Effect on gene loss because of compartmentalisation of plastids/mitochondria/endosymbiont?

Effect on gene loss because of compartmentalisation of plastids/mitochondria/endosymbiont?

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Considering the transfer of genes during endosymbiosis a gene transfer event (at least fundamentally, even if it's a special case), how does the fact that in this case the genes are inside a compartment, affect their gene loss, or incorporation into the host/recipient's genome (in context of gene transfer)?

I would imagine that the loss would be slower, recombination with other transferred genes less probable. But I can't find literature on the same. Any leads?

Integration of plastids with their hosts: Lessons learned from dinoflagellates

After their endosymbiotic acquisition, plastids become intimately connected with the biology of their host. For example, genes essential for plastid function may be relocated from the genomes of plastids to the host nucleus, and pathways may evolve within the host to support the plastid. In this review, we consider the different degrees of integration observed in dinoflagellates and their associated plastids, which have been acquired through multiple different endosymbiotic events. Most dinoflagellate species possess plastids that contain the pigment peridinin and show extreme reduction and integration with the host biology. In some species, these plastids have been replaced through serial endosymbiosis with plastids derived from a different phylogenetic derivation, of which some have become intimately connected with the biology of the host whereas others have not. We discuss in particular the evolution of the fucoxanthin-containing dinoflagellates, which have adapted pathways retained from the ancestral peridinin plastid symbiosis for transcript processing in their current, serially acquired plastids. Finally, we consider why such a diversity of different degrees of integration between host and plastid is observed in different dinoflagellates and how dinoflagellates may thus inform our broader understanding of plastid evolution and function.

Plastids evolve through the endosymbiotic integration of two organisms: a eukaryotic host and a photosynthetic prokaryotic or eukaryotic symbiont. It is generally believed that the host initially consumes the symbiont through phagocytosis. Subsequently, over long evolutionary timescales, pathways evolve within the host to maintain the endosymbiont as a permanent, intracellular organelle (1). At least eight distinct plastid endosymbioses have been documented across the eukaryotes, giving rise to a diverse array of different photosynthetic lineages (reviewed in ref. 2). Understanding what processes underpin the integration of plastids with their hosts may provide valuable insights into the evolution and function of photosynthetic eukaryotes.

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Mechanisms facilitating endosymbiosis

Mutualism often originates from asymmetrical, even exploitative interactions [12] most of them are facultative, and many have relatively recent origins [65]. Obligate mutualisms are rare and considered less stable, since there is a higher chance of (functional) degradation by occasional loss of partner [50, 65, 70]. Symbiosis is shaped by conflicts of interests which are probably harder to manage at the early stage of the association [14, 71]. Consequently, it is unlikely that the ancestors of mitochondria and host first met with perfect metabolic complementarity, so that their symbiosis was immediately mutually beneficial. On the other hand, these specialized obligate symbioses do exist and are persistent for millions of years despite any conflicts, indicative of stabilizing mechanism. In turn, we will discuss mechanisms that can stabilize an emerging though suboptimal interaction so that in can be selected for.

Group selection in endosymbioses

If groups (associations) form among cells and these groups affect the selection of individual cells, selection appears at multiple levels: individual selection favors the interest of individual cells, while group selection acts in the interest of the associations [11, 72, 73], e.g., of symbiotic pairs. However, multilevel selection almost inevitably leads to between-level conflicts. To better understand group formation, multilevel selection was conceptually characterized into two types, multilevel selection 1 and 2 (MLS1, 2).

In case of MLS1, only temporary groups form that periodically disappear to revert to an unstructured population of cells (also called transient compartmentation) [74]. Facultative (endo- or ecto-) symbioses realize MLS1: partners re-associate better-than-random. Fixed spatial structure of cells can also act as implicit group structure. In dense biofilms, cells are practically immobile and the limited diffusion of exchanged molecules localizes interactions. As a result, mutualist partners stay close and their implicit group can withstand cheating mutants or harmful competitors appearing at group edges [75]. In this case, splitting up the population into explicit, reproductively isolated groups is not required for selection to prefer mutualists [76]. It is yet unknown if endosymbiosis could or have ever evolved in biofilms.

