TCA cycle signalling and the evolution of eukaryotes

Abstract

A major question remaining in the field of evolutionary biology is how prokaryotic organisms made the leap to complex eukaryotic life. The prevailing theory depicts the origin of eukaryotic cell complexity as emerging from the symbiosis between an α-proteobacterium, the ancestor of present-day mitochondria, and an archaeal host (endosymbiont theory). A primary contribution of mitochondria to eukaryogenesis has been attributed to the mitochondrial genome, which enabled the successful internalisation of bioenergetic membranes and facilitated remarkable genome expansion. It has also been postulated that a key contribution of the archaeal host during eukaryogenesis was in providing 'archaeal histones' that would enable compaction and regulation of an expanded genome. Yet, how the communication between the host and the symbiont evolved is unclear. Here, we propose an evolutionary concept in which mitochondrial TCA cycle signalling was also a crucial player during eukaryogenesis enabling the dynamic control of an expanded genome via regulation of DNA and histone modifications. Furthermore, we discuss how TCA cycle remodelling is a common evolutionary strategy invoked by eukaryotic organisms to coordinate stress responses and gene expression programmes, with a particular focus on the TCA cycle-derived metabolite itaconate.

Figure 1. The TCA cycle

Overview of all 8 chemical reactions of the TCA cycle and it’s stoichiometry. This stoichiometry is achieved by the complete oxidation of acetyl-CoA to CO2, GTP/ATP and the reducing equivalents NADH and FADH2. The cycle is composed of 8 enzymes and includes citrate synthase (CS), Aconitase (ACO2), Isocitrate dehydrogenase (IDH), oxoglutarate dehydrogenase complex (OGDH), succinyl-CoA synthetase, succinate dehydrogenase (SDH), fumarate hydrates (FH) and malate dehydrogenase (MDH).

Figure 2. The endosymbiont and entangle-engulf-endogenize (E3) hypothesis

Overview of the endosymbiont/E3 hypothesis. (A) Lokiarchaeon (archaeal host) found itself in a symbiotic relationship with a sulfate-reducing bacterium and an αλπηα-proteobacterium (mitoprecursor), which helped it to detoxify O2 after the great oxygenation event spurred on by photosynthesis and cyanobacteria. (B) The mitoprecursor became entangled in Lokiarchaeon protrusions and eventually led to the endogenization of the mitoprecursor and the development of primitive nuclear structures. (C) This proto-eukaroyte would initially have bioenergetic pathways in both the host archaeon and the mitoprecursor, living off amino acids as fuel. (D) Delegation of ATP production to the mitoprecursor results in the loss it’s genome, except for key genes needed for respiration and local translation, both to the archaeal host and through lack of necessity. This enabled genome expansion in the host, the development of complex genome structures and the emergence of intracellular complexity and organelle formation.

Figure 3. The acquisition of mitochondria supported the emergence of multicellularity

Heterotrophic prokaryotes with low yields but high rates of ATP (via fermentation for example) compete for shared food sources with other heterotrophic that can lead to food source exhaustion and low reproductive rates. The acquisition of mitochondria supports high yields of ATP but at low rates that triggers cooperation, food source sharing and is better for reproduction. This evolutionary trade off suggests mitochondria were essential contributors to the emergence of multicellular life in the Eukarya domain.

Figure 4. An evolutionary timeline of eukaryotic cell development

In our proposed timeline, the TCA cycle emerged in the pre-biotic era and was later adopted by early life forms as means to assimilate CO₂ using the reductive TCA cycle (rTCA) and build organic compounds. At the same time, photosynthetic organisms evolved that lead to a major production of O₂, the great oxygenation event and the evolution of aerobes and facultative anaerobes that use O₂ as a terminal electron acceptor. The coupling of a reversible rTCA, the oxidative TCA cycle (oxTCA), that can also break down fuel molecules and couple to respiration that uses O₂ in a highly exergonic process is selected for. The mitochondrion precursor, likely with a reversable TCA, is endogenized by an archaeon as it acted as an important O₂ scavenger. This leads to the favouring of the oxTCA cycle, the delegation of ATP production and O₂ detoxification to the mitochondrion precursor, the formation of nuclear structures and eventually the first eukaryote emerges. The acquisition of eukaroytes leads to cooperation for food sources that leads to the emergence of multicellular and morphologically complex life. The eukarya domain undergoes massive expansion to form diverse kingdoms of complex living creatures, including the animal kingdom and the human species of great ape.

Figure 5. How TCA cycle signalling may have contributed to eukaryogenesis by acting as a driver of genome expansion, chromatin architecture and gene expression

In our hypothesis, the acquisition of mitochondria acted as a driver of eukaryogenesis as it facilitated the expansion of the genome by removing the bioenergetic constraints imposed by the expression large quantities of proteins, while at the same provide key nutrient signals that promoted the formation of chromatin architecture and resulted in the ability to dynamically control this expanded genome. Furthermore, The TCA cycle and the electron transport chain (ETC) resulted in high yields of ATP that likely also enabled the evolution of multicellular organisms. Histones may have also played an important role in regulating mitochondrial function as the H3-H4 tetramer has recently been shown to function as a copper reductase that supplies bioavailable copper for respiratory chain function. This role of the TCA cycle in driving this response is supported by the fact that remodeling of the TCA cycle is intimately linked to the regulation of genome structure and gene expression in diverse eukaryotic organisms, a phenomenon only recently starting to come to light.