Lecture 8: The Origin and Evolution of Anaerobic Respiration

Ancient Hydrothermal Environments

Introduction to Hydrothermal Vents: 3.3 billion-year-old hydrothermal vents located in the Barberton greenstone belt, South Africa.
- Organic Matter Evidence: Inorganic compounds such as H2 and CO2 indicate that thermal fluids were a principal energy source for early life.
- Chemolithotrophic Metabolisms: The study of how these early organic compounds facilitated microbial life and energy metabolism.

Types of Anaerobic Metabolisms

Amino Acid Fermentation

Peptidases Role: Autotrophic organisms utilize peptidases for digestion of proteins in their environment.
- Mechanism: Peptidases exit the cell, digest proteins, and release amino acids or small peptides.
- Nutrient Utilization: The released amino acids serve as a source of carbon, nitrogen, and energy.

RNA Fermentation

Bacterial Types: Acetogenic and methanogenic bacteria can derive carbon, nitrogen, and energy through purine and pyrimidine fermentation.

Unfermentable Substrates Impact

Impact of High Concentrations: Presence of compounds like lipids and fatty acids creates an environment favorable for anaerobic respiration.
- Environmental Electron Acceptors: Respiration occurs as cells use external electron acceptors with more positive midpoint potentials than H2, thereby allowing anaerobic activity to flourish.

Conditions in Primitive Ecosystems

Oxidant Availability: Early crust ecosystems likely lacked oxidants essential for anaerobic respiration.
- Elemental Sulfur (S0): Can accumulate in the presence of O2, which oxidizes sulfur compounds to S0.
- Midpoint Potential of Elemental Sulfur: The midpoint potential is noted as Eo' = -260 mV, allowing it to serve as an electron acceptor, similar to protons (H+) in fermentation.
Example of Pyrococcus furiosus: This archaeal fermenter utilizes a specific isoform of Mbh called Mbs for sulfur reduction, creating reduced sulfane species (S3^2−) that subsequently disproportionate into H2S and S0.

Mechanisms of Fermentation and Respiration

Redox Reactions: Both fermentation and respiration are fundamentally redox reactions.
- Fermentation: Utilizes internally generated electron acceptors.
- Respiration: Involves external electron acceptors, a critical step for starving fermenters seeking new energy pathways.
Example of Shewanella:
- Can grow anaerobically on lactate using Fe3O4 as an electron acceptor, illustrating a possible evolutionary link to anaerobic respiration origins.

Evolution of Cytochromes

Cytochrome Synthesis: Ancestors of respiratory organisms evolved to produce multiheme cytochromes, forming protein-based nanowires for electron transfer to solid-phase Fe3O4.
- Absence of Heme in Early Bacteria: Methanogens and acetogens likely predate the development of heme, suggesting an evolutionary progression towards utilizing external electron acceptors required for respiration.

Origin of Heme and Cytochromes

Structure of Heme: Defined as a tetrapyrrole, with iron at the center acting as a cofactor for electron transfer.
Biosynthetic Pathway: Begins with glutamate, transforming into aminolevulinic acid and subsequently into porphobilinogen and uroporphyrinogen III, critical for heme synthesis.
- Significance: Heme production is among the most ancient metabolic pathways, with cobalamin found in early H2-utilizing organisms.

Electron Transfer Mechanism in Fermenters

Conditions for Electron Acceptance: Starving fermenters have access to electron acceptors like Fe3O4 but lack the means to utilize them.
- Heme Interaction: Heme's hydrophobic nature allows it to facilitate cytochrome formation, leading to the development of extracellular nanowires enabling electron transfer.
Nanowire Functionality: Cytochromes with covalent bonds to heme permit electron hopping between heme groups due to their spatial organization within nanowires, facilitating electron transport to external acceptors.

Conductive Nanowires

Shewanella Nanowires: Electron microscopy reveals conductive nanowires containing heme molecules that streamline electron transfer.
- Tunneling Mechanism: Electron transfer relies on proximity (<14 Å) and quantum tunneling, where electrons transition between reduced and oxidized heme forms by overcoming energy barriers.

Formation of Quinones

Importance of Quinones: Ubiquitous two-electron carriers in microbial metabolism, essential for electron transport in anaerobic conditions.
- Synthesis Origins: Start from chorismate, tied to aromatic amino acid biosynthesis, and coupled with isoprenoid synthesis for membrane stability.

Evolution of Anaerobic Respiratory Pathways

Electron Acceptors in Hydrothermal Systems: Presence of Fe3O4 from serpentinization processes providing accessible electron acceptors for organisms.
Thermodynamic Necessity for Electron Transfer: Without an electron transfer chain, non-fermantable growth is thermodynamically unviable.
Membrane-Associated Electron Transport: Initially comprised quinones and cytochromes, hinting at ancestral respiration forms.

