Evolutionary rewiring of gene regulatory network linkages at divergence of the echinoid subclasses

Abstract

Evolution of animal body plans occurs with changes in the encoded genomic programs that direct development, by alterations in the structure of encoded developmental gene-regulatory networks (GRNs). However, study of this most fundamental of evolutionary processes requires experimentally tractable, phylogenetically divergent organisms that differ morphologically while belonging to the same monophyletic clade, plus knowledge of the relevant GRNs operating in at least one of the species. These conditions are met in the divergent embryogenesis of the two extant, morphologically distinct, echinoid (sea urchin) subclasses, Euechinoidea and Cidaroidea, which diverged from a common late Paleozoic ancestor. Here we focus on striking differences in the mode of embryonic skeletogenesis in a euechinoid, the well-known model Strongylocentrotus purpuratus (Sp), vs. the cidaroid Eucidaris tribuloides (Et). At the level of descriptive embryology, skeletogenesis in Sp and Et has long been known to occur by distinct means. The complete GRN controlling this process is known for Sp. We carried out targeted functional analyses on Et skeletogenesis to identify the presence, or demonstrate the absence, of specific regulatory linkages and subcircuits key to the operation of the Sp skeletogenic GRN. Remarkably, most of the canonical design features of the Sp skeletogenic GRN that we examined are either missing or operate differently in Et. This work directly implies a dramatic reorganization of genomic regulatory circuitry concomitant with the divergence of the euechinoids, which began before the end-Permian extinction.GRN evolution | network linkages | embryonic skeletogenesis | sea urchin embryogenesis T he mechanisms responsible for evolutionary divergence of animal body plans, as so extensively documented in the Phanerozoic fossil record, lie in alterations of the encoded genomic regulatory programs that direct development. This principle has long been evident a priori (1), and overwhelmingly, accumulating current evidence precludes any other general explanation (2). However, it still remains a challenge to adduce specific examples in which evolutionary rewiring of developmental gene-regulatory networks (GRNs) can be seen to account for observed differences in morphogenetic processes that distinguish descendants of a common ancestor. Knowledge of developmental GRNs remains insufficiently extensive, and it is not trivial to locate useful examples, which require comparison within a monophyletic clade at just sufficient distance so that the diverged morphology is clearly the output of homologous networks of developmental regulatory gene interactions.In recent years, largely complete developmental GRN models have been solved that causally explain spatial specification in large domains of the embryo of the sea urchin Strongylocentrotus purpuratus (Sp), up to gastrulation (3-5). The explanatory power of these networks was demonstrated, in these pages, by a predictive computational analysis that showed that they contain sufficient informat...

Divergence of ectodermal and mesodermal gene regulatory network linkages in early development of sea urchins

“…Sequential unfolding of NSM regulatory states in Et has diverged, although evidence presented here indicates that gcm and ese are spatially distributed in a similar fashion to that in euechinoids. In the Et archenteron, previously reported observations suggested that the euechinoid SM-specific regulatory genes ets1/2 and tbrain are distributed broadly in the mesoderm (17). I confirmed that result by double-fluorescent WMISH (SI Appendix, Fig.…”

“…Interestingly, in cidaroids, the micromere embryonic address is the location at which numerous euechinoid SM genes are first activated (17,47). These observations suggest that in the ancestral echinoid lineage, the adult skeletogenesis program was co-opted to run in the micromeres.…”

“…Previous analyses of embryonic regulatory states in Et surveyed SM regulatory factors (17,47) and anterior neural ectoderm specification (75). In addition, two previous studies investigated SM and early endomesodermal micromere regulatory factors in the Pacific-dwelling cidaroid Prionocidaris baculosa (16,99).…”

“…Although there is evidence of minor alterations to these GRNs, such as a heterochronic shift in snail expression in Lv and Sp (22), numerous studies have made clear the striking conservation of GRN linkages in these lineages. Recent studies of early development of the distantly related, indirect-developing cidaroid sea urchin Eucidaris tribuloides (Et) have revealed that skeletogenic mesoderm specification in this clade is markedly different from that observed in euechinoids (17,18,47). The foregoing observations suggest that comparative analyses of GRN circuitry in early Significance Sea urchins (echinoids) consist of two subclasses, cidaroids and euechinoids.…”

“…Importantly, an excellent fossil record affords dating of evolutionary events (9), which has established that the sister subclasses of sea urchins-cidaroids and euechinoidsdiverged at least 268 million years ago (mya) (10). Differences in the timing of developmental events in embryogenesis of cidaroids and euechinoids have long been a topic of interest, but have become the subject of molecular research only recently (11)(12)(13)(14)(15)(16)(17)(18).…”