MLS2, on the other hand, involves explicit group structure, i.e., groups that last and reproduce indefinitely. In symbiosis terms, this means exclusive partnership with strict vertical inheritance. If the group is selected for and can stably inherit group-related adaptations, it is a bona fide evolutionary unit (an informational replicator [77]). When obligate codependence of endosymbiotic partners is established, a new unit of evolution emerges [78] and selection of associations dominates over selection of individuals. A major evolutionary transition happens when multilevel selection results in irreversible coupling where individuals forfeit their autonomous replication and gives rise to an association with potential for higher complexity [11]. For group selection to be effective, group members must reproduce together better than random and there must be a selective advantage at the group level. In turn, we will discuss mechanisms that can ensure positive assortativity of partners.

The theory of group selection predicts that the group is favored by selection over individuals if there is a reasonable selective advantage for the group, even if the net of benefits and costs is negative at certain times (i.e., the per capita growth rate of the association is smaller than that of individual cells under certain conditions). Accordingly, the initial partnership does not need to be directly mutually beneficial for both parties at all times, as long as the partnership together enjoys selective advantage averaged over some time or over different environments. Nevertheless, there must be at least a hidden benefit for each party, so that reduced mean fitness in certain periods is compensated. There are at least two general mechanisms to draw such indirect benefits. One is to exploit heterogenous environments, for example temporally fluctuating or spatially differentiated, so that the mean fitness over a wider temporal or spatial range is larger than those of competitors. The other is bet-hedging, that compensates a reduced mean fitness with reduced fitness variance, e.g., with wider tolerance of harsh conditions [79]. This renders the species less prone to extinction in certain selective environments that are truncating, though rare. A prudent strategy counters or even anticipates the effects of a heterogenous environment (see the farming hypothesis, explored theoretically [53]).

Partner choice mechanisms

Pre- or post-infection partner choice can stabilize (partially) beneficial interactions [80]. Pre-infection partner choice is based on cues or signals or screening mechanisms to filter partner quality before actually establishing any association with the partner [65, 80, 81]. Quorum sensing, including intra- and inter-species communication, exists both in bacteria and archaea [82, 83]. There is, however, no guarantee that interacting cells are indeed of the cooperative type, as cheating in the form of dishonest signals can arise [84, 85]. Signals can be of two types: diffusive or contact molecules. Surface contact requires close proximity and these signals are usually partner-specific. Diffusive signal molecules can reach a larger number of cells, but are less effective (being diluted easily) and are usually not partner-specific, hence are less reliable. The specificity and reliability required for obligate pairwise symbiosis suggest that surface contact is preferred over diffusive signals (Fig. 4).

Basic steps of endosymbiosis and organellogenesis. Geometric shapes represent various benefits (e.g., metabolites), solid black arrows represent the source and flow of the various benefits, dashed arrows indicate investments, and colored arrows indicate the option to leave the host. Note that the last step, if involves nuclear integration and protein import, is irreversible

Post-infection partner choice is based on conditional investments, and involves various rewarding or sanctioning mechanisms, including the selective termination of the interaction and the possibility of switching partners [65, 86]. The prerequisite of post-infection partner choice is spatial separation of the multiple partners, so that the host can differentiate and then selectively treat high- or low-quality partners a set-up often referred to as biological markets [13, 80, 87, 88]. The quality of preferable partners depends on multiple factors [65, 87, 88], and often, a low-quality partner is better than no partner at all.

For most of the cases, there is an asymmetry between the mutualist partners in many aspects, such as power of control over the partner, strategic options, availability of alternative partners, etc.[86]. The party with more power or control is expected to gain the higher profit from the interaction, which can even drive the interaction towards unilateral exploitation [58, 65, 88]. Nevertheless, such selectivity by partner control mechanisms can shift the balance in favor of high-quality partners in the population in spite of their competitive inferiority to low-quality partners without the intervention of the mutualist [65]. Additionally, control mechanisms may allow the host to manipulate symbiont behavior and to force higher returns from investing into the symbiont, and may also allow for context-dependent treatment of the partner [56, 58, 89].

