Emergence, development and diversification of the TGF-beta signalling pathway within the animal kingdom

Abstract

Background: The question of how genomic processes, such as gene duplication, give rise to co-ordinated organismal properties, such as emergence of new body plans, organs and lifestyles, is of importance in developmental and evolutionary biology. Herein, we focus on the diversification of the transforming growth factor-beta (TGF-beta) pathway -- one of the fundamental and versatile metazoan signal transduction engines.

Results: After an investigation of 33 genomes, we show that the emergence of the TGF-beta pathway coincided with appearance of the first known animal species. The primordial pathway repertoire consisted of four Smads and four receptors, similar to those observed in the extant genome of the early diverging tablet animal (Trichoplax adhaerens). We subsequently retrace duplications in ancestral genomes on the lineage leading to humans, as well as lineage-specific duplications, such as those which gave rise to novel Smads and receptors in teleost fishes. We conclude that the diversification of the TGF-beta pathway can be parsimoniously explained according to the 2R model, with additional rounds of duplications in teleost fishes. Finally, we investigate duplications followed by accelerated evolution which gave rise to an atypical TGF-beta pathway in free-living bacterial feeding nematodes of the genus Rhabditis.

Conclusion: Our results challenge the view of well-conserved developmental pathways. The TGF-beta signal transduction engine has expanded through gene duplication, continually adopting new functions, as animals grew in anatomical complexity, colonized new environments, and developed an active immune system.

Figure 1

Evolution of Smads and TGF-β receptors in Bilateria. The species tree, not-to-scale, displays the phylogenetic relationship between humans and the other species, using the monophyletic Ecdysozoa hypothesis. Each point of divergence (POD) group joins together species which share the same ancestor with the evolutionary line leading to humans. POD nodes are marked by yellow boxes. Please, note that PODs differ in strength of available supporting evidence (shown by the species tree). The gene table, at the bottom, describes the relationship between human Smads or receptors (right column of the table, and the adjacent gene trees) and orthologs in POD groups. POD groups are described in the top row of the table, and linked by discontinuous lines to respective POD nodes on the above-mentioned species tree. Inside the cells of the table: blue lines represent one to one orthology (all species of the POD group); red lines represent one (human) to two or more orthology (at least one species of the POD group). Finally, an empty cell signifies a failure to identify an ortholog within a given POD group.

Figure 2

Amino-acid Bayesian tree of Smads focusing on worm and fly proteins. The four canonical fly Smads: Mad, dSmad2, dSmad4, and Dad (in black) define the three functional classes of Smads: receptor Smads, Co-Smads and inhibitory Smads. Worm Smads are shown in pale green. Branch lengths are shown in red. Node probabilities are shown in black. The tree is rooted using the N. vectensis I-Smad: EDO39628 (in red).

Figure 3

Multiple additional Smads are present in teleost fishes. Letters in brackets signify additional teleost fish Smads (co-orthologs in relation to human genes). Fly genes are also shown for comparison. Table 5 lists accession numbers for the relevant genes. The tree is produced using TreeBeST and rooted on time. Red boxes signify duplication nodes, while green boxes signify speciation nodes (inferred using the speciation and duplication inference algorithm).

Figure 4

Basal metazoan repertoire of Smads. Trichoplax adhaerens (prefix Ta – in blue), Nematostella vectensis (prefix Nv – in green) and fly proteins (Dad, Medea, dSmad2 and Mad) are shown. The Bayesian tree reveals ancestral metazoan duplications (AMD1, 2 and 3) of the hypothetical single primeval common mediator/receptor activated Smad – note high probability values for all the nodes. N. vectensis sequences were retrieved from GenBank: NvSMAD1 (EDO47037), NvSMAD2 (EDO39594), NvSMAD4 (EDO31382), and NvSMAD6 (EDO39628). The tree is rooted using Dad. Branch lengths are shown in red. Node probabilities are shown in black.

Figure 5

Amino-acid Bayesian tree showing basal metazoan repertoire of type II/I receptors. Trichoplax adhaerens (prefix Ta – in blue), Nematostella vectensis (in green) and fly proteins (Babo, Tkv, Sax, Put, wit) are shown. N. vectensis sequences were retrieved from GenBank: type I receptors – EDO30434, EDO41833, EDO49083; type II receptors – EDO41379, and EDO49370 (with splice variant AAS77521). The tree is rooted using EDO41379. Branch lengths are shown in red. Node probabilities are shown in black.