Unique Functionality of Quinones

Menaquinone's Role: In Shewanella fermentation, menaquinone's function is primarily electron transport, distinct from dual roles in other microbial processes.
Absence of Specific Interactions: No strict enzyme-substrate fitting for electron transfers; any interaction suffices for electron transfer from reduced hemes to mineral acceptors.
Positive Midpoint Potential Advantage: Cytochromes' ability to more readily accept electrons from lactate and transfer to diverse environmental acceptors demonstrates their evolutionary benefit in anaerobic respiration.

Trophic Succession and Colonization**

Pattern of Colonization: Following the emergence of chemolithoautotrophs, early fermenters helped establish an ecological wave, leading to those capable of anaerobic respiration using cytochromes and quinones.
Consequences of Succession: Resulted in the vibrant microbial ecosystems filling niches in hydrothermal vents—transitioning from primary production to fermentation to respiration, which shaped the Earth's crust habitats.

The End of the Dark Age

Evolution of the reverse Citric Acid Cycle (rTCA): Evolved during early colonization by anaerobic respiratory organisms; required ATP for CO2 fixation indicates dependence on developed ATP synthesis pathways.
Crustal Ecosystems: Highlight the reliance of anaerobic breakdowns and redox reactions in sustaining ecosystems constrained to hydrothermal vents.
Development of Photosynthesis: Required for soil escape, asserting no other sustainable electron donors existed pre-photosynthesis.

Isotope Fractionation and Evidence of Microbial Activity

Isotopes: Variants of the same element with differing neutron counts leading to distinct behaviors in kinetic and thermodynamic reactions.
- Isotope Fractionation: Process reflecting preferential incorporation or exclusion of isotopes based on reactions.
Mass-Dependent Isotope Fractionation (MDF): Predictable changes in isotopic abundances based on mass.
Mass-Independent Isotope Fractionation (MIF): Deviations from MDF that inform past geochemical conditions, e.g., photolysis reactions creating sulfate aerosols.

Applications of Isotope Research

Contextualizing Microbial Evolution: MDF/MIF isotopes help assess origins and interactions of various microbial metabolisms against geological phenomena like the Great Oxygenation Event.
Microbial Sulfate Reduction: A metabolic process that reduces sulfate (SO₄²⁻) to hydrogen sulfide (H₂S), revealing carbon and sulfur isotopes as markers of microbial activity.

Geological Survey of Earth's History

Timeline of Geological Events: Illustrated with major milestones such as rise of oxygen levels, eukaryotic emergence, and formation of supercontinents across billion-year scales.

Conclusion: Pathways to Life Post-Dark Age

Emergence and Colonization: With improved mechanisms in making use of diverse substrates and electron acceptors, life flourished dominantly in dark oceanic environments before the advent of photosynthesis allowed surface diversification.

Ancient Hydrothermal Environments

What are Hydrothermal Vents?: Really old deep-sea hot springs (3.3 billion years old!) found in South Africa.
Signs of Early Life: Simple molecules like hydrogen (H2) and carbon dioxide (CO2) show that the hot fluids from these vents gave early life its energy.
How Early Life Got Energy: This part looks at how these simple compounds helped tiny life forms get energy and grow.

Types of Anaerobic Metabolisms

Amino Acid Fermentation

How Organisms Use Proteins: Simple life forms use special tools called peptidases to break down proteins around them.
The Process: Peptidases leave the cell, chop up proteins, and release smaller pieces like amino acids.
What Amino Acids Provide: These amino acids are used as food (carbon, nitrogen) and energy.

RNA Fermentation

Bacteria Using RNA: Certain bacteria can get energy, carbon, and nitrogen by breaking down parts of RNA (purines and pyrimidines).

When Non-Fermentable Foods Are Around

Good for Anaerobic Life: Lots of fats and fatty acids create an environment suitable for life forms that do not need oxygen to breathe (anaerobic respiration).
Using Outside Helpers: These cells "breathe" by using things outside the cell (electron acceptors) that are better at taking electrons than hydrogen (H_2). This lets them live without oxygen.

Conditions in Primitive Ecosystems

Lack of Breathing Partners: Early Earth's crust likely did not have many chemicals (oxidants) needed for anaerobic respiration.
Elemental Sulfur (S^0): This sulfur can build up when oxygen is around, as oxygen turns other sulfur compounds into S^0.
Sulfur's Role as an Electron Taker: It has an energy potential (Eo' = -260 mV) that lets it take electrons, just like protons (H^+) do in fermentation.
Example: Pyrococcus furiosus: This archaeal microbe takes sulfur (S^0) using a protein called Mbs, making reduced sulfur compounds (S3^{2−}) which then break down into hydrogen sulfide (H2S) and more S^0.

Mechanisms of Fermentation and Respiration

Both are Energy Swaps: Both fermentation and respiration are about moving electrons around.
Fermentation: Uses electron takers found inside the cell.
Respiration: Uses electron takers found outside the cell. This is a big step for starving fermenters looking for new ways to get energy.
Example: Shewanella:
- Can grow without oxygen by using a sugar (lactate) and rust (Fe3O4) as an electron taker. This hints at how anaerobic respiration might have started.

