24: Microbial Evolution Notes

Origins of Life

• The earliest life forms with clear fossil evidence are bacterial communities called stromatolites.
  • These are bulbous masses of sedimentary layers of limestone (CaCO_3) approximately 3.4 billion years old.
• Before cells evolved, essential conditions were required.
  • Essential elements: To compose organic molecules.
  • Continual source of energy: Mainly from the sun.
  • Temperature range permitting liquid water: Metabolic reactions cease if it's too cold (freezing) or too hot (desiccation).

The Prebiotic Soup Model

• Small organic molecules arose abiotically from simple reduced chemicals, sparked by lightning, generating organic building blocks.
• These building blocks produced complex macromolecules that eventually acquired mechanisms for self-replication and membrane compartmentalization.

Miller-Urey Experiment

• Simulated conditions thought to be present on early Earth.
  • Sterilized to prevent contamination.
  • Began with hydrogen, ammonia, methane, and water.
  • Produced glycine, alanine, other amino acids, and their derivatives.
  • Subsequent experiments generated nucleic acids from hydrogen cyanide and ammonia.

The Metabolist Model

• Self-sustaining abiotic chemical reactions could have formed the basis of cellular metabolism.
• The genetic code may have originated from the synthesis of an amino acid complexed to a dinucleotide.

The RNA World

• Hypothesis: RNA was the first "information molecule".
  • Precursor to DNA.
  • Used as the genome by some viruses.
  • Has catalytic activity (ribozymes).
    • Splices introns.
    • Regulates gene expression (riboswitches).
    • Synthesizes proteins.
    • RNA performs major functions of the ribosome.
  • Over time, ribozymes acquired protein subunits that took over most functions.
  • Remnants of the RNA world.
    • Nucleotide cofactors (e.g., NAD^+/NADH, ATP).

Biological Information Flow

• Replication: DNA (genes) → RNA (transcription) → Protein (translation).

The Origin of Life

• No model fully explains how we go from biological molecules to a functional cell with a replicating genome to pass on hereditary information.
• Evolution has occurred since the earliest life forms.
• Once cells with genetic information formed, evolutionary change can be measured.

Molecular Clocks

• The molecular clock is the temporal information contained in a macromolecular sequence.
• Based on the acquisition of new random mutations in each round of DNA (or RNA for some viruses) replication.

Criteria for a Good Molecular Clock

• Must be able to align molecules to determine genetic relatedness.

• Universal molecule found in all organisms.

• Has conserved functions in all organisms.

• Strictly vertically transferred (heritable):

  • Cannot be picked up from the environment or different cells.

• Constant substitution rate: Sequence divergence proportional to time.

• Genes that show the most consistent measures of evolutionary time encode components of the transcription and translation apparatus.

  • Ribosomal RNA and proteins, tRNA, and RNA polymerase.

• The most widely used molecular clock is the gene encoding the small subunit rRNA (SSU rRNA).

  • 16S rRNA (bacteria) or 18S rRNA (eukaryotes).

The 16S rRNA Gene

• Approximately 1500 base pairs in length.
• Part of the small subunit of the prokaryotic ribosome.
• Conserved regions across all life forms.
• Variable regions specific to species, genus, phylum, or domain are used as the clock.

How to Extract rRNA Genes and Analyze Evolutionary Relationships

1. Isolate DNA from cells.
2. Use PCR (Polymerase Chain Reaction) to amplify the gene encoding ribosomal RNA.
3. Sequence the amplified DNA.
4. Align multiple rRNA gene sequences.
5. Generate a phylogenetic tree based on sequence similarities and differences.

• Example:
  • SSU rDNA sequences from uncultured soil bacteria are aligned.
  • A phylogenetic tree is constructed, showing similarity and divergence.

Three Domains of Life

• In 1977, Carl Woese studied prokaryotes living in hot springs that produce methane.
• Analysis of their 16S rRNA genes revealed they were NOT bacteria.

Phylogenetics

• The study of evolutionary relationships among biological individuals (species, groups of organisms, genetic sequences).
• Involves the construction of trees (phylogenies) to show evolutionary relationships.
• Organisms with similar nucleic acid sequences are closer on the tree.

Modern Phylogenetics

• Computational and molecular, not morphology-based.
• 16S rRNA genes are most often used in bacteria.

Archaea vs. Bacteria and Eukaryotes

Evolution of Eukaryotes

• DNA is more like archaeal DNA than bacterial DNA.
• Mitochondrial and chloroplast DNA are similar to bacterial DNA.
• Endosymbiont theory:
  • Mitochondria were bacteria.
  • Chloroplasts were cyanobacteria.
• They were infected or eaten by other species and ended up living together inside host cells.

Endosymbiosis

• Endosymbionts are microbes living symbiotically inside a larger organism.
• Endosymbiotic Rhizobia bacteria induce legume roots to form nodules, facilitating bacterial nitrogen fixation.
• Endosymbiotic microbes provide essential nutritional contributions to host animals.

Lynn Margulis & Endosymbiont Theory

• Eukaryotic flagellum contains [9(2) + 2] microtubules.

Mitochondria and Chloroplasts

• Organelles were bacteria.

  • Chloroplast: cyanobacteria.
  • Mitochondria: Rickettsia (proteobacteria).

• Double membranes.

• Electron transport components in the inner membrane of mitochondria.

• Photosynthetic complexes are similar to cyanobacteria.

• Behave like endosymbiotic organisms.

  • Live inside another organism.
  • Reproduce independently.

• Extreme reductive evolution: Organisms lose genes from their genome.

  • Mitochondria/chloroplasts don’t need all their genes; the host makes some of their proteins for them.

  Characteristics of Mitochondria and Chloroplasts

• Circular chromosomes

• Prokaryotic, 70S ribosomes

• 16S rRNA with sequences similar to those of bacteria

• Same antibiotics inhibit ribosome function in bacteria, mitochondria, and chloroplasts

• 10% sequence change in 16S rRNA gene phylogeny separates E. coli and Mitochondria.

Endosymbiont Theory

• The endosymbiosis theory was very controversial.
• It implied a polyphyletic ancestry of living species, instead of the assumption that species evolve only by divergence from a common ancestor (monophyletic ancestry).