Monday, April 13, 2009
LUCA
On page 86, Carroll states, "... there was a common ancestor of all threee domains (the last "universal" common ancestor, or LUCA) that then split into two domains, the Bacteria and Archaea, and the eukaryotes arose later from a branch of the Archaea." Explain the evidence that supports this idea, both from the book and from outside research, and discuss how the "tree of life", as Carroll calls it, grew from LUCA into what it is today. Also, discuss any information scientists may have about LUCA in terms of basic traits, how old it is, etc.
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ReplyDeleteLUCA is believed to be the most common universal ancestor because it has numerous factors that are in common with all living creatures that exist today. The LUCA is estimated to have lived 3.5 to 3.8 billion years ago around the time in the paleoarchean era. What binds all the living organisms on earth to LUCA is that the genetic code contains DNA. It has the four basic nucleotides of deoyadenosine, deoxycytidine, deocythymidine, and deoxyguanosine. The genetic code is also composed of three nucleotide codons.
ReplyDeleteThe codons are crucial to the entire life of an organism. It instructs how an organism creates polypeptide chains that influence the structure and actions of an organism. First there is codon recognition where the mRNA codon in site A of the ribosome forms a hydrogen bond with the anticodon and the attached amino acid of an incoming molecule of tRNA. The rRNA molecule of a large ribosomal subunit, used as a ribozyme, catalyze the formation of the peptide bond that joins the polypeptide extending from the p site of the newly arrived amino acid in the A site. The ribosome now translocates the tRNA in the a site to the p site and as the t RNA moves, the anti codon remains bonded to the mRNA codon and brings another codon to be translated. Then the codon in the p site is moved to the e site as it exits the ribosome. The translocation requires energy and the mRNA moves through the ribosome in one direction only. This unique and universal process justifies how we all must originate from distinct ancestor.
Other characteristics about LUCA is that the DNA is double stranged and requires DNA polymerase to read in order to duplicate the DNA in order to grow. The entire DNA strand is maintained by a group of topoisomerase, ligase, histones, and repair enzymes that all are there to maintain and help reproduce and duplicate the cell multiple times. The DNA strand is all expressed through transcription and translation where RNA polymerase reads the DNA and translates the mRNA into poly peptides. All proteins are made from amino acids and described in the process above. The cell’s membrane contains a distinct lipid bilayer.
“Once a list of these genes has been made, they also lead to another possibility: perhaps this list captures the essence of cellular life — the minimum number of genes required to make a cell. In 1996, with the sequences of the first two bacterial genomes (_Mycoplasma genitalium_ & _Haemophilus influenzae_) in hand, Arcady Mushegian & Eugene Koonin [Mushegian & Koonin 1996] tried exactly this. The most striking features of their minimal genome were: * A mere 256 genes * No biosynthetic machinery for making the building blocks of DNA From this they tentatively concluded that LUCA stored its genetic information in RNA, not DNA, and made suggestions on how to further reduce the number of genes in their minimal genome. The work heralded the arrival of comparative genome studies, and there is no doubt that a good number of the genes in their 256-strong list do date back to the LUCA.” IT shows that the basic genes of life all 256 the most crucial ones are extremely low. This then relates to how complexity must have stemmed from simplicity which allows scientists to believe that LUCA must have contained all 256 which makes it a huge qualifier for the most common ancestor.
“Candidatus ruddii, a bacterium, took the title again, with a genome only 159,662 base pairs long. The LUCA probably had a genomic complexity in this general range.” It is said that the LUCA resembles more closely to the bacteria and archaea domain. From there the necessities and complexities of life stemmed forward.
http://en.wikipedia.org/wiki/Last_universal_ancestor
http://www.actionbioscience.org/newfrontiers/poolepaper.html
http://www.wisegeek.com/what-is-the-last-universal-common-ancestor-luca.htm
During earlier studies of the tree of life, the origins of bacteria, archaea and eukaryotes were very indistinct. Different research showed similarities between all three, but the question was which two had the most in common. Recently, this was determined as eukaryotes and archaea. It is believed that the universal ancestor (LUCA) descended to archaea and bacteria. Then, archaea branched off to show eukaryotes.
