Bacterial Genetics and Taxonomy Flashcards

Genetic Transmission in Bacteria

  • Genotype and Phenotype

    • Organisms use their genes in specific combinations to produce what is called a physical manifestation, known as the phenotype.
    • During reproduction, bacteria (the "Mom" cell) make a copy of the nucleoid and split into two daughter cells.
    • This process produces clones, which are genetically identical offspring.
    • Because they share the same genotype, clones will also possess the same phenotypes.
    • This traditional passing of genetic information from parent to offspring is a form of transmission where no change in the genotype occurred during the copying process.

  • Horizontal Gene Transmission (HGT)

    • Bacteria exhibit vertical transmission (reproduction), but they can also perform horizontal transmission.
    • Horizontal transmission allows bacteria to pass genetic information from one cell to another through means other than reproduction.

The Discovery of Transformation: Frederick Griffith (1928)

  • The Experimenter and the Organism

    • Frederick Griffith was a microbiologist who investigated Streptococcus pneumoniae in 1928 as a significant medical problem.

  • Bacterial Variants (Morphovars)

    • Wild Type (Smooth Cells): Normal Streptococcus. When grown on solid media (agar plates), these colonies appear smooth, wet, glistening, and sticky. This appearance is due to the presence of a capsule.
    • Mutant Type (Rough Cells): These colonies appear rough because they have lost the ability to produce a capsule due to a mutation. Most mutations represent a loss of function.

  • The Capsule and Pathogenicity

    • The capsule is a virulence factor that helps the bacterial cell hide from the host's immune system.
    • It is harder for the immune system to mount a fast and effective response against a pathogen with a capsule.
    • Consequently, the smooth strain is an effective pathogen, while the rough strain is less effective.

  • Griffith’s Four-Step Experimental Process

    1. Injection of Live Smooth Cells: He injected smooth Streptococcus into mice. The mice died. He recovered living smooth cells from the mice.
    2. Injection of Live Rough Cells: He injected rough Streptococcus into a second batch of mice. The mice survived. Autopsies showed very few living rough cells remained.
    3. Injection of Heat-Killed Smooth Cells: He boiled the smooth cells to kill them and injected the dead bacteria into mice. The mice survived.
    4. Injection of Heat-Killed Smooth and Live Rough Mix: He mixed the dead smooth cells with the live rough cells and injected the mixture. Unexpectedly, the mice died. The autopsy revealed living smooth Streptococcus cells in the mice.

  • The "Transforming Principle"

    • In 1928, it was not yet known that DNA was the genetic material; the prevailing guess was protein.
    • Griffith concluded that a "transforming principle" from the dead smooth cells had transformed the live rough cells into smooth cells.

Mechanisms of Transformation

  • Transformation Process

    • Transformation occurs when bacterial cells find pieces of DNA in their environment, absorb them, and pull them into the cell.
    • These DNA fragments must be patched into the chromosome to be maintained. Fragments cannot exist indefinitely outside the chromosome because they lack the mechanisms to be replicated and passed to daughter cells.
    • If incorporated via homologous recombination, the new genes are inherited by all future offspring, permanently changing the genotype.

  • Homologous Recombination

    • The mechanism for molecule recombination works best if the two DNA sequences are highly similar (homologous).
    • In Griffith's experiment, the rough cells were genetically nearly identical to the smooth cells, except for the mutation in the capsule-synthesis gene.
    • This high similarity made homologous recombination very frequent and efficient once the rough cells picked up DNA fragments from the heat-killed smooth cells.

  • Competence

    • Bacteria capable of performing transformation are described as being "competent."
    • Natural Competence: Some cells are naturally capable of absorbing DNA from the environment.
    • Artificial Competence: In the lab, scientists can force cells to become competent to absorb DNA.

  • Plasmids in Transformation

    • Plasmids are small, circular pieces of DNA that exist separately from the chromosome.
    • If a cell takes up a plasmid through transformation, the plasmid can be replicated separately without needing to be integrated into the chromosome via homologous recombination.
    • This makes genetic engineering easier, as it simplifies the process to a single step (getting the DNA inside).

Conjugation and the F Plasmid

  • The F Plasmid

    • The F (Fertility) plasmid contains genes that allow a cell to initiate conjugation.
    • A cell containing this plasmid is called an F+F^{+} cell.
    • A cell lacking the plasmid is called an F−F^{-} cell.

  • The Pilus and Transfer

    • The F plasmid encodes the ability to create an F-pilus, a structure used for attachment.
    • The F-pilus of an F+F^{+} cell attaches specifically to an F−F^{-} cell.
    • Once attached, the F plasmid is replicated, and a copy is passed through the connection to the F−F^{-} cell.
    • This changes the genotype and phenotype of the recipient; at the very least, it becomes an F+F^{+} cell capable of creating its own pilus.

