What is the name of the hypothesis that explains the origin of eukaryotes?

Evidence

Much of the evidence for the endosymbiotic theory comes from the structure and handling of these organelles’ genetic codes. Both mitochondria and plastids have DNA sequences in circles as that of bacteria. Their DNA also lacks histones (proteins that the DNA is wrapped around) which are present in eukaryotes and some archea. In addition, mitochondria and plastid transcription begin with the amino acid fMet (formylmethionine) as in bacteria, not Met (methionine) as in eukaryotes.

Ribosome sizes are questionable evidence for the endosymbiotic theory. Bacteria usually have ribosomes of 70s (Svedberg units) and eukaryotes usually have around 80s in their cytoplasm. While the mitochondrial and plastid ribosomes are usually of around 70s, they do in fact vary among species from around 60s to 80s, thus overlapping both bacterial and cytoplasmic eukaryote ribosome sizes.

Other evidence for the endosymbiotic theory comes from the two membranes usually surrounding these organelles. The inner membrane belongs to that of the original bacteria and outer membrane presumably a result from the original engulfment. The outer membrane has approximately a 1:1 protein–lipid ratio by dry weight, similar to many eukaryotic cytoplasmic membranes, while the inner membrane (which is made of two layers) has approximately a 3:1, similar to many bacteria. These organelles and bacteria also both utilize electron transport enzymes lacking elsewhere in eukaryotes.

Some of the best evidence for the endosymbiotic theory however comes from bioinformatics. Phylogenetic analyses of various bacteria, mitochondria from various hosts from various kingdoms, and nuclear DNA from those hosts usually place mitochondria as most related to a group of bacteria known as proteobacteria, often placed closest to Rickettsia and other α-proteobacteria. The α-proteobacteria as a group are almost entirely symbiotic or parasitic which may have predisposed the mitochondrial ancestor to an existence within its host. Chloroplasts are most often placed next to cyanobacteria and both contain thylakoids and chlorophyll a; cyanobacteria are also involved in a number of symbioses including lichens and corals.

II Introduction

Chloroplasts are the prominent organelles of green plant tissue. According to the widely accepted endosymbiotic theory [1] they originated from an ancient cyanobacterium, which was engulfed by a eukaryotic host cell. The metamorphosis of the autonomous cyanobacterium into a cell organelle included the transfer of the cyanobacterial genes to the host nucleus. About 98% of all chloroplast genes are now found in the nuclear genome. Consequently, the vast majority of chloroplast proteins is synthesized on cytosolic ribosomes and has to be transported posttranslationally into the plastid. This includes specific targeting to the organelle, binding to receptor proteins on the organellar surface and translocation across the double envelope membranes. Most of the proteins destined for a plastidic subcompartment are synthesized as precursor proteins with a cleavable N‐terminal presequence. Targeting sequences reveal only little similarity at the level of primary sequence or length [2], but all contain predominantly positively charged and hydroxylated amino acids such as threonine and serine [3]. Proteins which are located in the outer envelope use a different, yet mostly unknown, mechanism for targeting and insertion [4]. Translocation itself is mediated by two complex machineries, called Translocon at the outer envelope of chloroplasts (Toc) and Translocon at the inner envelope of chloroplasts (Tic).

The characteristics of Toc are extensively described by D. Schnell in this volume. Here, we will delineate the knowledge about Tic, which is still rather scarce at this point. In general, single subunits have been characterized by biochemical approaches, especially focusing on interaction with precursor proteins. For each member convincing evidence has been provided of it being a Tic component, even though their specific function in most cases remains to be clarified. The same applies to the exact composition of the complex under different conditions and the regulation of the import process across the inner envelope. Due to the growing number of available mutant lines of Arabidopsis, also genetic approaches shed further light on the possible function of Tic constituents. The analysis of knockout or antisense mutants of the respective Tic genes is a very valuable tool for gaining more insight into protein translocation into chloroplasts. We will focus on the characterization of the single subunits and try to fit all known facts into a larger picture of Tic function and regulation.