Partner fidelity feedback and internalization

Partner fidelity mechanisms are able to reduce the conflict of interest between partners as the symbiont survival depends on the survival of the host [90]. Increasing investment toward the partner increases the amount or possibility of reciprocated investment, i.e., it is a favor returned [48, 80]. The higher the quality of the mutualist, the higher the chances for survival [65]. Such feedbacks can be interpreted in two time-frames: in-generation or cross-generation. In a generation of a long-term partnership, increasing investments induce higher rates of nutrient flows (in nutrition mutualisms) or higher quality of services (in protection mutualisms) by the partner. Partner fidelity can also manifest as a cross-generational effect, where the investment into a high-quality partner will also benefit the progeny [65].

Cross-generational partner fidelity is usually coupled with vertical (or pseudo-vertical) transmission mechanisms, and is similar in effect to spatial structure: it ensures that offspring can form associations with the same selection of partners as parents did. Strict vertical transmission is very rare (besides endosymbiotic organelles, and some cases of parasitism, like Wolbachia in wasps [48, 91]). Imperfect correlation between partners across generations, called pseudo-vertical transmission, is more frequent [48, 92]. Such loose correlations and feedbacks can stabilize mutualism and pave the way for the evolution of perfect cross-generational correlation of partners.

Theory predicts that the evolution of symbiont capture and vertical transmission is driven by host mechanisms to control symbiont transmission [93]. First, because symbiont capture involves the genome reduction of the symbiont while providing increasingly more benefit to hosts, second, because the processes during cell division affecting the distribution and the frequency of reproduction of both parties are controlled by the host, which thus can have the power of selecting which symbionts to transfer (probably restricted to multicellular eukaryotes, e.g., in Buchnera–aphid interactions [94].

Undoubtedly, physical inclusion is the most advanced method of vertical transmission, but at the start of a symbiotic partnership, it is rarely available. In most prokaryotic symbioses, physical inclusion never happens, or is limited to a periplasmic space (e.g., Bdellovibrio [95], Chlorochromatium aggregatum [96]). There are some rare cases where the symbiont can enter the host’s cytoplasm, but, e.g., parasitic Daptobacter ultimately kills its host [97]. Phagotrophic eukaryotes could store their captured symbionts in phagosomes (symbiont-bearing vesicles or symbiosomes [98, 99]), but whether phagocytosis was the means of mitochondrial inclusion is not known yet. According to some hypotheses, the early host for mitochondria trapped its surface–contact partners in membrane protrusions [100, 101]. In case of a heterotrophic host capable of secreting extracellular digestive enzymes, such entrapment could serve as a poor-man’s phagocytosis [102]. A mixed vertical and horizontal transmission seems to be in effect in Burkholderia-infected Dictyostelium [103], indicative of facultative endosymbiosis.

Central control and organellogenesis

As partners become more dependent on each other, and as one party starts to dominate the other, central control evolves. Its ultimate form is the nuclear transfer of symbiont genes, requiring the presence of a nucleus and a mechanism to import proteins from the host cytosol to the symbiont. Evolved dependence on protein and lipid import mechanisms is a sign of endosymbiosis becoming irreversible.

For mitochondrial genes to undergo nuclear transfer, the host must have already been a (proto-)eukaryote. The ancestor of mitochondria could have been acquired before the nucleus, but only with the evolution of the true karyon could compartmentalized, safe transcription (safe from hybridization) be implemented. Symbiont genes relocating into the host nucleus are minimizing the effect of lower level of selection of the multilevel selection situation. With this step, eukaryotes left the prokaryotic domain for good.

After nuclear transfer of genes, it is necessary that proteins not produced by the symbiont anymore find their way back into the symbiont. Usually, this is a translocon-mediated protein import system installed by the host. With a protein import system in effect and a sufficient number of genes transferred to the nucleus, the symbiont could relinquish its protein-coding genes and protein-producing machinery, leveraging its genome. Moreover, this allows the host to introduce proteins of its own interest into the symbiont’s membrane.

