Micro. Lecture 15 (2001) Diana Nemergut

Diana Nemergut

nemergut@colorado.edu

Chapters 13 and 14

Ziebuhr, W., K. Ohlsen, H. Karch, T. Korhonen and J. Hacker. 1999. Evolution of bacterial pathogenesis. Cellular and Molecular Life Sciences. 56: 719-728

link to reference

Generation of variation in Bacteria

Mechanisms that generate variation:

    Outline:

  1. Mutational processes
  2. Horizontal gene transfer
    1. Acquisition of foreign DNA that can remain extrachromosomal
    2. Acquisition of foreign DNA that can be integrated into the chromosome
  3. Within-genome recombination

1. Mutational processes

- general definitions (top of table 13.2)
  1. DNA level definitions

    2. Substitution- change of one nucleotide for another

    1.Transitions- purine for purine or

    pyrimidine for pyrimidine

    Adenine(A)-Guanine(G)

    Cytosine(C)-Thymine(T)

    2.Transversions —purine for pyrimidine

    or vice-versa, less common

    Addition or deletion of base pairs

  2. Protein level definitions

Silent mutation- triplet codes for same amino acid

AGG -----> CGG

Arg ------> Arg

Neutral mutation- triplet codes for different but functionally similar amino acid

AAA ------> AGA

Lys -----> Arg

Missense mutation- triplet codes for a different (functionally) amino acid

AAA ------> GAA

Lys -------> Glu

Nonsense mutation- triplet codes for a premature stop codon

CAG -----> UAG

Gln -------> STOP

Frameshift mutation- addition or deletion of base pairs that changes the reading frame of the mRNA

AAAAGACGG -------> AAAGACGG

Lys Arg Arg -------> Lys Asp
  1. Mutational processes
    1. point mutations (antibiotic resistance)
    2. mutator strains (increased mutation rates)
    3. slipped strand mispairing (phase variation in antigenic determinants)

 

  1. Point mutations- Antibiotic resistance, mutations in rRNAs or proteins that confer resistance to antibiotics

    2. Rifampin/Mycobacterium

    -inhibits transcription

    -mutations in RNA polymerase enzyme confer resistance

    -example of a change in a single amino acid that can have a HUGE effect on fitness

    Streptomycin/Mycobacterium

    -binds 16S rRNA, inhibits translation

    -several 1 base substitutions in 16S rRNA confer resistance

  2. Mutator strains- mutations in polymerase or proofreading genes that lead to increased general mutation rates. Good for adapting to continually changing environments

    3. Cystic Fibrosis

    -mutation in transmembrane proteins, leads to hyperosmolar, viscous mucous in the lungs

    -colonized by Pseudomonas aeruginosa, must adapt to heterogeneous environment

    Pseudomonas aeruginosa isolates from CF patients have a much higher rate of mutator strains than from non-CF patients

    -way to quickly generate variation and adapt to a heterogeneous environment

  3. Slipped strand mispairing- DNA polymerase slips during replication because of repeats in promoter or protein coding regions

-phase variation- repeats increase rate of SSM and lead to increased variation

Mycoplasma- vlp gene family codes for surface antigen proteins

-a "pure" culture of Mycoplasma always has a mix in surface antigens

-promoter has a polyA tract that increases the rate of polymerase slippage, leading to differential expression of these proteins

-variation in antigens is good way to evade the host immune system

2. Horizontal Gene transfer

- transfer of DNA between independent organisms

General mechanisms of DNA uptake by microbes (pg 290- 298)

    1. Transformation- uptake of naked DNA by cells (mistake in book)

      2. -competent cells

      -Figure 14.16

    2. Conjugation- transferring DNA by cell to cell contact

      3. -Figure 14.14

    3. Transduction- transferring DNA by viruses-

-Figure 14.18

All mechanisms can transfer DNA that remains extrachromosomal or that integrates into the host chromosome.

  1. Foreign DNA elements that can remain extrachromosomal
  1. plasmids (Figure 14.16B)

-circular (generally) DNAs with origin of replication that are passed on to daughter cells

—ex.-Rhodococcus virulence plasmid

-mechanisms- conjugation, transformation and transduction
  1. Foreign DNA elements that can be integrated into the chromosome
  1. Episomes- plasmids that integrate into host chromosomes

    2. -mechanisms- conjugation and transformation OR transduction AND integration

  2. phage (Figure 14.18b)

    3. -mechanism- transduction and integration (lysogeney)

    -integration is usually site-specific

  3. "pathogenicity islands"- huge cassettes, arrays of genes that are up to 200 Kb in

    4. size with virulence genes

    ex. PAIS

    -mechanisms- transduction, transformation OR conjugation AND integration into host genome

  4. transposons/ insertion sequences (pg 285-289)

    5. -mobile DNAs with genes needed for transposition, flanked by repeat sequences

    -simplest elements are insertion sequences (IS)

    -IS with other genes are transposons

    -ex. composite

    -mechanisms- hitch a ride on plasmids

    (transformation, conjugation or

    transduction) or on phage genomes

    (transduction) AND integration

  5. mobile gene cassettes- small, circular DNAs that generally contain one ORF with little regulatory information

-can be integrated and expressed by integrons

-mechanism- transformation (probably) and integration behind promoter of integrons, integration is site-specific

 

 

3. Within genome recombination,

    1. within genome homologous recombination- mediated by regions of sequence similarity
      • Niesseria gonorrhea- lots of genes for antigenic determinants. Like regions of these genes can pair and swap genetic material to increase the variability of these proteins
  1. transposable elements

-insertion sequences and transposons can move around the genome and insert themselves randomly

-insertion can interrupt coding regions and result in a non-functional protein or can interrupt regulatory regions (promoters) to change expression of genes