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Writing Assignment 1

by: Jacob Decker

Writing Assignment 1 ZOL 425

Jacob Decker
GPA 3.71
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This is the Writing Assignment 1 for the lecture portion of the class by Dr. Bello
Cells and Development (W)
D. Bello-Deocampo
Class Notes




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This 6 page Class Notes was uploaded by Jacob Decker on Saturday February 13, 2016. The Class Notes belongs to ZOL 425 at Michigan State University taught by D. Bello-Deocampo in Spring 2016. Since its upload, it has received 23 views. For similar materials see Cells and Development (W) in Microbiology at Michigan State University.

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Date Created: 02/13/16
Decker 1 William Decker Dr. D. Bello­DeOcampo ZOL 425 Jan. 18th “An archaeal origin of eukaryotes supports only two primary domains of life”  Carl Woese changed the world in 1977, proposing that there are three primary domains of cellular life. This hypothesis suggest that eukaryotes and archaea share a common ancestor,  prokaryotic cells, and was named the well­known ‘universal’ tree of life. However, because  eukarya and archaea are more closely related, there has been building evidence of the possibility  that eukarya actually descend from archaea rather than prokarya. This would suggest the  presence of only two primary domains, and the most support for this idea is found in the eocyte  hypothesis. The true phylogenetic tree is yet still debatable due to the many strains in discovering all  of the evolutionary divergences that took place billions of years ago. One of the many challenges of reconstructing ancient relationships is the fact that the oldest confirmed eukaryote was found  in a fossil that dated back to 1.8 billion years ago, giving protein and DNA substitutions more  than enough time to have any connection between eukaryotes and archaea be completely  untraceable. Studies supporting the three­domains phylogenetic tree didn’t take into account the  possibility of similar bases or amino acids grouping together. Assuming complete homogeneity  of specific bases and the rate at which they evolve can result in false phylogenetic trees, as  similarly­composed may group together even if they are not associated.  Decker 2 Similarly, when analyzing ribosomal RNA and protein­coding genes to develop a  phylogenetic tree, there is usually strong evidence of series of long branches. Called long branch  attraction (LBA), these long sequences will cluster together regardless of their ancestors which,  in effect, will result in many errors in the tree. Imposing a method to reduce this effect, the  eocyte hypothesis was suggested when analyzing rRNA sequences. When focusing on RNA  polymerase sequences, archaea was favored to monophyletic, but in opposition, the eocyte  hypothesis was again more favorable when taking into consideration the among­site variation of  the rRNA and RNA polymerase sequences together. To make sense of the flustering  observations, it was suggested that short branches may have clustered to form the eocytes and  long branches of eukaryotes and it was much more challenging to create the eocyte tree using  these naive methods.  Another critical factor to consider in this phylogenetic tree debate is the analysis of  proteins shown to be conserved on all genomes, called the “genetic core.” Analyzing the proteins of the genetic core have produced opposing phylogenetic hypotheses in many cases, however.  One reason for this may be the various sequencing­aligning methods, while another could be the  phylogenetic method used. Brown et al. found that using model­based methods produced a  results suggesting the eocyte hypothesis, but using maximum frugality revealed the three­domain topology. Models used over the past few years have implemented methods that are less  susceptible to LBA and other errors seem to go hand­in­hand with molecular sequence data  much better. All of these studies have interestingly produced an eocyte topology, although not  many have been conducted.  Decker  3 With the help of enhanced sampling, relatives of eocytes have recently been discovered.  These lineages in the “TACK” superphylum are comprised of Thauumarchaeota, Aigarchaeota,  and Korarchaeota. Tubulin, actin, and a number of genes that play primary roles in transcription  and translation found in these relatives are homologous to eukaryotic genes. None of these  eukaryotic cell relatives contain all of the genes though, suggesting that the patterns of  distributing between the genomes of eukarya and archaea was completed by either horizontal  gene transfer (HGT) or total loss of that missing gene. Comparative genomics has exhibited and established that the genomes of eukaryotic cells contain many different genes that are found to be of various origins. However, the preserved,  core proteins mentioned previously do not have much relationship to those of archaea. This  evidence provides clarity that there is not a phylogenetic tree that fully describes the history of  genomic information of eukaryotic cells. As it is becoming more apparent the power of HGT and the fact that this occurs mainly within