Evolution of Cytochromes

Building Electron Highways: Early breathing organisms learned to make special proteins called multiheme cytochromes. These act like tiny wires (nanowires) to move electrons to solid rust (Fe3O4).
No Heme in Very Early Life: Simple early life like methanogens did not have heme (a key part of cytochromes), suggesting that using outside electron takers came later in evolution.

Origin of Heme and Cytochromes

What is Heme?: Heme is a special ring-shaped molecule with iron in its center. The iron helps move electrons.
How Heme is Made: It is made from a starting molecule called glutamate, which goes through several steps to become the final heme structure.
Its Importance: Making heme is one of the oldest ways living things created energy. A similar molecule (cobalamin) is found in very early organisms that used hydrogen.

Electron Transfer Mechanism in Fermenters

Opportunity for Starving Cells: Fermenters might be surrounded by electron takers like rust (Fe3O4) but cannot use them directly.
Heme's Help: Heme can easily form cytochromes because of its structure. These cytochromes then create tiny wires (nanowires) that stick out of the cell to transfer electrons.
How Nanowires Work: Cytochromes with heme attached form a chain. Electrons "hop" from one heme to the next in these nanowires, moving them to outside electron takers.

Conductive Nanowires

Shewanella's Wires: Pictures from electron microscopes show that Shewanella bacteria have these tiny, electron-carrying wires made of heme molecules.
Electron Jumps: Electrons move by "tunneling" between heme groups that are very close (less than 14 Å apart). They can jump across small energy barriers.

Formation of Quinones

Why Quinones are Important: These are common two-electron carriers in microbes, vital for moving electrons when there is no oxygen.
How They are Made: They start from a molecule called chorismate (also used for making specific amino acids) and are linked to making other molecules that help cell membranes stay stable.

Evolution of Anaerobic Respiratory Pathways

Electron Takers in Hot Springs: Rust (Fe3O4) produced from geological processes in hydrothermal vents provided easy-to-reach electron takers for early life.
Need for Electron Transfer: Without a way to move electrons around, life could not grow using things other than fermentation.
Membrane-Linked Transport: Early respiration likely involved quinones and cytochromes located in the cell membrane.

Unique Functionality of Quinones

Menaquinone's Specific Job: In Shewanella fermentation, menaquinone mainly just moves electrons, which is different from its other roles in other microbes.
No Strict Matching Needed: Electron transfer does not need a perfect fit between molecules; any interaction between reduced hemes and mineral takers is enough.
Cytochromes' Advantage: Cytochromes are good at taking electrons from things like lactate and passing them to various outside acceptors. This made them very useful for anaerobic respiration.

Trophic Succession and Colonization

How Life Spread: After initial life forms appeared, early fermenters created a wave of new life, leading to organisms that could "breathe" without oxygen using cytochromes and quinones.
What Happened Next: This led to diverse life in hydrothermal vents, moving from basic energy creation to fermentation and then to respiration, shaping early Earth's environments.

The End of the Dark Age

Evolution of a Special Cycle (rTCA): The reverse Citric Acid Cycle (rTCA) developed when anaerobic respirers were colonizing places. It needed energy (ATP) to fix CO_2, meaning advanced ways to make ATP were already present.
Life in the Crust: Life in early Earth's crust relied heavily on anaerobic processes and electron exchange to survive, mainly in hydrothermal vents.
Why Photosynthesis Was Needed: Life could not leave these isolated environments until photosynthesis developed, as there were no other sustainable ways to get electrons outside of these vents.

Isotope Fractionation and Evidence of Microbial Activity

Isotopes: These are versions of the same element with different weights (different numbers of neutrons). They act a bit differently in chemical reactions.
Isotope Fractionation: This is when reactions prefer to use or exclude certain isotopes.
Mass-Dependent Isotope Fractionation (MDF): Changes in isotope amounts that can be predicted based on their mass.
Mass-Independent Isotope Fractionation (MIF): Changes that do not follow the mass rule. These tell us about unique past conditions, like how sunlight broke down chemicals to make sulfate aerosols.

Applications of Isotope Research

Understanding Microbial History: MDF/MIF isotopes help us figure out when and how different microbial ways of life appeared and interacted with big geological events like the Great Oxygenation Event.
Microbial Sulfate Reduction: When microbes turn sulfate (SO4^{2−}) into hydrogen sulfide (H2S), they leave specific carbon and sulfur isotope signatures, showing their activity.

Geological Survey of Earth's History

Earth's Key Moments: A timeline showing major events like the rise of oxygen, the appearance of complex cells (eukaryotes), and the formation of supercontinents, spanning billions of years.

Conclusion: Pathways to Life Post-Dark Age

Life's Expansion: With better ways to use different food sources and electron takers, life thrived mainly in the dark parts of the ocean before photosynthesis allowed it to spread to the surface.