ReplyDeleteLUCA stands for last universal common ancestor. It is guessed that this single cell lived about 3 or 4 billion years ago and that all life evolved from it. There is proof that everything on Earth is related to this common cell and it is shown in genetic code. One example is the huge similarities between bacteria and humans. Their DNA is so similar that human DNA can be injected into bacteria to produce proteins. This is how insulin is artificially made for humans with diabetes.
Before the tree of life was fully established, the three branches that we know use were not fully understood. Archaea were just recently given their own branch and it was earlier thought that there were two main branches: prokaryotes (bacteria and archaea) and eukaryotes (plants, animals and fungi). The differences between bacteria and archaea were then unclear. Now, scientists realize the strict differences and the tree of life was reconstructed. The initial decision to split the branches between eukaryotes and prokaryotes were the basic and distinct differences between the two. Eukaryotes all have a nucleus while prokaryotes don’t. However, both bacteria and archaea don’t have a nucleus, but they are now realized to be different enough to end up in two different branches.
Changes are made all the time to the research done on LUCA. It was, until recently, thought that the LUCA craved heat and was a hyperthermophilic organism. However, recent studies show that the LUCA was actually sensitive to heat and lived in an environment of 50 degrees Fahrenheit or cooler. This just shows how much the branches of life have changed so readily. Changes even in the LUCA are still being found, changing much of what we’ve thought of organisms today.
LUCA started out with RNA instead of DNA. This was a mystery for many scientists because RNA is sensitive to heat and early Earth had very high temperatures. However, studies done on the micro climate of the Earth found an environment where this cell could live. Proof of evolution was then found as the RNE evolved to DNA. DNA is much more stable in hot or changing environments, therefore making it a selective advantage to have DNA over RNA. This evolution helped the organism survive and branch out into what we know as the tree of life.
http://www.actionbioscience.org/newfrontiers/poolearticle.html
http://www.sciencedaily.com/releases/2008/12/081217124200.htm
LUCA
ReplyDeleteOn page 86, Carroll states, "... there was a common ancestor of all three domains (the last "universal" common ancestor, or LUCA) that then split into two domains, the Bacteria and Archaea, and the eukaryotes arose later from a branch of the Archaea." Explain the evidence that supports this idea, both from the book and from outside research, and discuss how the "tree of life", as Carroll calls it, grew from LUCA into what it is today. Also, discuss any information scientists may have about LUCA in terms of basic traits, how old it is, etc.
Answer:
The LUCA is not the first living thing ever or the most primitive possible living organism, just the universal common ancestor of all extant organisms. The evidence that the book gives about the three domains and LUCA is that Archaea and eukaryotes are more closely related than to bacteria therefore eukaryotes had to branch off from Archaea. But much research showed that the majority of Achaean genes showed the greatest similarity to bacteria. This makes resolving the tree of life more difficult. But when more research was conducted, it was noted that “similarities between eukaryotes and bacteria were in operational genes involved in the metabolism of various nutrients and basic cellular materials” (87). Comprehensive analysis at UCLA showed that the eukaryote genome is the product of a fusion between a relative of Archaea and a relative of bacteria. This intertwines with the theory of endosymbiosis.
As a compellation of all of this research, the tree of life now grew into more of a ring, not a conventional trunk, from which the tree ascends and branches. Researchers are trying to reconstruct LUCA, the cell from which all life has evolved. Although it sounds easy: compare all three groups and choose the features that are common to all. In actuality, many genes were lost or swapped throughout horizontal transfer of genes. “There is still much uncertainty about LUCA and we’re not sure we can ever find out the truth. LUCA's genetic redundancy predicts loss of paralogous gene copies in divergent lineages to be a significant source of phylogenetic anomalies”. Carl Woese, one of the key researchers in reconstructing the tree of life is suggesting that there might have been more than one LUCA’s.
