Survey of Genomes - Even Most Eukaryotes are Microbial
Brad sets up the last two student-hosted episodes by bringing up a not so obvious point to us “macrobes” (organisms visible to the naked eye) - even most members of the domain Eukarya are microbial!
Welcome back to Genomics Revolution. Brad Goodner jumping back in to our Survey of Genomes guest-hosted by students from the 2019 Hiram College Genetics course. You have probably been wondering “hey, when are they going to talk about the human genome?” We will get to it in time, but I am big believer that we humans need to see the biological world through a non-human dominated lens. Life on Earth, contrary to what our eyes tell us, is actually dominated by microbes – in cell number, in biomass, and in diversity. That is even true for the major branch of the tree of life where we humans sit – the eukaryotes.
As you probably know, we humans are in the evolutionary family commonly known as the great apes. We are in the order Primates, the class Mammalia, the phylum Chordata meaning we have a notochord during our development (different from a spinal cord) and the kingdom Metazoa better known as the animals. Yet, did you know that there are microscopic animals? Some of the most numerous animals on Earth are tiny roundworms, mites, and tardigrades (commonly called water bears).
We humans are also in the domain Eucarya or Eucaryota. All eukaryotes – animals, plants, algae, fungi and amoebas to name just a few, share a common ancestor whose cells had, among other things, a double membrane-bound nucleus, a double-membrane-bound organelle called a mitochondria, some other membranous organelles such as endoplasmic reticulum (ER) and Golgi apparatus, well-developed actin- and tubulin-based cytoskeleton systems and a special way to separate their chromosomes called mitosis. Yes, mitosis is only seen in eukaryotes. You don’t see these features in the domains Bacteria and Archaea. Yes, the available data suggests that Bacteria invented the ancestral forms of actin and tubulin, but these cytoskeleton systems in Bacteria are nowhere near as complex as we see in eukaryotes especially in terms of molecular motors and regulatory proteins. Yes, Archaea invented new ways of organizing and compacting DNA, but eukaryotes have taken DNA organization and compaction to multiple levels of complexity that are critically linked to regulating gene expression. To finish this line of thought, there is growing evidence that the earliest proto-eukaryote was a cell from the Archaea lineage that engulfed a member of the Bacteria lineage, specifically an organism from the alpha-Proteobacteria. Instead of only one cell winning, the engulfer and the engulfed ended up as a co-dependent “cell of cells” as aptly described by Carl Woese and his collaborators. The engulfed alpha-Proteobacteria cell evolved into what we now call the mitochondria – keeping a small subset of genes (in our case as mammals, keeping about 15 or so genes), losing most of its now non-essential genes, and having some other genes move into what would become the nucleus. Other genes in current eukaryotic nuclear DNA appear to be of Archaea origin.
Now eukaryotes are found in virtually all habitats, large and small, on Earth. We usually think of the blue whale, the human, the redwood, the daisy, the kelps of the brown algae and the button mushroom. These macrobes, as we might call them, are visible to the naked eye because each organism is composed of millions to trillions of cells working with and/or signaling each other. In episode 12, Kaitlyn Morse discussed the genome of the most well-understood macrobe, the fruit fly Drosophila melanogaster. Each fruit fly is made up of 5 million or so cells. However, for every macrobe we can easily see, there are billions, if not trillions, of single-celled eukaryotes or multicellular eukaryotes with just a few hundred to a few thousand cells in the body. In episode 14, Brett Bentkowski introduced us to the unicellular fission yeast, Schizosaccharomyces pombe. In the next couple of episodes we will hear about some more important yet tiny eukaryotes. So I hope you will stay tuned, listen and learn. Until then, take care.
As you probably know, we humans are in the evolutionary family commonly known as the great apes. We are in the order Primates, the class Mammalia, the phylum Chordata meaning we have a notochord during our development (different from a spinal cord) and the kingdom Metazoa better known as the animals. Yet, did you know that there are microscopic animals? Some of the most numerous animals on Earth are tiny roundworms, mites, and tardigrades (commonly called water bears).
We humans are also in the domain Eucarya or Eucaryota. All eukaryotes – animals, plants, algae, fungi and amoebas to name just a few, share a common ancestor whose cells had, among other things, a double membrane-bound nucleus, a double-membrane-bound organelle called a mitochondria, some other membranous organelles such as endoplasmic reticulum (ER) and Golgi apparatus, well-developed actin- and tubulin-based cytoskeleton systems and a special way to separate their chromosomes called mitosis. Yes, mitosis is only seen in eukaryotes. You don’t see these features in the domains Bacteria and Archaea. Yes, the available data suggests that Bacteria invented the ancestral forms of actin and tubulin, but these cytoskeleton systems in Bacteria are nowhere near as complex as we see in eukaryotes especially in terms of molecular motors and regulatory proteins. Yes, Archaea invented new ways of organizing and compacting DNA, but eukaryotes have taken DNA organization and compaction to multiple levels of complexity that are critically linked to regulating gene expression. To finish this line of thought, there is growing evidence that the earliest proto-eukaryote was a cell from the Archaea lineage that engulfed a member of the Bacteria lineage, specifically an organism from the alpha-Proteobacteria. Instead of only one cell winning, the engulfer and the engulfed ended up as a co-dependent “cell of cells” as aptly described by Carl Woese and his collaborators. The engulfed alpha-Proteobacteria cell evolved into what we now call the mitochondria – keeping a small subset of genes (in our case as mammals, keeping about 15 or so genes), losing most of its now non-essential genes, and having some other genes move into what would become the nucleus. Other genes in current eukaryotic nuclear DNA appear to be of Archaea origin.
Now eukaryotes are found in virtually all habitats, large and small, on Earth. We usually think of the blue whale, the human, the redwood, the daisy, the kelps of the brown algae and the button mushroom. These macrobes, as we might call them, are visible to the naked eye because each organism is composed of millions to trillions of cells working with and/or signaling each other. In episode 12, Kaitlyn Morse discussed the genome of the most well-understood macrobe, the fruit fly Drosophila melanogaster. Each fruit fly is made up of 5 million or so cells. However, for every macrobe we can easily see, there are billions, if not trillions, of single-celled eukaryotes or multicellular eukaryotes with just a few hundred to a few thousand cells in the body. In episode 14, Brett Bentkowski introduced us to the unicellular fission yeast, Schizosaccharomyces pombe. In the next couple of episodes we will hear about some more important yet tiny eukaryotes. So I hope you will stay tuned, listen and learn. Until then, take care.