Monthly Archives: February 2017

The Great Mystery of Biology: The Eukaryote Cell’s Origin

The origin of eukaryotes is one of the hardest and most intriguing problems in the study of the evolution of life, and arguably, in the whole of biology.”(Koonin, 2015)
All living things are composed of either prokaryote or eukaryote cells. The prokaryote cells are simple, basically a blob of protoplasm encased in a cell membrane while the eukaryote cell is larger, possesses a nucleus, (a kind of DNA-packed control room safely enclosed in a membrane), as well as a set of specialized organelles (“little organs”) that are able to perform necessary tasks like storing molecules or protein manufacture. Significantly the eukaryote cell has its own power plant in the form of mitochondria.
For nearly 2 billion years after the appearance of life on Earth, the prokaryote model had Earth to itself. It was and continues to be highly successful at not only surviving but also thriving. Prokaryotes can be found in all of Earth’s habitats from clouds to the depths of the sea, using a repertoire of ways to survive, from the ability to cause disease, use noxious substances like crude oil for food, power themselves with energy from the Sun, and even to swap genes with one another. (Yong, 2014)
The eukaryote cell with its nucleus and mitochondria, doesn’t appear until much later in Earth’s history, about 1.5 billion years ago.
While the prokaryotes “have repeatedly nudged along the path to complexity” and while some groups of prokaryotic cells move in colonies that resemble complex life, “none of them have acquired the full suite of features that define eukaryotes: large size, the nucleus, internal compartments, mitochondria…” (Yong, 2014)
This is why the appearance of the eukaryote (“eukaryogensis”) is “regarded as one of the major evolutionary innovations in the history of our planet” because the eukaryote cell with its mitochondria, its own power plant provides “the host cell with a bonanza of energy, allowing it to evolve in new directions that other prokaryotes could never reach,” and accounts for the reason why all multicellular life is based on the eurkaryotic cell. (Zaremba-Niedzwiedzka et al., 2017 & Yong, 2014)
In an article in Nature published in January 2017, the authors argue that “most recent insights” support a variety of symbiogenesis of eukaryotic evolution. Evidence is that a still mysterious host cell from the domain Archaea merged with “an alphaprotobacterial (mitochondrial) endosymbiont.” (Zaremba-Niedzwiedzka et al., 2017)
That the mitochondria in the eukaryote cell was once a free living bacteria was first proposed by Lynn Margulis in 1967, at the time a graduate student.
Margulis argued that one driver of evolution was symbiosis, with evidence based on the fact that the mitochondria in eukaryotic cells look remarkably like bacteria. Another example for this endosymbiosis are chloroplasts which also look like bacteria. With the coming of new genetic tools, analysis of the chloroplast genome by the University of Illinois’ Carl Woese showed that the chloroplast genes were not at all like the genes in the host cells, but turned out to be the DNA of cyanobacteria. It was also found that the mitochondrial DNA resembles that which is found in the group of bacteria that causes typhus.
New technologies have expanded the tools that are available to track the relationships between organisms, adding new data to the quest to solve the mystery surrounding eukaroygenesis. While the bacteria that contributed the mitochondria to the eukaryote was from the group known as alphaproteobacteria, a group well-known to take up life within the cells of plants and animals as both mutualists and pathogens.(Williams, Sobral, & Dickerman, 2007)
But less is known about the organism from the domain Archaea that was the presumed host in the merger.
In 2015 a team from Sweden’s Uppsala University collected and analysed sediments from an ocean floor field of hydrothermal vents lying between Norway and Greenland called Loki’s Castle. The DNA found in the sample show that these Lokiarchaeota are the “best approximations that we have for that ancestral archaeon that gave rise to us all.” (Yong, 2017)
More searches in places like North Carolina, Yellowstone National Park, and New Zealand, have revealed many more varieties from this group of archaea, which the group has named Asgard (a name from Norse mythology).
The DNA from these organisms have turned up genes that until now that were thought to be unique to eukaryotes. There are genes in the asgard archaea that serve in eukaryotes for building internal skeletons, although the archaea do not have internal skeletons. Other genes are associated with the pinching off of the outer membrane of cells to create little pockets that are used to move molecules around, another eukaryotic capability not found in archaea.
It would be wrong to say that these discoveries have solved the mystery of eukaryogenesis. A lead researcher in this field describes these cells, not as eukaryotes but “primed to become eukaryotes.”(Yong, 2017)
The Agard archaea are perhaps the link that connects the most ancient life to our own.

Resources:
Koonin, E. V. (2015). Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier? Philosophical Transactions of the Royal Society B, 370(1678). Retrieved from http://rstb.royalsocietypublishing.org/content/370/1678/20140333
Williams, K. P., Sobral, B. W., & Dickerman, A. W. (2007). A Robust Species Tree for the Alphaproteobacteria. Journal of Bacteriology, 189(13). Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1913456/
Yong, E. (2014). The Unique Merger That Made You (and Ewe, and Yew). Retrieved from http://nautil.us/issue/10/mergers–acquisitions/the-unique-merger-that-made-you-and-ewe-and-yew
Yong, E. (2017). A Break in the Search for the Origin of Complex Life. The Atlantic. Retrieved from https://www.theatlantic.com/science/archive/2017/01/our-origins-in-asgard/512645/
Zaremba-Niedzwiedzka, Caceres, E. F., Saw, J. H., Bäckström, D., Juzokaite, L., & Vancaester, E. (2017). Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature Immunology, 541(7637), 353-358. Retrieved from http://www.nature.com/nature/journal/v541/n7637/full/nature21031.html
See the South Carolina Academic Standards and Performance Indicators for Science 2014: Biology I, Cells as a System, H.B.2.
tags:
South Carolina Biology Standards, eukaryotes, prokaryotes, Eukarya, Archaea, Bacteria, domains, Carl Woese, Lynn Margulis

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Nature in the Front Yard: Evolution in the City

 

The voyage on H.M.S. Beagle that led to the theory of evolution took Charles Darwin to many remote places, most famously, the Galápagos Islands, 1000 km off the coast of Ecuador in the Pacific Ocean.