The adenine nucleotide translocase (ANT) was probably introduced by the host into the mitochondrial membrane to exchange host-cytosolic ADP with symbiont ATP [36, 104]. ANT was most likely evolved within eukaryotes after the engulfment of the ancestral symbiont [105,106,107]. It was certainly in the host’s best interest to exploit the symbiont. If, however, it was the symbiont who invented ANT to give up ATP for the host, then any cheater bacterium capable of turning off its ANT while inside the host would have been under positive selection leading to the overpopulation of defecting symbionts, as was pointed out [108]. Group selection could have stabilized against cheaters, but only if a population of endosymbionts payed enough ATP to the host, so that host replicated faster (compared to other host cells) since the symbiont replicated with the host, the benefit was shared [109]. Other partner control mechanisms screening out cheaters are unknown yet.

No prokaryotic analogies of karyogenesis were found yet, though nuclear transfer is known in many eukaryotes [110]. Further features thought to be exclusive to mitochondrial and plastid integration have been recognized in more recent endosymbioses [71, 111, 112], drawing a picture of a continuum from symbiosis to organellogenesis (see Fig. 4). While nuclear integration renders the partnership obligate and irreversible, preventing the escape of the reduced partner, such mechanisms by no means represent an end state. They do not even ensure the survival of the symbiont, as amitochondriate eukaryotes attest. In the next section, we explore mechanisms that work against and could even ruin endosymbioses.

Engineering of plastid genomes

The invention of the particle gun provided a universal method for DNA delivery into living cells and subcellular compartments, including organelles. Stable transformation of the chloroplast genome by particle gun-mediated (biolistic) DNA delivery was first accomplished in the unicellular green alga C. reinhardtii (Boynton et al., 1988 ), followed by success in the seed plant species N. tabacum (tobacco Svab et al., 1990 Svab and Maliga, 1993 ). For more than 20 years, these two species have remained the organisms of choice for plastid transformation, and its application in both basic research and biotechnology. Although a few important crop species can now also be transformed (Sidorov et al., 1999 Ruf et al., 2001 Dufourmantel et al., 2004 ), progress with developing plastid transformation protocols for additional species has been somewhat slow, and many genetic model species and agriculturally relevant crops are still not transformable, notably including A. thaliana and all monocotyledonous species (Maliga, 2004 Maliga and Bock, 2011 Bock, 2014 ).

The integration of foreign DNA into the plastid genome occurs exclusively via homologous recombination, thus allowing very precise manipulations of the plastid genome, such as the introduction of point mutations at defined positions (Przibilla et al., 1991 Bock et al., 1994 ). The extraordinarily high activity of the homologous recombination system of plastids also facilitates the simultaneous modification of two distinct regions of the plastid genome by co-transformation experiments, in which two or more plasmid vectors are loaded on the microprojectiles for bombardment (Kindle et al., 1991 Carrer and Maliga, 1995 Krech et al., 2013 ). Amazingly, this approach can even be used to co-transform the nuclear genome (by non-homologous end joining) and the plastid genome (by homologous recombination) in a single experiment (Elghabi et al., 2011 ).

Over the years, plastid transformation in the two model systems, Chlamydomonas and tobacco, has become more and more routine, with the efficiency of plastid transformation now approaching that of nuclear transformation. This cannot be ascribed to a single methodological breakthrough, but rather is the result of many incremental improvements in the procedures involved in generating transplastomic cells and plants: the biolistic protocol, the transformation vectors, selectable markers and expression cassettes, and the tissue culture, selection and regeneration protocols. Along the way, a large toolkit for plastid genome engineering has been put together by both the tobacco and the Chlamydomonas communities (Maliga, 2004 Day and Goldschmidt-Clermont, 2011 Maliga and Bock, 2011 Bock, 2013 , 2014 ). This toolkit contains, for example, various selectable marker genes, reporter genes, and promoters and untranslated regions (5′- and 3′- UTRs) that confer widely different transgene expression levels. Recently, significant progress has also been made with improving plastid transgene expression in non-green plastid types, such as amyloplasts and chromoplasts (Valkov et al., 2011 Zhang et al., 2012 Caroca et al., 2013 ), and with developing methods for the inducible expression of plastid transgenes (Mühlbauer and Koop, 2005 Surzycki et al., 2007 Verhounig et al., 2010 ).

