC, 91767 (DPU_G0073930). GenBank accession numbers for Ddis sequences: ACB, [GenBank:AAD50121]; GCA, [GenBank:CAB42641]; ACA, [GenBank:AAA33163]; ACG, [GenBank:Q03101]; GbpC, [GenBank:AAM34041]; GbpD, [GenBank:AAM34042]; PdeD, [GenBank:AAL06059]; PdeE, [GenBank:AAL06060]; PkaR, [GenBank:P05987]; cAR1, [GenBank:AAA33177]; cAR2, [GenBank:AAB25436]; cAR3, [GenBank:AAB25437]; cAR4, [GenBank:AAB32419]; Pde3, [GenBank:B0G0Y8]; Pde4, [GenBank:AAO59486]; PdsA, [GenBank:XP_637948]; Pde7, [GenBank:EAL62880]. GenBank accession numbers for Dmuc sequences: cAR1, [GenBank:ACF17575]; cAR2, [GenBank:ACF17576]; cAR3, [GenBank:ACF17577]; cAR4, [GenBank:ACF17578]. GenBank accession numbers for Dros sequences: cAR1, [GenBank:AAW24476]; cAR2, [GenBank:AAW24477]; cAR3, [GenBank:ACF17573]; cAR4, [GenBank:ACF17574]. GenBank accession number for Dmin cAR, [GenBank:AAS59250].