Lynn Margulis’ Serial Endosymbiotic Theory

Our modern notions of symbiogenesis come from Lynn Margulis (Sagan, 1967), who from the 1960s onward, has introduced the Serial Endosymbiotic Theory (SET) (Sagan, 1967; Margulis, 1970, 1991, 1998; Margulis and Fester, 1991; Margulis and Dolan, 2001; Margulis and Sagan, 2002). Besides advancing a symbiogenetic origin for mitochondria and chloroplasts, according to SET also the eukaryotic nucleus evolved by symbiogenesis. In fact, according to Margulis, who endorsed a five-kingdom classification of life (Whittaker and Margulis, 1978; Margulis and Schwartz, 1997), all four eukaryotic kingdoms evolved as a result of three distinct symbiogenetic events (Figure 6).

SET gives the following chronological sequence of events (Margulis et al., 2000; Margulis, 2010). In a first merger, fermenting thermoplasma-like archaebacteria (Thermoplasma acidophilum) merged with motile spirochete-like eubacteria, and evolved into the first anaerobe proto-eukaryotic cells (cells with a beginning nucleus). This first symbiosis is called motility symbiosis (Figure 7), because it presumably led to the evolution of undulipodia and cilia (eukaryotic motility organelles that resemble tails and hairs) as well as centrioli (that form the centrosome which is the microtubule-organizing center that enables mitosis).

Evidence for motility symbiosis is found in the structure of undulipodia and centrioli. In cross section, centrioli are made up of microtubules organized according to a [9(3)+0] pattern (Figure 2(a)). The same pattern is found in the cross section of the basal bodies (kinetosomes) of undulipodia and cilia (Figure 8). In their shaft (the axoneme), undulipodia and cilia have a [9(2)+2] microtubular pattern. The structure of eukaryotic undulipodia is universal, and its morphological resemblance to the microtubular organization of centrioli makes Margulis assume that they share an evolutionary homologous origin, which she attributes to come from spirochete-like bacterial ancestors (Margulis et al., 2000, 2006).

In a second merger, oxygen-respiring proteobacteria entered the cell’s cytoplasm and engaged in permanent and hereditary symbiosis. The endosymbiotic bacteria evolved into mitochondria. Aerobic protoctists evolved, that, amongst others, includes amoebozoa and tailed (mastigote) cells, and from here all fungi and animals evolved.

In a third merger, early aerobic protoctists additionally engulfed photosynthesizing cyanobacteria that evolved into chloroplasts and gave way to the plant kingdom.

Biology and Genetics

In contrast to chromosomal DNA, which is present as two parental copies in the nucleus, a cell contains up to multiple thousand copies of mtDNA. According to the endosymbiotic theory, mitochondria derive from archeo bacteria, which built a structural and functional association with the cell. Some of the features of the mitochondrial molecule are remnants of this past, such as the independent replication to the nuclear DNA (nDNA) and the deviating translation code. However, extensive transfer of mtDNA into the nucleus has occurred throughout evolution and is still ongoing, which becomes evident in the form of so-called numts (nuclear elements of mtDNA).

Human mtDNA is believed to be inherited solely via the maternal lineage, although paternal leakage and a doubly uniparental mode of transmission are established in some animal species. There are at least two mechanisms by which the inheritance of paternal mtDNA is prevented in humans. First, mitochondria in the sperm cell are outnumbered by those in the egg by at least three orders of magnitude (50–100 in sperms vs. 100000–200000 in the oocyte). Second, in mammals, sperm mitochondria are tagged by ubiquitin which leads to proteolytic digestion in early embryonic development. It has been suggested that the exclusively uniparental pathway has evolved to both mitigate lethal intermitochondrial gene conflicts and prevent the inheritance of sperm mtDNA damaged by free radicals. The analysis of large pedigrees and mother–child pairs has thus far confirmed the maternal mode of inheritance; and while both paternal leakage and recombination of human mtDNA have been proposed, the underlying data and/or methods applied in most of these studies have been challenged. However, in a single yet unrefuted study of a male patient suffering myopathy, paternal transmission of mtDNA was observed. The muscle tissue of the patient showed a mixture of the mtDNA of both parents. The paternal contribution differed from the mtDNA of the father by a 2 bp deletion, which was associated with the disease. Other tissues of the patient as well as tissues of other family members did not show the paternal haplotype.

