LECT_Notes_Phylogeny

LECT_Notes_Phylogeny - Diversity and Phylogeny of Microbes...

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Unformatted text preview: Diversity and Phylogeny of Microbes Methods for Determining the Relatedness of Organisms Morphology Morphology worked very well to tell us how macroscopic organisms are relate to each other. This yielded the five-kingdom view: plants, animals, fungi, protests, and monera (a.k.a. the prokaryotes). This method did not work very well for prokaryotic organisms, as they do not look very different from one another. Darwin and Wallace, by closely studying such things as the morphology of finch beaks on the Galapagos Islands, developed the theory of evolution. This theory stated that all life forms have a common origin. How all of life was related to each other could not be discerned from morphology. 16S rRNA Understanding what united all life forms (DNARNAprotein) gave us the means to analyze the relatedness of organisms. What was chosen was 16S rRNA (equivalent to the 18S rRNA of eukaryotes). This yielded the current view of the three domains of life: the bacteria, the archea, and the eukarya. Textbook Reading Phylogenetic Classification, pg. 489-494 What you should get out of this text: 1. Know the four criteria that are used to choose genes to construct the universal tree of life. a) universally distributed b) functionally homologous c) have regions of sequence similarity d) have regions that differ 2. Be able to explain why each of these four criteria are critical. 3. Know that 16S rRNA is the molecule of choice for most phylogenetic analyses. Constructing the Tree of Life…Or is it a Ring? Phyogenetic Trees Phylogenetic trees based on a gene such as that for the 16S rRNA are now the standard for understanding how all organisms are related to each other. The textbook reading provides a explanation of how a tree is constructed. Textbook Reading Phylogenetic Trees, pg. 494-495 What you should get out of this text: Understand how a simple tree is constructed based on evolutionary distance. a) align sequences 1 b) determine the fraction of the total number of bases analyzed that are different between each pair of two organisms (i.e. evolutionary distance) c) construct tree where the sum of the branch lengths that connect two organisms add up to the fraction determined in b) d) know what nodes and branches represent A Ring of Life? With the entire genome sequence of hundreds of organisms now available, efforts are now on going to determine the relatedness of organisms based on the whole genome sequence. This effort may be answering some of the questions that have arisen when looking at genes other than that for the 16S rRNA. For example, depending on the genes used, trees could show the Eukarya as being more closely related to the Archea or the Bacteria. In general the pattern that has emerged is that eukaryotic informational genes (genes involved in transcription, translation and other related processes) are most closely related to archaeal genes, whereas eukaryotic operational genes (genes involved in cellular metabolic processes such as amino acid biosynthesis, cell envelope and lipid synthesis, and so on) are most closely related to bacterial genes. Dr. James Lake and Maria Rivera, here at UCLA, used whole genome comparison of 10 organisms representing the three domains of life. What they found that the best fit to the data was not a tree, but a ring with the Eukaryotes have been formed by genome fusion of a member of the Bacteria and a member of the Archea. For more information, I have provided a link to the website for this paper (very optional reading). From the following article: The ring of life provides evidence for a genome fusion origin of eukaryotes Maria C. Rivera and James A. Lake Nature 431, 152-155 (9 September 2004) doi:10.1038/nature02848 2 Microbial Diversity Discovery of Microbial Diversity A revolution in our understanding of microbial diversity was brought about by the knowledge that 16S rRNA could be used to reveal the relatedness of organisms. Scientist started looking at the 16S/18S rRNA from all the known organisms. What it revealed was that the diversity of prokaryotes was far, far, far greater than anything observed with plants or animals (see Figure 11.16 on page 314). Morphology had not even come close to revealing this level of diversity for prokaryotes. And this finding is not because 16S rRNA underestimates the diversity of plants and animals. In fact, the morphological and 16S rRNA analyses agree quite well about the relatedness of plants and animals. It had long been known that we could not culture in the laboratory the majority of cells from an environmental sample that could be observed under a microscope. If we could not grow these microorganisms in the laboratory, we had no way to study them. PCR (polymerase chain reaction) changed all this. We could ask what genes were present in the DNA of these environmental samples. PCR allowed scientist to amplify sufficient quantities of a particular DNA sequence that they could subject that DNA to sequence analysis. PCR amplifying 16S rRNA genes from environmental samples revealed the diversity of organisms present. There generally would be 100’s to 1000’s of different prokaryotic organisms in an environmental sample. Many of these organisms were from groups that had never been studied in the laboratory before. These types of analyses have increased our depth of appreciation of the diversity of microbial life. Textbook Reading Sequencing 16S rDNA, pg. 495 What you should get out of this text: Understand the general mechanism by which you can determine the diversity of organism present in a microbial sample. a) isolate DNA from an environmental sample b) PCR amplify 16S rRNA gene using primers that are general for all 16S rRNA genes or more specific primers. c) separate the individual pieces amplified pieces of DNA (by cloning or other method) d) sequence and then generate a tree 3 Bioprospecting Bioprospecting is the “panning” of the microbial world for new products and processes. Current estimates are that, for every one prokaryotic species we have studied in the laboratory, there are as many as 1000 species in the environment that we have not studied. This translates to 5 to 8 million species waiting to be discovered. Now scientist can isolate DNA from environments, break it up, clone pieces into a bacterium like Escherichia coli, and then determine whether the E. coli clones express an interesting activity. 4 ...
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