lesson 7

• Evolution


  The process by which living organisms phenotypically change over time, due to heritable changes in the genome (mutations) or horizontal gene transfer
• Evolution is random or non-random, but adaptive evolution is driven by natural selection
• Natural selection doesn't 'cause' mutations
• Wild-Type (WT) Strain

  Strain isolated from nature; contains WT genome
• Mutant

  Derived from WT strain; contains a mutation
• Genotype


  Nucleotide sequence of genome, gene, etc
• Phenotype


  Observable properties of organism
• Mutations can be beneficial or deleterious, but most are neutral
• Isolation of Mutants by "Replica Plating"

  1. Select for antibiotic resistance; nutrient utilization

  2. Mutant with additional nutrient requirements = auxotroph

  3. Screen for colour changes, morphology changes

  
• Point mutation


  Mutation in a single base pair
• Spontaneous rate of point mutations is slow, but exponential growth = rapid accumulation
• Point mutations can be "induced" by mutagens like UV, chemicals, humans
• Frameshift mutations

  Insertions or deletions that shift the reading frame, usually very serious
• Horizontal Gene Transfer


  Transfer of genes from "donor" to "recipient" instead of parent to progeny

  
• Fate of Horizontally Transferred DNA

  1. Degraded by restriction enzymes

  2. Replicate on its own (requires origin of replication)

  3. Recombine with host chromosome (requires RecA)

  
• Transformation


  Free DNA released by one cell is taken up by another
• Very few species are naturally competent for transformation: e.g. Bacillus, Streptococcus (some other G+). Most are not: e.g. E. coli (most other G-)
• Competence can be induced chemically (Ca2+ neutralizes DNA and membrane charge) or by electroporation (high voltage permeabilizes membrane)
• DNA Binding Protein

  Usually Type IV pilus
• Transduction

  DNA transferred from one cell to another via a virus (bacteriophage)

  
• Transduction by Lytic Viruses


  Accidental packaging of host DNA into viral particles instead of viral genome, injected into donor, recombination

  
• Transduction by Lysogenic Viruses

  Virus integrates into host genome (prophage), replicates with host, when virus enters lytic cycle it can accidentally pick up adjacent genes, lyse donor, infect and integrate into recipient cell with donor genes

  
• Conjugation


  Conjugative plasmids (F plasmids = fertility plasmid) transferred via cell-cell contact through sex pilus (F pilus)
• F Plasmid of E. coli

  tra region encodes sex pilus, OriV for normal replication, OriT for replication during conjugation, IS for potential recombination with genome, Tn1000 for transposable elements
• Rolling Circle Replication


  Pulls cells together, forming mating bridge at oriT
• Hfr Cell


  F+ but F plasmid has integrated into genome, can transfer chromosomal elements

  
• Homologs


  Genes inherited from common ancestors, with similar sequences
• Paralogs


  Results from gene duplication followed by mutation, different functions

  
• Orthologs


  Results from slow mutation over time from a common ancestor, same functions
• Gene Duplication


  Spare copy of gene is free to undergo mutations without sacrificing function of original gene
• Transposons


  Mobile genetic elements that move between chromosomes, plasmids, viruses via the enzyme "transposase", can create duplications, deletions, inversions

  
• Systematics


  Phylogeny (evolutionary relationships) + taxonomy (naming/characterizing/classifying based on predetermined criteria)

  
• Endosymbiotic Origins of Eukaryotes

  Mitochondria = aerobic bacterium engulfed by early eukaryote, Chloroplast = cyanobacterium engulfed by early eukaryote, both contain 16S rRNA and 70S ribosomes
• Woese and the Tree of Life: in the 1970s, sequence of ribosomal RNA (rRNA) genes used to infer evolutionary relationships between organisms (phylogeny)</b>

  
• rRNA genes are excellent candidates for phylogenetics because they are universally distributed, functionally constant, highly conserved, and adequate length to provide information
• Phylogenetic analysis focuses on orthologs (genes with the same function)

  
• Sequence Alignment


  Allows determination of differences between sequences, factors in insertions/deletions
• Phylogenetic Trees


  Diagrams that depict evolutionary relationships, with nodes representing ancestor divergence and branches containing unique species or lineages

  
• Phylogenetic trees assume vertical gene transfer, but horizontal gene transfer interferes with this
• rRNA genes are very rarely horizontally transferred, making them excellent candidates for phylogenetics