Bacterial Genetics and Physiology

Posted on Nov 26, 2024 in Biology

Transposable Elements: Transposons

The genes in living organisms are not static and may change their sequence under certain conditions, for example, through insertion sequences.

  • Insertion occurs through single-strand breakage by the enzyme transposase.
  • Transposons, or “jumping genes,” are DNA segments that can move within the genome, or between chromosomal DNA and plasmids.
  • The transposon attaches to the ends of single strands and repairs them after replication.
  • Transposition is important because these mobile elements can insert into plasmids, potentially promoting antimicrobial resistance.

Genetic Variation

Bacteria employ several mechanisms to vary their genetic information:

  • Mutations in DNA
  • Acquisition of new genes: transformation, conjugation, transduction, and transposition

Mutations are heritable changes resulting from alterations in the DNA base sequence. They can be lethal. Mutations occur spontaneously or can be induced by mutagens (physical or chemical).

  • Physical mutagens include UV light, X-rays, cosmic rays, and gamma radiation.
  • Chemical mutagens are classified into four groups: base analogs, alkylating agents, base modifiers, and intercalating agents.

Types of Mutations

Mutations can involve a single base or multiple bases through substitution, insertion, or deletion.

  • Substitutions are called transitions if a change occurs between bases of the same group (purine or pyrimidine), and transversions if the change is between different groups.
  • Changes in codon sequences can lead to the translation of different amino acids, resulting in a mutant protein or affecting translation itself.
  • Insertions or deletions cause a shift in the DNA base sequence, altering all triplets downstream. These mutations rarely occur spontaneously and are typically caused by ionizing radiation or certain chemicals.

Phenotypic Expression of Mutations

Mutations can result in the loss or gain of one or more traits in the mutant strain, such as:

  • Loss of ability to utilize certain carbon sources (e.g., lactose-deficient mutants, Lac-)
  • Loss of ability to synthesize amino acids or vitamins
  • Acquisition of antimicrobial resistance
  • Alteration of bacterial surface components (glycocalyx, flagella)
  • Loss of toxin synthesis (exotoxins and endotoxins)

Genetic Recombination

Genetic recombination occurs when two genetically distinct elements combine. It involves three processes: transformation, transduction, and conjugation.

Transformation is the acquisition of new genes by some bacterial species. It was discovered by Griffith in 1928 while studying pneumococcal infection in mice. Griffith found that pneumococcal virulence was related to the presence of a polysaccharide capsule. Transformation can be natural or artificial. Some naturally transformable pathogenic bacteria include Streptococcus pneumoniae, Neisseria gonorrhoeae, and Haemophilus influenzae. Artificial transformation has been crucial for the advancement of DNA technology (genetic engineering).

Genetic Recombination: Conjugation

Conjugation is the transfer of chromosomal or plasmid DNA from a donor to a recipient bacterium through physical contact. In Gram-negative bacteria, DNA transfer occurs via pili. In Gram-positive bacteria, donor cells form surface proteins (adhesins) that bind to receptors (lipoteichoic acid) on recipient cells lacking plasmids. This interaction induces pheromone synthesis (e.g., in Streptococcus faecalis). Conjugative R plasmids (resistance to antibiotics) have been found in Gram-positive bacteria like Streptococcus, Streptomyces, and Clostridium.

Genetic Recombination: Transduction

Transduction is DNA transfer mediated by bacteriophages. Phages can infect bacteria and replicate (lytic cycle) or integrate into the bacterial genome (lysogenic cycle), delaying phage release. Phage integration can occur at specific or random chromosomal locations. Generalized transduction typically occurs during the lytic cycle, where any genomic sequence can be packaged into the virus and transferred to other bacteria. Specialized transduction occurs primarily during the lysogenic cycle, transferring specific genes. An example is the lambda phage in E. coli.

Water

Sources of water:

  • Endogenous (from oxidation-reduction reactions)
  • Exogenous (primary source)

Water availability is measured as water activity (aw).

  • Oligotrophic bacteria: aw close to 1
  • Bacteria in blood and fluids: aw = 0.995
  • Marine bacteria: aw = 0.980
  • Certain Gram-positive bacilli: aw = 0.950
  • Xerophilic microorganisms: aw around 0.75
  • Extreme halophilic archaea (Halobacterium)
  • Saccharophilic yeasts in juices

Carbon Dioxide (CO2)

All prokaryotes require CO2.

  • Autotrophs use it as a carbon source:
    • Chemoautotrophs: with chemical energy
    • Photoautotrophs: with light energy
  • Methanogenic archaea can use CO2 as an electron acceptor from H2. Some also use it as a carbon source.
  • Heterotrophs require small amounts of CO2 for carboxylic metabolic pathways.

Phosphates

Phosphorus is usually required in the form of phosphates.

  • Bacteria using organic phosphates have extracellular phosphatases (secreted in Gram-positive bacteria, periplasmic in Gram-negative bacteria).
  • Inorganic phosphates are also utilized.

Mineral Salts: Cations

  • K+ (enzyme activation, teichoic acids in Gram-positive bacteria)
  • Mg2+ (stabilizes ribosomes, membranes, and nucleic acids; cofactor in ATP reactions, chlorophylls, and bacteriochlorophylls)
  • Ca2+ (cofactor for enzymes like proteinases)
  • Fe2+/Fe3+ (cytochromes, FeS proteins, enzyme cofactor)

Trace Elements (Micronutrients)

  • Mn (cofactor for certain enzymes)
  • Co (vitamin B12)
  • Zn (stabilizes DNA and RNA polymerases)
  • Mo (molybdo-flavoproteins, nitrogenase)
  • Ni (hydrogenases)

Specific Nutrients

Nitrogen and sulfur requirements can be met in various ways:

  • Oxidized inorganic forms:
    • NO3– (nitrate reductase and nitrite reductase) → NH3 → organic nitrogen
    • SO42- (activated by ATP, reduced to SO32- and then to H2S → incorporated into organic compounds)
  • Reduced forms:
    • Reduced inorganic nitrogen: NH4+
    • Reduced inorganic sulfur: S2-, HS–
    • Reduced organic nitrogen: amino acids, peptides
    • Reduced organic sulfur: cysteine

Measurements of Bacterial Mass in Liquid Culture

Common methods include:

  • Turbidity: Measures the opacity of the bacterial culture, estimating total bacteria (live or dead) using a spectrophotometer.
  • Viable cell count: Determines the number of living bacteria by counting colonies grown on a plate after plating a known volume (CFU). Plotting the logarithm of turbidity or viable cell count against time generates a growth curve. Generation time is the time required to double the bacterial mass.

Bacterial Genetics and Genomics

  • Bacterial genome: Covalently closed circular macromolecule composed of two nucleotide chains linked by hydrogen bonds.
  • DNA replication: The new chain forms where the double-stranded DNA breaks. Replication proceeds bidirectionally from the origin.
  • DNA polymerase requires precursor triphosphate nucleotides present in the cytoplasm.

Plasmids and Episomes

  • Genetic elements composed of double-stranded, covalently closed, supercoiled DNA.
  • Episomes can integrate into the bacterial genome, coming under its replication control.
  • Plasmids encode three main gene groups: replication, phenotypic traits, and pilus formation.
  • The F (fertility) plasmid in E. coli can be transferred and exist as an integrated episome.