LUCA is a single cell that lived perhaps 3 or 4 billion years ago, and from which all life has since evolved. LUCA stored its genetic information in RNA and had at least 256 genes. The LUA is estimated to have lived some 3.5 to 3.8 billion years ago. It is generally believed that LUCA was a heat-loving or hyperthermophilic organism. Another shared feature is the way DNA instructions are expressed via single-stranded RNA intermediates. These RNA intermediates lead to the construction of proteins by ribosomes, tRNA and a group of related proteins. These proteins are built from 20 amino acids, and the synthesis pathways are arbitrary but universal. All forms of life use glucose (simple sugar) as a source of energy and carbon. ATP is always used as the energy currency of the cell. The LUCA would have had a simple locomotion system based on microtubules. The main features of LUCA that we can figure out are features that are shared by all domains. We are still limited greatly on our knowledge of LUCA.
http://www.actionbioscience.org/newfrontiers/poolepaper.html
http://en.wikipedia.org/wiki/Last_universal_ancestor
http://www.biolbull.org/cgi/reprint/196/3/373.pdf
http://www.physorg.com/news148741334.html
http://www.biology-direct.com/content/3/1/29/abstract
http://www.sciencedaily.com/releases/2008/12/081217124200.htm
Seriously? Three people replied while I was still writing mine? Sigh...
ReplyDeleteThe LUCA is theorized as being the organism from which Archaeans and Bacteria originally split off evolutionarily. It is estimated to have existed around 3.5 to 3.8 billion years ago. While the LUCA is the ancestor to all modern-day organisms, it was not the first organism to have existed. The earliest life is believed to have been self-reproducing RNA molecules. From the existence of life and organisms, natural selection arose. Contrary to what the "conventional" genealogical tree may imply, the LUCA was not one particular organism. It was the communal grouping of primitive cells that evolved together and eventually broke off into the two evolutionary lines of Archaea and Bacteria (which later formed the third doman Eukarya through endosymbiosis). The evolution from the origin of life into the LUCA involved the development of DNA. Natural selection favored the efficiency of DNA replication, and this is the basic defining factor of the LUCA. All known living organisms, from complex animals like humans to a unicellular bacteria, use this same biochemical stucture - DNA. The branching of all life forms from a single LUCA explains how every organism can contain the same rudimentary structure. Due to the tendency of evolution to repeate itself, as Carroll has talked about extensively, it may not seem too far-fetched to wonder if DNA could evolved independently. After all, it is a relatively simple structure that provides an immense selective advantage. However, based on current research, Caroll points out that there are "about 500 genes that exist in all domains of life" (79). This essentially proves that all of these organisms did have a common ancestor, the LUCA.
The only point that I've mentioned that may be confusing is the idea that the LUCA was not a single organism but a commmon ancestral community of primitive cells. It is important to distinguish the differences between modern-day natural selection and the microbial natural selection that was taking place in this very early stage of life. Today, we understand the primary evolutionary mechanism to be reproduction. As an organism reproduces, sexually or asexually, the offspring contain mutations, which may be advantageous or not. Among microbial organisms we see the secondary evolutionary mechanism of horizontal gene transfer. This basically describes the process of an organism incorporating foreign genetic material into its own. In the very early stages of life, this horizontal gene transfer was the dominant force affecting natural selection, not reproduction. Because of this, these early cells would constantly mix their genetic information wthin this large community of cells. As a result, genealogical trees are essentially useless at distinguishing between these different cells but are also generally unimportant at this point. These communal cells, even if they do not technically make up a single organism, are the LUCA. From this community arose all life.
Sources:
http://en.wikipedia.org/wiki/Last_universal_ancestor
http://www.actionbioscience.org/newfrontiers/poolepaper.html
http://www.pnas.org/content/95/12/6854.full