Lecture_10-11 - BIOL 214 GENES, ECOLOGY AND EVOLUTION /...

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Unformatted text preview: BIOL 214 GENES, ECOLOGY AND EVOLUTION / PEPPER LECTURE 19 (October 11, 2006) SUPPLEMENT READING ASSIGNMENTS: Origins of Life and Precambrian Evolution, pages 370-392. "Genomics and the Tree of Life" Rokas, Science Sept. 29, 2006 (PDF) "What is the minimal genome for life?" see below. READING AHEAD: Mutation and Genetic Variation, pages 197-207. READ FOR FUN: "Solar-Powered Sea Slugs" Rumpho et al. 2000 (PDF) KEY CONCEPTS: `Scavenger hypothesis' for the origin of eukaryotes No early-branching thermophilic eukaryotic lineages May have been decomposers, heterotrophs at the periphery of hydrothermal vents Energy efficiency gained from endosymbbiote (protomitochondria) would have allowed for greater size and mobility in this lineage First eukaryotic fossils (approx. 2Ga) during a time of steep rise in oxygen levels Endosymbiotic theory of chloroplast origins Chloroplast circular genome (85-115 genes in most plants) Cyanobacteria (oxygenic photosynthetic Bacteria) Most numerous organisms in the biosphere, including photic zones of all the world's oceans Currently responsible for 30% of the world's primary productivity (CO2 fixation) Oxygenic photosynthesis CO2 fixed by Calvin Cycle enzymes Photosystems PSI and PSII in folds of inner membrane known as thylakoids The capacity to produce one's own food from light and CO2 would have conferred a massive advantage to organisms with endosymbiotic cyanobacteria/proto-chloroplasts Most of the genes from the endosymbiotic cyanobacteria can now be found in the plant nucleus Modern, living single-cell protists (Eukarya) with endosymbiotic cyanobacteria Modern, living multicellular animals, including molluscs (e.g. Elysia chlorotica) with endosymbiotic chloroplasts Endosymbiotic and other mutualistic interactions are a major theme in evolution (and in ecology) that was unknown to Darwin Different universal phylogenetic trees based on different genes give different topologies for the relationships of eukarya, bacteria and archea Suppl. to Lecture 19, page 1 Recent whole genome sequencing has recently discovered that whole large `blocks' of genes were transferred among the eukarya, bacteria and archea before, around, and soon after the major divergence of these lineages Horizontal gene flow (also known as lateral gene transfer): Is now more common in modern Bacteria and Archea than in Eukarya Was probably very common in the early ancestors to all three groups Many modern species in the domains of Archea and Bacteria will naturally take up naked DNA from the environment and incorporate it into their genomes (natural genetic transformation) Reticulate (net-like) evolution Cenancestors = last universal common ancestors (LUCA) "Minimal genome" of LUCAs ( 800 genes? Range of 400-1400?) Overall increase in predicted gene number and gene functions Increase in predicted gene number is correlated with increased complexity Assimilation of genes (aerobic respiration, oxidative photosynthesis) in eukaryote lineage Genes do not arise de novo (from nothing, or from random DNA sequences); New genes arise from previously existing genes, through duplication and divergence, and through `mixing and matching' of gene-sections known as `protein domains' WHAT IS THE MINIMAL GENOME FOR LIFE? Bacterial pathogens and parasites have some of the smallest predicted gene numbers of any organisms. Mycoplasmas are the smallest self-replicating organisms. They are often pathogens and parasites that like warm wet environments like human lung tissue. They can be difficult to detect and to treat. Unlike most bacteria, they lack a cell wall, and are thus can't be effectively treated with penicillin-type antibiotics (which inhibit cell wall formation). Mycoplasma genitalium is a parasite of mammalian genital and respiratory tracts. It has the smallest known genome of any living organism with just 517 predicted genes. Mutational studies suggest that less than 300 of these genes may actually be essential for life (on nutrient media in a Petri dish). Scientist and biotech CEO Craig Venter (who played a key role in directing the sequencing the human genome) has launched a new project to chemically synthesize the entire genome of Mycoplasma genitalium as a single large circular DNA. The DNA would then be inserted into a bacterial "shell" in which the host genome has been destroyed by radiation or other methods. Suppl. to Lecture 19, page 2 Craig Venter, a controversial genome scientist If properly designed, the host's DNA replication and gene expression machinery (proteins and RNAs required for replication, transcription, translation) should theoretically go to work replicating and expressing this new genome, and the organism should begin to divide. This is what is known as a `proof of concept experiment.' According to Venter, if this experiment works, it could open the way to building `designer' microorganisms that produce fuel or act as an agent for bioremediation of contaminated environments. Genes could theoretically be incorporated from other bacteria, from archea and from plant, animal, fungal and other eukaryotic genomes. This new `designer' organism would combine genes from archea, eukarya and bacterial domains. Organisms created this way would thus constitute a completely new domain (the name "Venteria" has been suggested ). STUDY QUESTIONS: 1. There are several evolutionarily distinct oxygenic-photosynthetic lineages in both Eukarya (e.g. Euglena, Plants, Chlamydomonas) and in Bacteria (e.g. Chlorobium, Chromatium, Cyanobacteria) in the rRNA-based tree of life presented in class. Do you think oxygenic photosynthesis evolved independently in each of these lineages, or can you think of any alternatifve explanations. 2. It has been said that plants have three genomes. Explain. 3. Do you think modern mycoplasmas have a set of genes that is very similar to the set the LUCAS would have had? How would it be similar; how would it be different? 4. Do you think an organism with 517 genes could survive as a free-living entity in an open environment (outside another living organism)? 5. What do you think are some of the moral and ethical issues surrounding the `designer organism' project described in "What is the minimal genome for life"? 6. If you were going to build an organism from the ground up for use as a bioremediation agent, or to make biofuels, would you start with the Mycoplasma genetalium genome? Suppl. to Lecture 19, page 3 7. The human genome is predicted to have approximately how many times as many genes as a typical genome from free-living organisms in the domain Bacteria (such as E. coli and cyanobacteria)? A. Twice as many genes B. Four times as many genes C. Ten times as many genes D. Forty times as many genes E. One hundred times as many genes Suppl. to Lecture 19, page 4 ...
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