Assuming that paternal leakage may still represent the very rare exception in mtDNA transmission, the observed variation in human mtDNA can only be explained by de novo mutations in germline cells that eventually become fixed within descendent individuals through the action of an intergenerational genetic bottleneck. Genuine mixtures of mtDNA molecules within single individuals have been described for humans and are known as heteroplasmy. For instance, the observation of point (sequence) heteroplasmy at ntp 16169 in the otherwise identical sequences of the putative remains of Tsar Nicholas II and those of his brother Georgij Romanov substantiated maternal relatedness and supported the identification of the remains of the Romanov family (Figure 2). In medical genetics, point heteroplasmy plays an important role in the diagnosis of mitochondrial-based diseases because pathogenic mutations are rarely present in homoplasmic form. Rather they must exceed a critical threshold in the mixture with the wild-type allele before a disease phenotype develops. It has recently been established that nonpathogenic point mutation mtDNA heteroplasmy is common. Extensive CR sequencing analyses of more than 5000 population samples showed heteroplasmy in 6% of individuals, but with the vast majority displaying the mixture exclusively at single sites (Table 1). Only very few sequences featured point heteroplasmy at two or three positions (0.14 and 0.02%, respectively) and cloning analysis showed that in all of these cases, the constituent haplotypes (three or four molecules, respectively) differed from one another at a single position only. Also, there was a clear tendency for heteroplasmy to occur at known evolutionary hotspots, for example, at ntps 16093, 152, 146, and 204 with exceptions only at positions 214 and 215. Heteroplasmy, when encountered in forensic samples, requires special attention for interpretation and evidence reporting (see the section ‘Practical Aspects of Forensic mtDNA Testing’).

Table 1. List of positions in the mtDNA control region at which heteroplasmy was observed more than once in a total of 5015 investigated haplotypes

PositionTrnTrvPositionTrnTrv1609342–16182–315220–2282114618–161842120418–642–19510–1832–161899–1982–1508–2072–2158–2272–16183–8161292–2147–161682–161927–161692–165197–161732–1514–162562–160924–162782–163114–162902–163624–162912–1533–163012–1893–163092–1943–163552–1993–163992–2343–1611111162613–1619011162943–1623411163903–1626611

Trn, transition; Trv, transversion.

Source: Reproduced from Irwin J, Saunier J, Niederstätter H, et al. (2009) Investigation of point heteroplasmy in the human mitochondrial DNA control region: A synthesis of observations from over 5000 global population samples. Journal of Molecular Evolution 68: 516–527.

2 MAMs structure and composition

Approximately 5–20% of the total surface of the mitochondrial network is estimated to be in close proximity to the ER (Rizzuto et al., 1998). Interestingly, according to the endosymbiotic theory, first proposed by the biologist Lynn Margulis, mitochondria are the result of the endocytosis of purple nonsulfur bacteria by early eukaryotes. However, close apposition of ER subdomains to mitochondria may have evolved in specialized membrane regions to regulate mitochondrial functions and metabolism, giving rise to MAMs.

Mitochondria and the ER are highly dynamic organelles that undergo continuous and coordinate remodeling in the intracellular space. Electron micrography studies showed overlapping apposition between the ER and mitochondria at distances of approximately 10–25 nm (Csordás et al., 2006). Over the years, with the development of subcellular fractionation methods, strong ER contamination was identified in mitochondrial fractions, supporting the presence of membrane contact sites between the ER and mitochondria. The first function for this interface was identified in 1990 through the characterization of a membrane fraction associated with mitochondria and implicated in phospholipid (PL) synthesis. This fraction, now frequently called the MAM, is a specialized subdomain of the ER with a particular lipid and protein composition and many similarities to microsomes (Vance, 1990).

