Lecture 24: Microbial Evolution

Introduction

This lecture explores the origins of life, the evolution of microbial diversity, and the molecular and genetic tools used to study evolutionary relationships. It also covers the endosymbiotic theory explaining the origin of mitochondria and chloroplasts in eukaryotes.

Origins of Life

Stromatolites and Early Life Evidence

• Stromatolites: Bacterial communities forming bulbous masses of sedimentary limestone (CaCO3), dating back ~3.4 billion years.

• Provide the earliest clear fossil evidence of life on Earth.

• Example: Modern stromatolites found in shallow marine environments.

Fundamental Conditions for Life

• Essential elements: Required to compose organic molecules (C, H, O, N, P, S).

• Continual energy source: Mainly from the sun, drives chemical reactions.

• Temperature range permitting liquid water: Necessary for metabolic reactions; extremes cause freezing or desiccation.

Prebiotic Models of Life's Origin

The Prebiotic Soup Model

• Small organic molecules arise abiotically from simple reduced chemicals, sparked by lightning or other energy sources.

• These molecules form complex macromolecules, eventually acquiring mechanisms for self-replication and membrane compartmentalization.

• Example: Formation of amino acids and nucleotides in simulated early Earth conditions.

Miller-Urey Experiment

• Simulated early Earth conditions using hydrogen, ammonia, methane, and water.

• Produced amino acids (glycine, alanine) and their derivatives.

• Subsequent experiments generated nucleic acids from hydrogen cyanide and ammonia.

• Demonstrated that organic molecules could form under prebiotic conditions.

The Metabolist Model

• Proposes that self-sustaining abiotic chemical reactions formed the basis of cellular metabolism.

• The genetic code may have originated from synthesis of amino acids complexed to dinucleotides.

• Example: Metabolic cycles forming key biomolecules before genetic information systems evolved.

The RNA World Hypothesis

• Suggests RNA was the first "information molecule" and precursor to DNA.

• RNA can act as a genome (in some viruses) and has catalytic activity (ribozymes).

• Functions include splicing introns, regulating gene expression, and synthesizing proteins.

• Remnants of the RNA world may be found in nucleotide cofactors (e.g., NAD/NADH, ATP).

Biological Information Flow

Central Dogma of Molecular Biology

• Information flows from DNA (genes) to RNA (transcription) to Protein (translation).

• Proteins determine cellular structure and activity.

• Energy is required to convert genetic information into functional cellular components.

Measuring Evolutionary Change

Molecular Clocks

• Molecular clock: Temporal information contained in macromolecular sequences, based on accumulation of random mutations during DNA/RNA replication.

• Used to estimate evolutionary divergence times between species.

Criteria for a Good Molecular Clock

• Ability to align molecules to determine genetic relatedness.

• Universal molecule found in all organisms.

• Conserved function across all organisms.

• Strictly vertically transferred (heritable from generation to generation).

• Constant substitution rate: sequence divergence proportional to time.

Genes Used as Molecular Clocks

• Genes encoding components of transcription and translation apparatus (ribosomal RNA, tRNA, RNA polymerase).

• The most widely used molecular clock: small subunit rRNA (SSU rRNA)—16S rRNA in bacteria, 18S rRNA in eukaryotes.

The 16S rRNA Gene

Structure and Use

• ~1500 base pairs in length.

• Part of the small subunit of the prokaryotic ribosome.

• Conserved regions: Used for universal applications.

• Variable regions: Used for species, genus, phylum, or domain-specific identification.

Extraction and Analysis

• DNA is extracted from cells, and the gene encoding 16S rRNA is amplified by PCR.

• Sequencing and alignment of rRNA genes allows comparison of evolutionary relationships.

• Phylogenetic trees are constructed based on sequence similarity.

Three Domains of Life

Bacteria, Archaea, and Eukarya

• Analysis of 16S rRNA genes led to the discovery of Archaea as a distinct domain, separate from Bacteria and Eukarya.

• Archaea were first identified by Carl Woese in 1977, studying prokaryotes from hot springs.

Phylogenetics

Principles and Methods

• Study of evolutionary relationships among biological individuals (species, groups, genetic sequences).

• Construction of phylogenetic trees (phylogenies) to visualize relationships.

• Organisms with similar nucleic acid sequences are placed closer together on the tree.

• Modern phylogenetics uses computational and molecular methods, often focusing on 16S rRNA genes in bacteria.

Microbial Biodiversity

Most Biodiversity is Microbial

• Microbes (Bacteria, Archaea, Eukaryotic microbes) represent the majority of Earth's biodiversity.

• Phylogenetic trees show extensive branching and diversity among microbial lineages.

Comparing Archaea, Bacteria, and Eukaryotes

Key Differences

Evolution of Eukaryotes

Endosymbiont Theory

• Explains the origin of mitochondria and chloroplasts in eukaryotic cells.

• Mitochondria were once bacteria; chloroplasts were cyanobacteria.

• These organelles were engulfed by ancestral eukaryotic cells and became permanent residents.

• Mitochondrial and chloroplast DNA is similar to bacterial DNA.

Endosymbiosis

• Endosymbionts: Microbes living symbiotically inside larger organisms.

• Examples: Rhizobia in legumes (nitrogen fixation), essential nutritional contributions to host animals.

Lynn Margulis and the Endosymbiont Theory

• Lynn Margulis proposed the endosymbiont theory, which was initially controversial.

• Implied a polyphyletic ancestry of living species, rather than a single common ancestor (monophyletic ancestry).

Mitochondria and Chloroplasts

Origin and Features

• Organelles were originally bacteria: Chloroplasts from cyanobacteria, Mitochondria from Rickettsia (proteobacteria).

• Double membranes, electron transport components, and photosynthetic complexes similar to their bacterial ancestors.

• Behave like endosymbiotic organisms: live inside another organism, reproduce independently, undergo extreme reductive evolution (loss of genes).

Genomic Evidence

• Mitochondria and chloroplasts have circular chromosomes, prokaryotic 70S ribosomes, and 16S rRNA sequences similar to bacteria.

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

16S rRNA Gene Phylogeny

• Phylogenetic trees based on 16S rRNA show mitochondria clustering with Rickettsia and other bacteria, supporting their bacterial origin.

Endosymbiont Theory: Implications

• Suggests multiple origins for eukaryotic organelles (polyphyletic ancestry).

• Challenges the traditional view of species evolving only by divergence from a common ancestor.

Summary Table: Key Features of Mitochondria and Chloroplasts

Conclusion

Microbial evolution is central to understanding the origins and diversity of life. Molecular tools such as 16S rRNA gene sequencing and phylogenetic analysis have revolutionized our ability to classify organisms and trace evolutionary relationships. The endosymbiont theory provides a compelling explanation for the origin of key eukaryotic organelles, highlighting the importance of symbiosis in evolution.