Mitochondria and Anaerobic Energy Metabolism in Eukaryotes

Biochemistry and Evolution

William F. Martin, Aloysius G. M. Tielens, Marek Mentel

• Publisher: De Gruyter
• Year: 2020
• ISBN:
  9783110612721
• Edition: 1
• Topic: Ciencias biológicas
• Subtopic: Biología celular

Mitochondria are sometimes called the powerhouses of eukaryotic cells, because mitochondria are the site of ATP synthesis in the cell. ATP is the universal energy currency, it provides the power that runs all other life processes. Humans need oxygen to survive because of ATP synthesis in mitochondria. The sugars from our diet are converted to carbon dioxide in mitochondria in a process that requires oxygen. Just like a fire needs oxygen to burn, our mitochondria need oxygen to make ATP. From textbooks and popular literature one can easily get the impression that all mitochondria require oxygen. But that is not the case. There are many groups of organismsm known that make ATP in mitochondria without the help of oxygen. They have preserved biochemical relicts from the early evolution of eukaryotic cells, which took place during times in Earth history when there was hardly any oxygen avaiable, certainly not enough to breathe. How the anaerobic forms of mitochondria work, in which organisms they occur, and how the eukaryotic anaerobes that possess them fit into the larger picture of rising atmospheric oxygen during Earth history are the topic of this book.

Part I: Basics

Eukaryotes are important for understanding the history of life on the blue planet. Cells on Earth are classified as prokaryotes which have no nucleus, or eukaryotes which have a cell nucleus. Eukaryotes encompass all the genuinely complex organisms, like plants, fungi, and animals. In comparison with eukaryotic cells, prokaryotic cells are less complex from the cytological, genetic, and genomic point of view. Prokaryotes encompass archaea (called archaebacteria until the 1990s) and bacteria. Prokaryotes lack a nucleus. They also do not have a complex cytoskeleton, peroxisomes, vacuoles/lysosomes, or any organelles of endosymbiotic origin − mitochondria and plastids. The flagella of prokaryotes are not homologous with eukaryotic flagella, which are based on microtubules composed of tubulin. The flagella of prokaryotes represent analogous structures: even the flagella of archaea and bacteria are not homologous, for which reason the archaeal flagellum is called an archaellum. Homologous in this book means similar by virtue of common ancestry.

In general, eukaryotic cells are more complex than prokaryotic cells. Their linear chromosomes are localized in the nucleus. The nuclear membrane is contiguous with the endoplasmic reticulum, which is in contact with the Golgi apparatus through membrane vesicles. As complex as the eukaryotic nucleus might seem, it can be induced to form spontaneously in cell-free extracts. Newport (1987) showed that a mixture containing 100 µL of Xenopus egg extract, 2 mM ATP (along with 20 mM creatine phosphate and some creatine kinase to provide continuous ATP supply), and 1.6 µg of bacteriophage lambda DNA incubated at 22 °C will spontaneously form nuclei around the lambda DNA, with two lamina (inner and outer leaves of the nuclear membrane) along with nuclear pores, in about an hour. Another specific feature of eukaryotes is the presence of mitochondria in different biochemical variations: as aerobic mitochondria, (facultative) anaerobic mitochondria, hydrogenosomes, and mitosomes (Müller et al. 2012). Complex structures in eukaryotic cells require ATP for their formation; ATP synthesis in eukaryotes is the legacy of mitochondria.

Eukaryotes and prokaryotes have followed different trajectories in evolution. Prokaryotes have boundless biochemical diversity, but they are always packaged into small single celled units of life. Prokaryotes can grow with a broad diversity of energy sources (chemotrophic or phototrophic), carbon sources (autotrophic or heterotrophic), and electron sources (organotrophic or lithotrophic) (Madigan and Martinko 2006). Prokaryotes can colonize environments with temperatures ranging from ca. −30 °C to ca. +115 °C and pH varying between ~3 and ~12. Eukaryotes persist in more restricted ranges of temperature (from ca. −20 °C to ca. +50 °C) and pH (from ~1 to ~10) (Nealson and Conrad 1999). In terms of carbon and energy metabolism, eukaryotes are far narrower in scope than prokaryotes. In fact, the full breadth of energy metabolic diversity known in eukaryotes is less than that found in a single, generalist bacterium like members of the genus Rhodobacter (Müller et al. 2012), with the exception of course, of oxygenic photosynthesis in plants, which is an inheritance from cyanobacteria via the endosymbiotic origin of plastids (Zimorski et al. 2014). However, the cellular complexity of eukaryotes comes at a cost of being less robust, that is, less resistant to extreme or changing external conditions.

Diversity in eukaryotic energy metabolism encompasses a narrow spectrum of electron donors and acceptors compared to prokaryotes. Moreover, the energy metabolic diversity that eukaryotes have is linked to mitochondria. The narrow sample of prokaryotic energy metabolic diversity in eukaryotes, together with the association of anaerobic energy metabolism with the mitochondrion, reflects the single endosymbiotic origin of mitochondria, the event that gave rise to eukaryotes roughly 1.5 billion years ago.