  • Hfr (High Frequency Recombinant)

    • Sometimes, the F plasmid integrates into the host cell's chromosome through homologous recombination.
    • This type of cell is called an Hfr cell. All the genetic information is still present, but the arrangement has changed.
    • When an Hfr cell attempts conjugation, it tries to transfer the plasmid, but because the plasmid is now part of the chromosome, it attempts to transfer the entire chromosome.
    • The bacterial chromosome is too large to pass through the fragile conjugation bridge before it breaks.
    • The sequences that mark the F plasmid for transfer are at the end of the line, meaning the donor sends a large chunk of chromosomal DNA but usually fails to send the full F plasmid sequences.
    • The recipient remains F−F^{-} but gains new chromosomal genes that may be incorporated into its own chromosome.

Transduction: Virus-Mediated Transfer

  • Normal Viral Cycle (Lytic)

    1. Attachment: The protein shell of a virus attaches to a bacterial cell.
    2. Injection: The virus injects its nucleic acid into the cell.
    3. Takeover: Viral nucleic acid destroys the bacterial chromosome, breaking it into fragments.
    4. Replication: The cell copies viral nucleic acid and produces viral proteins.
    5. Assembly and Release: New viruses are packaged and the cell bursts (lyses) to release them.

  • Transduction Mechanism (The Error)

    • Occasionally, during assembly, the viral protein shell mistakenly packages a fragment of the host bacterial chromosome instead of the viral nucleic acid.
    • This resulting particle is not a functional virus; it is a protein shell carrying bacterial DNA.
    • When this shell attaches to a new bacterial cell, it injects the previous host's DNA into the new cell, allowing for horizontal gene transfer.

Taxonomy and Classification

  • Hierarchy of Taxonomy

    • Domains are the highest level of taxonomy. Each domain is divided into Kingdoms.
    • Kingdoms are divided into Phyla.
    • Phyla are divided into Classes, which are further divided into Groups, and eventually Genus and Species.

  • History of Nomenclature

    • Carolus Linnaeus: In the late 1600s (concurrent with Leeuwenhoek and Hooke), Linnaeus developed a taxonomy and the system of binomial nomenclature.
    • Frederick Cohn: A German bacteriologist (era of Pasteur and Koch) who classified bacteria based on phenotypes, specifically cell shape and arrangement (e.g., Bacillus, Vibrio, Staphylococcus).

  • Rules of Binomial Nomenclature

    • Scientific names consist of the Genus and the species.
    • Example: Staphylococcus aureus.
    • Capitalization: Genus is always capitalized; species is always lowercase.
    • Formatting: Names should be italicized. If handwritten, they must be underlined.
    • Abbreviation: After the full name has been used once, it can be abbreviated using the first letter of the Genus followed by the full species name (e.g., S. aureus).

  • Problems with Common Names

    • Common names like "ringworm" are problematic because they can refer to organisms that are not actually worms or can encompass multiple different species under one name.
    • Conversely, a single species might have many names (e.g., cougar, mountain lion, painter).

Modern Species Definition in Microbiology

  • Inadequacy of the Biological Species Concept

    • The standard definition of a species involves organisms that can breed and produce fertile offspring. This does not apply to bacteria because they reproduce asexually.

  • Woese and Fox’s Proposals

    • Carl Woese and George Fox proposed that the five-kingdom system was inadequate because it lumped all prokaryotes (Bacteria and Archaea) into a single kingdom called Monera.
    • They introduced the Domain level of taxonomy to separate these groups.

  • Molecular Standards for Bacterial Species

    • Small Ribosomal Subunit (16S rRNA): This is the preferred method for distinguishing species because everything has ribosomes, and they mutate very slowly (fatal mutations occur if essential ribosomal sequences are mucked around with).
    • Identity Thresholds for the Same Species:
      1. Small Ribosomal Subunit Sequence: Requires 97%97\% identity or higher.
      2. Genomic DNA Identity: Requires 95%95\% identity or higher.
      3. DNA-DNA Hybridization: Requires 70%70\% or higher hybridization.

Bacterial Strains (Subspecies)

  • Groups within a single species that meet the identity thresholds but have distinguishable differences are called strains.

    • Morphovars: Strains with visible physical or morphological differences (e.g., the smooth vs. rough Streptococcus).
    • Biovars: Strains with metabolic or physiological differences (e.g., a histidine auxotroph that cannot produce its own histidine).
    • Serovars (Serotypes): Strains distinguished using serology (serum proteins/antibodies).

  • Antigens and Antibodies

    • Antibodies are serum proteins that recognize and bind to specific molecular shapes.
    • The molecule an antibody grabs onto is called an antigen.
    • In Gram-negative bacteria, the Lipopolysaccharide (LPS) contains a long chain of sugars sticking up from the core oligosaccharide called the O antigen. Variants in the O antigen are often used to define different serovars.