domains rather than between, we can assume from current  evidence that prokaryotes have been transferring their bacterial data long before eukaryotes  obtained their plastid and mitochondrial endosymbionts. The reason that HGT occurs in metabolic pathways rather than in the core (preserved)  genes involved in translation and transcription is currently assumed that because if these genes  are substituted, the cell will likely become more susceptible to become extinct by means of  natural selection as they plan an extremely important role in cellular communications. The  universal core genes are then the most believed genes to have been available to track ancestrial  DNA because of their vertically­restricted dependence. In the universal tree hypothesis, these  Decker 4 genes are as historic as archaea but the eocyte hypotheses implies that these genes were derived  from within archaea, meaning that eukaryotes are comparatively young.  Other information insinuates the presence of photosynthetic bacteria in microfossils and  stromatolites which date back to 3.4 billion years ago, while biological methane (methanogenic  euryarchaeota) depicts archaea as being 3.5 billion years old. Based on these two analyses,  eukaryotes might be about 2 billion years younger. One can also focus on the timing of  eukaryotic endosymbiosis of mitochondria when searching for the origin of eukarya. Archezoans were hypothesized to have descended from eukaryotes that never obtained mitochondria, but  were found to have a mitochondrial homologue which implies that mitochondrion were obtained  even before eukaryotes. This also supplies firm indication that the mitochondrial­endosymbiotic  alphaproteabacteria are actually older in history than eukaryotes. Additionally, if all eukaryotes  contain a mitochondrion and a nucleus, it is impossible to tell which came first. Cells that  obtained mitochondrion didn’t necessarily have to have already had a nucleus and this  strengthens theories of prokaryotes being the cells that obtained mitochondria via endosymbiosis. Focusing on eukaryotic cell membranes can also bring enlightenment in the search for the origin of eukaryotes. Plasma membranes of bacteria and eukaryotes mainly entail the same  phospholipids containing fatty acids with ester bonds to sn­glycerol­3­phosphate, but archaea  mostly contain phospholipids containing isoprenoid chains with ether bonds to sn­glycerol­1­ phosphate. To survive and preserve its membrane in more extreme environments, archaea may  have evolved to using this compositionally­different membrane. Many may ask how the  membrane composition was reversed among the the eukaryotes when doubting the eocyte  hypothesis, but the genes required to produce both types of plasma membranes have been  Decker  5 discovered in all three of these groups while experimental data has proven that mixtures of these  membrane lipids are unwavering. The molecular sequencing experiment by Carl Woese was no doubt a ground­breaking  discovery, as it recognized bacteria, archaea, and eukarya as being the three primary domains of  cellular existence. However, the extreme impact of HGT suggest tat it is impossible to have a  single phylogenetic tree that truly depicts the evolutionary history of eukaryotes and prokaryotes. In light of this, some version of the eocyte tree is the most logical hypothesis for the origin of  genes associated predominantly in translation and are also found to be most resilient to the  likelihood of HGT. Supposing the eocyte tree hypothesis is true would indicate that archaea of  the TACK group possibly hold information that would help solve the mystery of complicated  eukaryotic configurations while also rejecting the 3­domain hypothesis of eukaryotes as being an elemental source of cellular evolution. In effect, this would reduce our primary domains to a  number of two, archaea and bacteria and completely undermine the hypothesis of the universal,  three­domain hypothesis. To have been told that there were three primary domains all throughout grade school and  then have read these articles is very eye­opening. I understand Woese’s hypothesis has been  accepted as the universal phylogenetic tree of life, as it was a revolutionary idea to everybody  and that it provides a basis for us all to comprehend the origins of living microbial cells.  However, these articles have made me realize the endless questions that are left unanswered and  the information that is yet to be uncovered. The human population has made unbelievable  discoveries regarding eukaryotic cells and where they came from, as there is abundant scientific  evidence to suggest these hypotheses. However, the two­domain eocyte topology and the many  Decker 6 other theories that has been proposed in this review are defined as hypotheses. This means that  they have not been confirmed. I do admit, this article was very persuasive and an extremely  interesting read and I am not disagreeing with the eocyte hypothesis as it may very well be true.  Although I do deem that there is much more for us to discover regarding the origin of cellular  lineage and I am very eager to see what the future has in store for our breakthroughs.


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