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.
DwN
14 November 2024, Nature Communications. DOI: 10.1038/s41467-024-54152-x
Scientists Create an “Extraordinary” Mouse Using Gene Older than Animal Life Itself
Queen Mary University of London
November 19, 2024
New research unveils the evolutionary origins of stem cells through a groundbreaking experiment that successfully created a mouse using ancient genetic tools.
Published in Nature Communications, an international team of researchers has achieved a groundbreaking milestone: the creation of mouse stem cells capable of generating a fully developed mouse. This was accomplished using genetic tools derived from a unicellular organism with which we share a common ancestor that predates animals. This breakthrough not only reshapes our understanding of the genetic origins of stem cells, but also offers a new perspective on the evolutionary connections between animals and their ancient single-celled relatives.
In an experiment that sounds like science fiction, Dr. Alex de Mendoza of Queen Mary University of London collaborated with researchers from The University of Hong Kong to use a gene found in choanoflagellates, a single-celled organism related to animals, to create stem cells which they then used to give rise to a living, breathing mouse.
Choanoflagellates are the closest living relatives of animals, and their genomes contain versions of the genes Sox and POU, known for driving pluripotency — the cellular potential to develop into any cell type — within mammalian stem cells. This unexpected discovery challenges a longstanding belief that these genes evolved exclusively within animals (rather than in one-cell organisms that evolutionarily preceded multicellular earliest animals).
“By successfully creating a mouse using molecular tools derived from our single-celled relatives, we’re witnessing an extraordinary continuity of function across nearly a billion years of evolution,” said Dr de Mendoza. “The study implies that key genes involved in stem cell formation might have originated far earlier than the stem cells themselves, perhaps helping pave the way for the multicellular life we see today.”
From Single-Celled Relatives to Multicellular Applications
The 2012 Nobel Prize to Shinya Yamanaka demonstrated that it is possible to obtain stem cells from “differentiated” cells just by expressing four factors, including a Sox (Sox2) and a POU (Oct4) gene.
In this new research, through a set of experiments conducted in collaboration with Dr Ralf Jauch’s lab in The University of Hong Kong / Centre for Translational Stem Cell Biology, the team introduced the choanoflagellate Sox gene into mouse cells, replacing the native Sox2 gene — achieving reprogramming towards the pluripotent stem cell state.
To validate the efficacy of these reprogrammed cells, they were injected into a developing mouse embryo. The resulting chimeric mouse displayed physical traits from both the donor embryo and the lab-induced stem cells, such as black fur patches and dark eyes, confirming that these ancient genes played a crucial role in making stem cells compatible with the animal’s development.
Evolutionary Roots of Stem Cell Machinery
The study traces how early versions of Sox and POU proteins, which bind DNA and regulate other genes, were used by unicellular ancestors for functions that would later become integral to stem cell formation and animal development.
“Choanoflagellates don’t have stem cells; they’re single-celled organisms, but they have these genes, likely to control basic cellular processes that multicellular animals probably later repurposed for building complex bodies,” explained Dr de Mendoza.
This novel insight emphasizes the evolutionary versatility of genetic tools and offers a glimpse into how early life forms might have harnessed similar mechanisms to drive cellular specialization, long before true multicellular organisms came into being, and into the importance of recycling in evolution.
This discovery has implications beyond evolutionary biology, potentially informing new advances in regenerative medicine. By deepening our understanding of how stem cell machinery evolved, scientists may identify new ways to optimize stem cell therapies and improve cell reprogramming techniques for treating diseases or repairing damaged tissue.
“Studying the ancient roots of these genetic tools lets us innovate with a clearer view of how pluripotency mechanisms can be tweaked or optimized,” Dr. Jauch said, noting that advancements could arise from experimenting with synthetic versions of these genes that might perform even better than native animal genes in certain contexts.
Reference: “The emergence of Sox and POU transcription factors predates the origins of animal stem cells” by Ya Gao et al., Ralf Jauch Laboratory, 14 November 2024, Nature Communications. DOI: 10.1038/s41467-024-54152-x