Analysis of septins across kingdoms reveals orthology and new motifs

Abstract

Background: Septins are cytoskeletal GTPase proteins first discovered in the fungus Saccharomyces cerevisiae where they organize the septum and link nuclear division with cell division. More recently septins have been found in animals where they are important in processes ranging from actin and microtubule organization to embryonic patterning and where defects in septins have been implicated in human disease. Previous studies suggested that many animal septins fell into independent evolutionary groups, confounding cross-kingdom comparison.

Results: In the current work, we identified 162 septins from fungi, microsporidia and animals and analyzed their phylogenetic relationships. There was support for five groups of septins with orthology between kingdoms. Group 1 (which includes S. cerevisiae Cdc10p and human Sept9) and Group 2 (which includes S. cerevisiae Cdc3p and human Sept7) contain sequences from fungi and animals. Group 3 (which includes S. cerevisiae Cdc11p) and Group 4 (which includes S. cerevisiae Cdc12p) contain sequences from fungi and microsporidia. Group 5 (which includes Aspergillus nidulans AspE) contains sequences from filamentous fungi. We suggest a modified nomenclature based on these phylogenetic relationships. Comparative sequence alignments revealed septin derivatives of already known G1, G3 and G4 GTPase motifs, four new motifs from two to twelve amino acids long and six conserved single amino acid positions. One of these new motifs is septin-specific and several are group specific.

Conclusion: Our studies provide an evolutionary history for this important family of proteins and a framework and consistent nomenclature for comparison of septin orthologs across kingdoms.

Figure 1

Typical septin structure. Septin sequences range from about three hundred to six hundred amino acids. Septins contain the conserved GTP_CDC binding domain with three motifs: G1, GxxxxGK [ST] (amino acids 126–135 in S. cerevisiae Cdc3p); G3, DxxG (amino acids 204–209 in S. cerevisiae Cdc3p); and G4, xKxD (amino acids 280–289 in S. cerevisiae Cdc3p). The previously described polybasic region (amino acids 110–120 in S. cerevisiae Cdc3p; [19, 21]) is shown as a black box and the previously described "septin unique element" (amino acids 360–413 in S. cerevisiae Cdc3p [21]); is shown as a grey box. S1-S4 mark positions of new septin motifs (Table 2b; amino acid 237–242, 247–259, 261–268, 364–365 in S. cerevisiae Cdc3p) and lines below diagram show conserved single amino acid positions (Table 2c; amino acids 117, 295, 300, 339, 360, 396 in S. cerevisiae Cdc3p). Many septins also have a predicted coiled-coil domain at the C-terminus (amino acids 476–507 in S. cerevisiae Cdc3p; [21]).

Figure 2

Overview phylogenetic tree of septin gene family. Half-compat consensus phylogram of 1.5 million generations of the MCMC analysis of the Bayesian phylogenetic analysis, discarding 400,000 generations as burn-in. Nodal numbers in front of the slash are posterior probabilities for Bayesian analysis. At the nodes where the tree topology agrees with the Bayesian analysis, numbers after the slash are bootstrap percentages from maximum likelihood bootstrap analysis using 1024 replicates. Red branches indicate animal lineage, green indicate fungal lineage and blue indicate microsporidia. Names in parenthesis under Group names indicate the best characterized fungal septin (CDC10, CDC3, CDC11 and CDC12, ASPE) or the mammalian septin classification of Martinez and Ware (2004) (MI, MII, MIII). See figures 3-5 for species names.

Figure 3

Group 1 septin phylogenetic tree. Group 1 from figure 2 enlarged to show species names. Red branches indicate animal lineage and green indicate fungal lineage.

Figure 4

Group 2 septin phylogenetic tree. Group 2 from figure 2 enlarged to show species names. Red branches indicate animal lineage and green indicate fungal lineage.

Figure 5

Groups 3, 4 and 5 septin phylogenetic tree. Group 1 from figure 2 enlarged to show species names. Green branches indicate fungal lineage and blue indicate microsporidial lineage.

Figure 6

Postulated septin evolution. Summary phylogeny of 31 species used in this study. This tree summarizes the evolution of the septins in the 31 organisms whose septins were identified and used in this study [50–53]. Red branches indicate animal lineages and green branches indicate fungal lineages. The table on the right of the tree indicates different groups of septin genes. Group 1 is red, group 2 is orange, group 3 is yellow, group 4 is green, and group 5 is blue. A triangle means the complete genome sequence was not available when the initial search was executed, so some septins might not have been identified due to incomplete sequence information.