But whether on a Pacific island or in the middle of New York city, the forces of evolution are in operation because science assumes that the universe is a vast single system in which basic laws are consistent no matter where you look. (Quinn et al., 2013)

Actually urban areas are different in one important respect which is that the rapidity of evolutionary forces depends on the “strength of natural selection — the relative benefit that a particular characteristic bestows on its bearer — is strong.” Even a small difference can matter greatly, especially in an urban environment because it is about as extreme and stressful as it is possible to find with its temperatures (warmer than surrounding countryside); its noise (a constant and invasive din that drowns out the usual warning sounds); further the urban landscape is encased in concrete and other substances hostile to the gripping of claws or traction for paws.  Then there are lots of humans, with their tempting trash along with their deadly cats and dogs, their waste that pollutes water, air, and soil.  (Schilthuizen, 2016)

This means that as the world becomes increasingly urbanized, more and more organisms are either being engulfed by urban areas or are gravitating to opportunities found in them.

Biologists therefore are “beginning to realize that the expanding urban sprawl is perhaps not something to be depressed about but something very exciting, as entirely new forms of life are evolving” in them. (Schilthuizen, 2016)

Jason Munshi-South, the director of the Munshi-South “Evolution in the Anthropocene” lab at Fordham University sees New York city as not only one of humanity’s greatest accomplishments but also as the home to native wildlife that are “subject to a grand evolutionary experiment.” (Munshi-South, Ted Ed talk)

Four hundred years ago the territory that makes up modern New York was covered by forest and meadow and was the home to a huge population of white-footed mice.

Four hundred years later the forests and meadows have largely been replaced by city streets, office buildings, multi-storied apartment buildings, and lots and lots of people, with their dangerously fast moving automobiles, noise, food waste, and trash while the white-footed mice are now crowded into the small patches of forest and meadows of the city’s parks. For Munshi-South the mice provide a model of what happens when wild organisms are engulfed by an urban ecosystem.

Advances in genetics have made it possible to identify changes that have occurred in a species because an organism’s genome is a record of its genetic history as well as that of its ancestors.

Genes are short segments of DNA which carry the recipes for creating the amino acids which are the building blocks for the proteins that actually do the cell’s work: its metabolism, its immune response, its reproduction, and so on.

If it happens that a single base pair on a gene changes and the change leads to an advantage for the mouse, for example, more babies, then this change will spread through a population because it will provide the individuals possessing the trait with increased fitness in the competition for survival. (Munshi-South, 2012)

After the examination of several thousand snippets of DNA from the genomes of 191 individual mice taken from 23 sites representing samples of both urban and “wild” environments, and then comparing the results with computer models the investigators were able to trace the history of the population of white-footed mice living in the area around New York.

About 12,000 years ago (coincident with the end of the last North American ice age) when rising sea levels separated Manhattan from the mainland, the genomes of the mice on Manhattan began to diverge from those on the mainland. Then about 400 years ago when Europeans began the settlement that soon became New York, more genetic divergence began to appear as the green space gave way to urban development. As Stephan Harris, a postdoctoral evolutionary biology researcher at Columbia University said, “The exciting thing is that the times of the divergence that we inferred lined up with the arrival of Europeans in New York.” (Netburn, 2016)

In the relatively brief time that New York has been populated by humans, the once genetically similar population of white-footed mice have evolved into genetically distinct populations each inhabiting a different park. The mice in one park are distinctive enough that the home park of a randomly selected New York white-footed mouse can be identified by examining just 18 snippets from its genome.

More significantly, the mice in different parks have developed park-specific traits related to their response to infection, their metabolism, and even their tolerance for environmentally occurring heavy metals like chromium and lead. (Munshi-South, 2012)

You don’t need a berth on the H.M.S. Beagle that will take you around the world to find evolution in action.

There are lots of great opportunities for “citizen science” projects where you can study nature in your home and neighborhood by tracking your local cats or the microscopic mites (Demodox) that are at home in the pores of your skin (yes, yours and mine).

You can find more about these projects at the Your Wild Life website.

 

Resources:

 

Menninger, Holly & Rob Dunn. Your Wild Life: Exploring biodiversity in our daily lives.

Munshi-South, Jason (2017). Evolution in Anthropocene. Retrieved from http://nycevolution.org

 

Munshi-South, Jason (2012). TED Ed.  Evolution in the Big City, retrieved from http://ed.ted.com/lessons/evolution-in-a-big-city

 

Netburn, D. (2016c). Why the City Mouse and the Country Mouse Have Different Genes. Los Angeles Times. Retrieved from http://www.latimes.com/science/sciencenow/la-sci-sn-city-mouse-20160415-story.html

 

Schilthuizen, Menno (2016). Evolution is Happening Faster Than We Thought.  New York Times, Sunday Review, July 23, 2016. Retrieved from https://www.nytimes.com/2016/07/24/opinion/sunday/evolution-is-happening-faster-than-we-thought.html?_r=0#st

 

Quinn, Helen R., Schweingruber, Heidi, Keller, Thomas, & others, A. A Framework for K-12 Science Education: Practices, Crosscutting Concepts, and Core Ideas. Washington, DC: National Research Council of the National Academies. Retrieved from http://www.nap.edu

 

tags:

evolution, urban ecosystem, fitness, gene, genome, genetics, white-footed mouse, New York, natural selection, citizen science, project-based curriculum