In recent years, multiple techniques have been developed to analyze the specific properties and composition of MAMs, using either biochemical (i.e., subcellular fractionation on a Percoll gradient) (Wieckowski et al., 2009) or fluorescence microscopy-based approaches (Cieri et al., 2018; Tubbs and Rieusset, 2016). Because of these multidisciplinary studies, we have vastly extended our comprehension of MAMs dynamics, structure and functions.

The close linkage between the ER/MAMs and mitochondria is reversible and does not involve membrane fusion. Live cell imaging has revealed that ER-mitochondria contact sites are constantly in flux dependent on intracellular signaling, suggesting that this interaction is a transient phenomenon (Rowland and Voeltz, 2012). From a molecular point of view, proteins and lipids residing in the OMM and the ER membrane interact to promote the formation of MAMs.

In addition to their role in supporting communication between the ER and mitochondria, these tethering structures also endow the associated organelles with new features.

Numerous works have indicated the variety of proteins involved in the composition of MAMs. Two independent mass spectrometry studies documented 991 (in the first study) and 1212 (in the second study) proteins localized to MAMs (Poston et al., 2013; Zhang et al., 2011). Despite the large number of proteins identified, only 44% were common to both studies. This difference may be due, in part, to differences between cell types, i.e., human fibroblasts versus mouse brain cells. The identification of molecular entities localizing at MAMs and their modifications following cellular environmental events provides important information about the processes orchestrating ER-mitochondria crosstalk.

Historically, the first roles associated with the MAM fraction were lipid synthesis and nonvesicular trafficking between the ER and mitochondria, due to the presence of the long-chain fatty acid-coenzyme A (CoA) ligase type 4 (FACL4) and phosphatidylserine synthase-1 (PSS-1) enzymes. Recently, Aufschnaiter et al. demonstrated that the modification of lipid composition in mitochondria and MAMs decisively influences cell death in neurodegenerative conditions (Poston et al., 2013). The ER and mitochondrial networks not only control different aspects of cellular metabolism but also, through their close and dynamic interaction, are involved in the transmission of physiological and pathological Ca2 + and reactive oxygen species (ROS) signals directly from the ER to mitochondria.

Kornmann et al. discovered the ER-mitochondria encounter structure (ERMES) through a genetic screen in Saccharomyces cerevisiae expressing artificial ER-mitochondria (Kornmann et al., 2009). This complex is a heterotetrameric protein complex comprising an ER transmembrane protein (Mmm1p), a cytosolic protein (Mdm12p), and OMM proteins (Mdm34p and Mdm10) (Lang et al., 2015). The subunits Mdm12p, Mdm34p, and Mmm1p contain the synaptotagmin-like lipid-binding protein (SMP) domain, which modulates contact site formation (Reinisch and De Camilli, 2016). Intriguingly, Kornmann showed that the number and activity of ERMES contact points are controlled by the Ca2 +-binding rho-like GTPase Gem1p (Kornmann et al., 2011). Despite its important role in regulating ER-mitochondria tethering in yeast, ERMES is not conserved through evolution (Wideman et al., 2013).

A human protein involved in ER-mitochondria tethering and MAM formation is the cytosolic protein phosphofurin acidic cluster sorting protein 2 (PACS-2) (Simmen et al., 2005). The mechanism by which PACS-2 mediates ER-mitochondria tethering is not yet known, but its knockdown separates the two organelles (Simmen et al., 2005). However, the activity of PACS-2 in the MAM fraction is regulated by the residue at position 437, whose phosphorylation mediated by phosphoinositide-dependent serine-threonine protein kinase (Akt) ensures that PACS-2 remains at MAMs (Betz et al., 2013). Moreover, mammalian target of rapamycin complex 2 (mTORC2), which itself localizes to MAMs, activates PACS-2 via Akt (Betz et al., 2013).

