Sterol and genomic analyses validate the sponge biomarker hypothesis

Abstract

Molecular fossils (or biomarkers) are key to unraveling the deep history of eukaryotes, especially in the absence of traditional fossils. In this regard, the sterane 24-isopropylcholestane has been proposed as a molecular fossil for sponges, and could represent the oldest evidence for animal life. The sterane is found in rocks ∼650-540 million y old, and its sterol precursor (24-isopropylcholesterol, or 24-ipc) is synthesized today by certain sea sponges. However, 24-ipc is also produced in trace amounts by distantly related pelagophyte algae, whereas only a few close relatives of sponges have been assayed for sterols. In this study, we analyzed the sterol and gene repertoires of four taxa (Salpingoeca rosetta, Capsaspora owczarzaki, Sphaeroforma arctica, and Creolimax fragrantissima), which collectively represent the major living animal outgroups. We discovered that all four taxa lack C 30 sterols, including 24-ipc. By building phylogenetic trees for key enzymes in 24-ipc biosynthesis, we identified a candidate gene (carbon-24/28 sterol methyltransferase, or SMT) responsible for 24-ipc production. Our results suggest that pelagophytes and sponges independently evolved C 30 sterol biosynthesis through clade-specific SMT duplications. Using a molecular clock approach, we demonstrate that the relevant sponge SMT duplication event overlapped with the appearance of 24-isopropylcholestanes in the Neoproterozoic, but that the algal SMT duplication event occurred later in the Phanerozoic. Subsequently, pelagophyte algae and their relatives are an unlikely alternative to sponges as a source of Neoproterozoic 24-isopropylcholestanes, consistent with growing evidence that sponges evolved long before the Cambrian explosion ∼542 million y ago.sponges | Porifera | sterols | steranes | Amorphea

Paleoproterozoic sterol biosynthesis and the rise of oxygen

“…This is based on several comparative genomic studies, which have concluded that the sterol biosynthesis pathway is present in the major eukaryotic clades, and that there is no compelling evidence for early horizontal gene transfer events between Eukaryotes (Desmond and Gribaldo, 2009;Gold et al, 2016a). This suite of genes includes sterol 24-C-methyltransferase (SMT), which allows for the methylation of sterol side chains and the biosynthesis of canonical C 26 -C 30 eukaryotic sterols.…”

The Holo-Transcriptome of a Calcified Early Branching Metazoan

“…sequence was then searched against the NCBI-nr database using BLASTx. Positive matches were aligned to the SMT protein alignment provided by Gold et al (2016) using clustalO. Phylogenetic analyses were conducted using MrBayes v 3.2.6 (Ronquist et al, 2012) with the following parameters: lset rates = gamma, preset aamodelpr = mixed, mcmcp, nruns = 4, ngen = 10,000,000, relburn = yes, burninfrac = 0.25, printfreq = 1,000, samplefreq = 100, nchains = 4, saveprlens = yes, and RAxML on the RAxML blackbox webserver (Stamatakis et al, 2008) using the combined bootstrapping and maximum likelihood search algorithm with the GTA model and 100 bootstraps.…”

Animal origins and the Tonian Earth system

“…The oldest evidence for animals in the biomarker record appears between 659 and 645 Ma, between the Sturtian and Marinoan glaciations, in the form of the 24-isopropylcholestane (24-ipc), commonly interpreted as a demosponge biomarker [57,58]. Cryostane (26-methylocholestane), which is restricted to the late Tonian, is another potential demosponge biomarker, as demosponges represent the only known extant organisms capable of methylating sterols in the 26-position [55,59].…”