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MICROBIOLOGY EXAM II- HGT is an important mechanism of evolution & diversity- Review: Evolutiono Mutationo Genetic change -> Phenotype changeo Different phenotypes among individuals in a populationo Different phenotypes confer differences in survival and/or reproductiono Environmental factors and ‘random’ events cause differential survival and reproduction o Differential survival and reproduction between individuals can cause population-level changes o The result is evolutionary change - Evolution of bacteria in the lab: Lenski experiment o Initially the bacteria used glucose as their carbon/energy source, but citrate was always in the mediao A decade in, the population emerged that could use citrate as its carbon source o How did this occur? Mutations  The E. coli don’t have taxonomic diversity, so NOT horizontal gene transfer Change in phenotype – enzyme change that could bind to/break down citrate instead of glucose  Survival advantage to using citrate – less competition for the carbon resource  Persistence of this sub-population due to survival and reproduction advantage - Microbial evolution in the wild o Proliferation of the early colonizer, followed by transient immigration of a late colonizer genotypeo DNA transfer from late colonizer to early colonizero Recombination in early colonizer to create Recombinant 1o Proliferation of recombinant 1o Transient immigration of late colonizer genotypeo DNA transfer from late colonizer to recombinant 1o Recombination to recombinant 1 creates recombinant 2o Proliferation of recombinant 2o Accumulation of single nucleotide polymorphisms in recombinant 2o Immigration of late colonizer genotypeo Proliferation of late colonizer genotype - Origin of microbial lifeo Prebiotic chemistryo RNA lifeo RNA and proteinso DNAo LUCAo Diversification of molecular biology, lipids, and cell wall structure o Dispersal to other habitats- Early evolution of microbial lifeo The first cells The first self-replicating entities may not have been cells  LUCA: common ancestral cell from which all cells descended We do not know the identity of this organism; its existence is inferred from genomic information o Hypothesis 1: Surface origin hypothesis The first membrane-enclosed, self-replicating cells arose out of primordialsoup rich in organic and inorganic compounds I ponds on Earth’s surface  Dramatic temperature fluctuations and mixing from meteor impacts, dustclouds, and storms argue against this hypothesis o Hypothesis 2: Subsurface origin hypothesis Life originated at hydrothermal springs on ocean floor- Conditions would have been more stable- Steady and abundant supply of energy (e.g., H2 and H2S) may have been available at these sites - Origin of microbial lifeo Prebiotic chemistry of early Earth set stage for self-replicating systemso First self-replicating systems may have been RNA-based (RNA world theory) RNA can bind small molecules (e.g., ATP, other nucleotides) RNA has catalytic activity; may have catalyzed its own synthesis o DNA, a more stable molecule, eventually became the genetic repositoryo Three-part systems (DNA, RNA, and protein) evolved and became universal among cells - Early evolution of microbial lifeo Earth formedo Oceans form, cover the majority of Eartho First cells appearedo Origin of microbial photosynthesiso Origin Aerobic respiration (bacterial) o Endosymbiosis between Bacteria + Archaea (?) Eukaryotic cells with mitochondria &/or chloroplasts o Archaeal and eukaryotic domains diverge o First multicellular eukaryotic animalso Rapid diversification of animal lifeo Large continents formo Diversification of terrestrial plant life- Three domains tree o Eukarya and archaea are clustered together, bacteria on other side - SSU rRNAo Evolutionary clocko Way to keep track of evolutionary timeo Amplify genomes and see which organisms have similar/different nucleotide sequences- Molecular clocks: models that calibrate gene sequence change with time - The microbiological species concepto Hard to distinguish a species due to horizontal gene transfer- Evolutionary processes – mutation + selection -> diversity - Topology of the three domains of lifeo Bacteria Own groupingo Archaea and eukaryea are more closely related to each other - Understanding evolutionary relationships using genetic informationo Extract DNAo Target the SSU rRNA gene – a “marker gene” (gene that can be used to track a specific trait of process of interest) SSU rRNA is a marker for evolutionary history because changes in its sequence are approximately proportional to base rates of mutation SSU rRNA gene encodes for a structure that is not subject to (much) selectiono Use PCR and sequencing to determine the nucleotide sequence of the marker gene in an individual organism, or in a mixed sampleo Compare the gene sequences to each other, and establish levels of similarity/difference between the sequenceso Compare to other “known” sequences – gene sequences that can be traced to previously described and/or cultured organisms - The bacterial domain contains the greatest amount of genetic/biological diversity - Challenges to defining a species in bacteriao High rates of mutation, horizontal gene transfer, asexual reproduction Viral Genetics - What are viruses?o Viruses are acellular or nonliving o Viruses are obligate intracellular parasiteso The genome of a virus enters a host cell and directs the production of the viral components, proteins and nucleic acids, needed to form new virus particles called virions  New virions are made in the host cell by assembly of viral componentso Most viruses will only be able to infect the cells of one or a few species of organism. This is called the host range - Viral replicationo Inoculation: inoculum of virus binds to cellso Eclipse: virions penetrate the cellso Burst: host cells release many viral particleso Burst size: number of virions released per bacterium - Lytic lifestyleso Viral attachment and penetration The phage infects a cello Integration The phage DNA becomes incorporated into the host genomeo Excision The phage is excised from the bacterial chromosome along with a short piece of bacterial DNA. The DNA is then packaged into newly formed capsidso Infection Phage containing both viral and bacterial DNA infect a new host cello Recombination The phage DNA, along with the attached bacterial DNA, are incorporated into the new cello Killing the

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