The topic today is most closely related to developmental biology, but these experiments are so mind-boggling because they also fit on the edge of gene-environment interactions, as related to evolution of life on Earth. First, we need A LOT of evo-devo background and definitions to get everyone on the same page.
Choanoflagellates are single-celled organisms (Protists) considered to be the closest living relatives to animals, providing important insights into the evolutionary origins of multicellularity (which defines Metazoa) in the Animal Kingdom. Choanoflagellates look like miniature tadpoles; they are tiny spherical, or egg-shaped, cells crowned with a “collar” of fingerlike protrusions surrounding a single flagellum that whips back and forth. They stir up water currents with their flagella, sweeping their next meal (usually bacteria) into their collars to eat.
Meanwhile, sponges are simple animals made up of many cell types, including choanocytes — collared, flagellated cells that line the chambers inside the sponge and capture its food. Choanocytes look and act remarkably like choanoflagellates, so much so — that some scientists (erroneously) proposed in the 1980s and ’90s that choanoflagellates might be animals that evolved from sponges and then “simplified down” to one cell.
Whereas (traditionally) sponges were thought to be the earliest animals, recent genetic analyses (e.g., whole genome sequencing; RNA-Seq transcription) now indicate that comb jellies (ctenophores) split off from the common ancestor (choanoflagellates) of all animals first, placing them as the earliest animal group; sponge is the next earliest. Choanoflagellates have complex life cycles that proceed through various cell states. These states essentially act as different cell types — but rather than all existing side by side — as in a multicellular organism, they arise sequentially in a single cell; this is called “temporal cell differentiation.”
Filasterea are another group of single-celled organisms related to animals and choanoflagellates; filasterea are a proposed clade Filozoans, sister to the clade that includes animals and choanoflagellates. Common features of filastereans are combined by the structure of their thread-like pseudopods (e.g., their varied shapes include amoebae, flagellates, cellular aggregations, and amoeboflagellates). As an aside, intriguingly, the sterol metabolism of filastereans comprises enzymatic activities that are usually considered exclusive to metazoans, or characteristic of fungi…!!
There are three different types of stem cells: [a] Adult Stem Cell (ASC) which can differentiate into various cell types specific to that tissue (e.g., new blood cells in bone marrow, skin cells in epidermis, or muscle cells in skeletal muscle — essentially replacing old or damaged cells within that particular organ or tissue); [b] Embryonic Stem Cell (ESC) which has the potential to become almost any cell type in the body (because they are considered “pluripotent”); and [c] Induced Pluripotent Stem Cell (iPSC) which essentially acts as a master cell that can be directed to become a specific cell type needed for therapeutic purposes.
The primary transcription factors used to induce pluripotent stem cells (iPSCs) are: Oct4 (Oct3/4), Sox2, Klf4, and c-Myc; collectively referred to as the “Yamanaka factors.” Shinya Yamanaka and Kazutoshi Takahashi won the 2012 Nobel Prize in Physiology or Medicine for their “discovery of iPSCs”; they discovered that adult cells can be reprogrammed to become pluripotent stem cells, which have the ability to develop into many different types of cells. They achieved this by introducing factors that turned on genes typically active in embryonic stem cells.
Authors [see attached article] state that “stem cells are a hallmark of animal multicellularity.” Sox and POU transcription factors are associated with “stemness” and were believed to be animal innovations — “reportedly absent in their unicellular relatives.” POU transcription factors are a family of proteins that bind to DNA to control gene expression; POU stands for Pit-Oct-Unc, and the family includes proteins from mammals and nematodes. POU proteins are known for their role in embryonic development and cellular fate decisions.
However, contrary to accepted dogma, authors [see attached article] show that Sox and POU factors ARE present in unicellular organisms. Choanoflagellate and filasterean Sox proteins were found to have DNA-binding specificity similar to mammalian Sox2. Choanoflagellate — but not filasterean — Sox can replace mammalian Sox2, which is then able to reprogram mouse somatic cells into induced pluripotent stem cells (iPSCs) through interacting with the mouse POU member, Oct4. In contrast, choanoflagellate POU exhibits a distinct DNA-binding profile and cannot generate iPSCs. Ancestrally reconstructed Sox proteins indicate that iPSC formation capacity is pervasive among resurrected sequences; therefore, loss of Sox2-like properties can stand-in for Sox family subfunctionalization (an evolutionary process where duplicated genes take on different functions, instead of retaining the original function of the ancestral gene).
These findings imply that evolution of animal stem cells might have involved the exaptation [i.e., a trait or feature that has evolved to serve a function other than its original one (e.g., feathers originally evolved to help regulate body temperature, but were later adapted for flight)] of a pre-existing set of transcription factors — in which “pre-animal Sox” was biochemically similar to present-day Sox, whereas POU factors required evolutionary innovations.
Below is a layman’s summary of what has just been written above as the scientific summary.
COMMENTS:
Dan,
This is an incredible study!
Comment:
Dave,
I also thought so. These results [see attached pdf] represent a Quantum Leap forward in our knowledge about early evolution of pre-animals versus animals. [I had not realized that choanoflagellates were first discovered/described in 1868 [see the brief review in Current Biology, 2 Dec 2019; Vol. 29: pp R1240-R1242] and, until the last decade of whole genome sequencing and RNA-Seq analysis, were believed to be the ancestors of sponge (not comb jellies, as has been established today).]
The last Quantum Leap forward (IMHO) was the demonstration that human and yeast transcription factors (TFs) were interchangeable: i.e., one could replace a yeast TF with the human homologous TF and show that the transcription apparatus worked perfectly fine (and vice versa). In yeast, upstream activation sites (UASs) are located roughly 100 bp upstream of the TATA box [Guarente et al., 1982; PNAS 79: 7410-14]; in mammals, enhancers are often as close as 30 bp upstream of the TATA box [Banerji et al., 1981; Cell 27: 299-308; Benoist & Chambon, 1981; Nature 290: 304-10; Fromm & Berg 1982; J Mol Appl Genet 1: 457-81]. Nevertheless, the mechanism of transcriptional activation is highly conserved between yeast and mammals. Thus, there was the realization (in some of us at that time) of how similar TFs and their functions were — across the tree of life.
The Quantum Leap forward in Nov 2024 — is that a TF in an organism (choanoflagellate) that precedes the evolutionary existence of the first animal (comb jelly) — is able to function just fine in the animal transcription machinery. Thus, Mother Nature is showing us that early evolution continues to be full of surprises.
DwN