The interactions between ER and mitochondria are modulated in different ways and by numerous proteins (Fig. 1), including the mitochondria-shaping proteins mitofusin1/-2 (MFN1/-2). Scorrano et al. demonstrated that loss of MFN2 alters Ca2 + signaling and reduces ER-mitochondria contacts due to the morphological changes in the ER mediated by MFN2 (de Brito and Scorrano, 2008). However, the activity and function of MFN2 have recently been questioned, leading to the opening of a rather heated debate. In fact, Filadi and colleagues demonstrated that MFN2 reduces the number of close contact sites between the two organelles, proposing a new model for ER-mitochondria tethering (Filadi et al., 2015). Nevertheless, Naon et al. re-evaluated the role of MFN2 defining it as a ER-mitochondria tether whose ablation decreases interorganellar juxtaposition and communication (Naon et al., 2016). This topic is still controversial with opposite results (Filadi et al., 2017) which allow for further considerations about MFN2 functions.

Another protein complex whose function is to modulate ER-mitochondria juxtaposition is the complex formed by inositol 1,4,5-trisphosphate receptors (IP3Rs), the voltage-dependent anion channel (VDAC) and the OMM chaperone Grp75 as described in Fig. 1 (Szabadkai et al., 2006). This interaction is considered functional because it promotes the efficient transfer of calcium from the ER to mitochondria. In fact, silencing of Grp75 in HeLa cells abolished Ca2 + accumulation in mitochondria, highlighting chaperone-mediated conformational coupling between the IP3R and mitochondrial machinery. Nevertheless, a recent study of Bartok et al. reveals a noncanonical and structural role for the IP3Rs independently from calcium flux (Bartok et al., 2019). They display that IP3Rs are required for maintaining ER-mitochondrial contacts.

Recently, a study of the Transglutaminase type 2 (TG2) interactome showed an enzymatic interaction with GRP75 in the MAM fraction (D'Eletto et al., 2018). In fact, silencing of the TG2-GRP75 complex leads to an increase in the interaction between IP3R-3 and GRP75, a reduction in the number of ER-mitochondria contact sites, impairment of ER-mitochondrial Ca2 + flux and an altered MAM proteome profile.

Furthermore, the complex formed between ER vesicle-associated membrane protein-associated protein B (VAPB) and PTPIP51 regulates the modulation of Ca2 + homeostasis by MAMs (De Vos et al., 2012).

The Ultimate Fate of the Symbiosome: Specialization into Host Organelles

A comparison of the rhizobia/legume and Buchnera/aphid symbioses underscores how endosymbiosis and the symbiosome can serve as a vehicle for the acquisition of novel metabolic organelles in the eukaryotic host. This is the essence of the endosymbiotic theory that describes how specialized biosynthetic organelles (e.g., chloroplasts) and bioenergetic organelles (e.g., mitochondria) find their origin as ancient symbioses involving cyanobacterial or α-proteobacterial endosymbionts, respectively. The picture that emerges from the analysis of obligate symbionts is that metabolic specialization leads to coevolution of the host and symbiont, and a genetic simplification of the endosymbiont with the loss of genes no longer essential for free-living physiological function. In other cases, symbiont genes essential for the symbiosis are transferred to the host genome, further simplifying the genetic complement of the endosymbiont, and placing these genes under host control. Ultimately, protein translocation machinery evolved to allow the uptake and assembly of these essential symbiotic gene products into the evolving organelle compartment. In this regard, metabolically specialized organelles such as chloroplasts and mitochondria can be viewed as relics of ancient symbiosome structures.

What is the name of the theory explaining how eukaryotes evolved?

What is the name of the theory that describes the origin of eukaryotic cells by one prokaryotic cell engulfing another?

What is the origin of eukaryotic organisms?