Students or specialists might wonder why this book is necessary. One can just turn to the internet, google some papers on “evolution of mitochondria” or “mitochondrial evolution” or “anaerobic mitochondria” and get the goods, everything one needs to know, maybe. It is not that simple. What we actually know about energy metabolism in mitochondria comes from biochemical laboratories where people measure enzyme activities, purify enzymes, reconstitute systems, and (very important for energy metabolism) measure end products of metabolism so that when one puts it all together one has an idea of what the organism might be doing, enzymatically, in order to generate ATP from a growth substrate en route to excreting the observed end products as waste. Doing that kind of work takes years or decades before one knows what is going on in the organism (its cells, its cytosol, and its mitochondria). In the old days, the enzymes needed to be highly purified and microsequenced (Edman degradation) in order to get information about the amino acid sequence or the gene. The assignment to the function of such purified proteins is certain because an enzymatic activity copurifies with a physical entity, the chemically sequenced protein, that was present at high activity in the organism.

For eukaryotes with anaerobic mitochondria, there are very few organisms where the physiological measurements have been done, and where we know what end products the organism is producing with the 10–100 genes that are devoted to energy metabolism (redox balanced ATP synthesis) out of the 30,000 genes that might be in the genome sequence (Müller 2003). The organisms that we cover in this book have physiology behind the maps. Why is that important?

In the age of genomes (2020) one can obtain an automatically annotated genome sequence for a given organism at a modest price in a couple of weeks. The annotations are made by automated sequence comparisons to genome sequences in the databases that were often annotated by automated sequence comparisons as well. However, metabolic maps generated from genomes without supporting physiology can foster very misleading results. An example is the case of Naegleria gruberi, a relative of the brain-eating amoeba, Naegleria fowleri, which causes a deadly brain infection in humans that only a handful of people have ever survived and that is so rapid (about a week) that the diagnosis often comes post mortem. The genome sequence (Fritz-Laylin et al. 2010) presented a map of N. gruberi metabolism based on some genes identifiable in the genome, suggested that the parasite might have an elaborate and sophisticated anaerobic metabolism of the type commonly found in anaerobic and microaerophilic eukaryotes such as Entamoeba, Giardia and Trichomonas. When one however goes to the effort of trying to grow N. gruberi anaerobically, one will see that it does not grow (Mach et al. 2018; Bexkens et al. 2018). It shuns sugars and amino acids, the substrates that the named protists use for ATP synthesis. But it devours the stuff that nerve cells have in abundance (lipids) and it has a high demand for O₂ (like the brain), which goes a long way to explaining why the brain-eating amoeba is a strict aerobe and why it feeds on brain tissue (Bexkens et al. 2018). We make this point to underscore the fact that the stories that can be read from, and into, genome sequences can differ substantially from the actual physiology of the organism. The organisms that we cover in this book have some physiology behind the maps that we present, which represent the results of measurements and experiments, not merely data from genome sequencing projects.

The main reactions of energy metabolism (core ATP synthesis) are catalyzed by proteins that are abundant in the cell and that are present in very high activities. Many glycolytic and Calvin cycle enzymes in eukaryotes (core carbon metabolism) can only be purified about 250-fold because they each typically constitute around 0.4% of the soluble protein in the cell. Energy metabolism is the chemical reaction that keeps us alive. A human adult who is not doing much exercise consumes about 500 liters of O₂ per day and generates about a bodyweight of ATP in the process. A 60 kg runner doing 20 km/h will consume roughly 50 ml O₂ per kg bodyweight per minute (Joyner and Coyle 2008), which translates to about 180 liters O₂ per hour. For 500 liters of O₂ consumed we generate about 500 liters of CO₂, which contain about 250 grams of carbon. A marathon runner burns about 500 grams of fat from start to finish to make the ATP to move the muscles to run the race, and synthesizes close to a bodyweight of ATP in the process.

We will hear a lot about redox balance in this book. Energy metabolism in eukaryotes involves redox reactions, typically generating CO₂ from organic substrates. The 500 liters of O₂ that a human consumes per day corresponds to about 22 moles of O₂, or about 5·10²⁵ electrons that have to change hands, most of them via NAD⁺ to reduced NADH that has to be reoxidized to NAD⁺ again in a human, daily, to keep life going. There is a strict requirement for NADH to be reoxidized, the electrons from oxidations have to be excreted as end products, otherwise life comes to a halt. That is the meaning of redox balance. In heterotrophs, the chemical reactions that release energy to support ATP synthesis involve the removal of electrons from food substrates and the deposition of those electrons onto products that can be excreted from the cell (or the organism). If the flow of electrons stops, the synthesis of ATP stops, and the chemical reaction that is life ultimately stops as a consequence. The evolution of energy metabolism is the evolution of staying alive. In eukaryotes, energy metabolism has everything to do with mitochondria, but in many lineages of modern eukaryotes, mitochondrial ATP synthesis does not involve O₂. How that works and why it is important for understanding evolution are the subject of the book.

The book is divided into three parts. Part I deals with basics and some general principles, Part II covers biochemically well-studied examples, and Part III covers evolutionary aspects. Earlier books dealing with aspects of the eukaryotic anaerobe evolution include Metazoan Life Without Oxygen edited by Bryant (1991) with an excellent overview of the metabolism of some of the animal groups that we discu...

Table of contents

• Title Page
• Copyright
• Contents
• Preface
• List of abbreviations
• Part I: Basics
• Part II: Well-studied examples
• Part III: Evolution
• Bibliography
• Index