This web page was produced as an assignment for an undergraduate course at Davidson College.
First assignment: Microbiology: Mind the gaps in cellular evolution
This is a review of this particular article: Mind the gaps in cellular evolution
1. What was the research project?
The research project was based on finding the origins of eukaryotic cells. Approximately 1.8 billion years ago, eukaryotic cells arose from cells that lack membrane bound organelles (prokaryotes) including protein based transport systems that enable the movement for molecules around the cell. The research project identified a superphylum branch of the prokaryotic family tree (asgard) that might be linked to some eukaryotes specific genes. The purpose of this research was to see where the eukaryotes originated from and if they originated from a different domain that is already present.
2. Were they testing a hypothesis or doing discovery science?
The actual hypothesis of this article states that eukaryotic cells arose form prokaryotic cells. However, this article is going more in depth to discover the connection between eukaryotes and prokaryotes making it a discovery science based article. The article expresses that eukaryotes derived form a merger that occurred when an archaeal cell engulfed a bacterial cell (as seen in figure 1). The discovery in this article lies in the connection between the early eukaryotic cells with now present eukaryotic cells and prokaryotic cells. The article proposes that within early eukaryotic cells the internalized proteobacterium evolved to form membrane bound organelles such as mitochondria. With different data being analyzed the article tries to discover the connection of early prokaryotes and eukaryotes.
3. What genomic technology was used in the project?
In order to analyze this research project, scientists obtained samples of aquatic sediments from seven locations worldwide. Short fragments of DNA have been extracted and more than 644 billion nucleotides have been sequenced. The article states that “The short fragments of sequence were assembled into longer pieces, and sequences containing at least six genes from an evolutionarily conserved ribosomal-protein gene cluster were identified.” While conducting this research, the researchers identified sequences that were most similar to previously sequenced Lokiarchaeota and Thorarchaeota (different archaeal species related to eukaryotes). DNA sequencing was used as a tool of genomic technology and a statistical method “as to classify the ribosomal sequences on the basis of similarities in the patterns of nucleotides used”, as expressed by this article.
4. What was the take home message?
Up to this point the archaea that have been identified as the most closely related ancestors of eukaryotic cells are Lokiarchaeota, which were identified by genome sequencing of organisms found in deep sea sediments. This special type of archaea contained features similar to a eukaryotic cell, such as genes that are found in the eukaryotic transportation system. Though the article states if a deeper understanding of the transition from prokaryotic to eukaryotic life should be made, more investigation must be done. During this research they identified a superphylum of Archaea “containing four major lineages of genetic material”: Lokiarchaeota, Thorarchaeota, Odinarchaeota and Heimdallarchaeota. The researchers named this the Asgard Superphylum. The analysis supports the existence of this superphylum. The research suggested that it is the closest related to eukaryotic cells and that the hypothesis that eukaryotes arose through a merger of cells from within archaea and bacteria is still valid. This newly discovered group has several linkages to eukaryotic cells that function in protein transport, signaling and degradation. Researchers have also discovered that it contains genes related to the cytoskeleton, with the formation of structural proteins and tubulin. Niedzwiedzka identified that “the tubulin in certain archea species (ordinaarcheaota) is closer in sequence to eukaryotic tubulin”. “Sequences have been identified relating to the protein complex ARP2/3 which regulates the cytoskeleton.” The Asgard superphylum has genes that encode eukaryotic membrane trafficking proteins. It is unclear how these genes might function due to prokaryotes small size and the lack of membrane bound organelles such as endoplasmatic reticulum and golgi complex. The general take home message is that it is still unclear how the eukaryotic cell formed and evolved during the course of time. Research might still reveal that major groups of life can still be discovered and that not everything has to make perfectly sense in the world of biology.
5. What is your evaluation of the project?
This project fully describes and analyses the difficulties of understanding the origin of eukaryotic cells. It makes good arguments and represents the data in a clear way, however the fact that the viewer does not have access to all the statistical data is one thing that this paper is lacking. The paper makes it clear that in biology unpredicted stuff can happen and that at times it is almost impossible finding an explanation for it without pursuing intensive research.
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