A salient feature of particle gun-mediated transformation is that DNA delivery is entirely based on a physical process. Thus, the biolistic method has no theoretical size limitation and large pieces of foreign DNA can be bombarded into the target compartment (Altpeter et al., 2005 ). So far, DNA pieces of up to 50 kb have been incorporated into the tobacco plastid genome (Adachi et al., 2007 ), and there is no reason to believe that much bigger pieces could not be introduced as well. Together with the small genome size (Figure 1) and the ease with which many genetic manipulations can be conducted, the capacity to accommodate large quantities of foreign DNA make the chloroplast an attractive target of synthetic biology. Based on pioneering work in microbial systems (Roodbeen and van Hest, 2009 Delaye and Moya, 2010 Cambray et al., 2011 ), two main branches of synthetic biology have emerged. Top-down synthetic biology approaches start from an existing biological system, and aim at reducing its complexity, ideally to a minimum-size system that consists of the smallest possible number of parts. Bottom-up synthetic biology approaches start with individual parts (building blocks) and try to construct artificial biological systems from first principles. The overarching goals of both approaches are very similar: (i) to further our understanding of the genetic elements and regulatory principles underlying functional biological systems and (ii) to design optimized biological systems for engineering applications. The latter goal brings synthetic biology in close proximity to biotechnology, and in fact many applications that nowadays come under the label of synthetic biology also could be viewed as advanced genetic engineering for biotechnological purposes (Peralta-Yahya et al., 2012 Paddon et al., 2013 ). This semantic issue notwithstanding, the amenability of plastids to large-scale genome manipulations with high precision facilitates both top-down and bottom-up approaches on the road to plant synthetic biology. In the following, the potential of plastids for synthetic biology is illustrated with two examples: (i) the design of minimum-size synthetic plastid genomes, a top-down approach and (ii) the build-up of new metabolic pathways in plastids via multigene engineering, a bottom-up approach.


Eukaryotes arose by the engulfment of prokaryotes and are thus genetic mosaics with two (animals and fungi) or three (plants) DNA-containing organelles. The integration of the third genetic compartment, the plastids, has led to photoautotrophic eukaryotes that are the nutritional basis for most life on earth. Plants had to evolve alternative means of metabolic coupling and organellar interaction hubs. We present a data set promoting the moss P. patens as a model organism for organelle biology, based on its evolutionary position and amenability to proteomics as well as microscopic studies. Comparative quantitative proteomics integrating validation on the single-protein level and metabolic pathway databases provides evidence that protein compartmentation and metabolic partitioning are highly flexible but well regulated in different kingdoms of life, different lineages within a kingdom, different tissues of a given species, between individual organelles of a single cell, and even at the suborganellar level by the formation of dynamic microcompartments in plastids and mitochondria.

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While the primary acquisition of the plastid from a free-living cyanobacterium is believed to have occurred only once [1], plastids have continued to spread through eukaryotes by means of secondary and tertiary endosymbiosis. This is the process whereby a plastid-containing, free-living eukaryote is consumed by another eukaryotic cell and becomes an organelle itself. Primary plastids (exemplified by those of plants) have two membranes, while secondary plastids have additional membranes corresponding to the outer membrane of the engulfed eukaryote and the phageosomal membrane of the host, as well as the original membranes of the primary plastid [2, 3], although in some lineages membranes have subsequently been lost. The nucleus of the engulfed cell is, in all but two described cases, absent, and the genes encoding plastid-targeted proteins having been relocated to the host nucleus [4–6]. The exceptions are the cryptomonads and chlorarachniophytes, which contain nucleomorphs, the remnant nuclei of the plastid-containing algae that were engulfed in the secondary endosymbioses that gave rise to these lineages (Figure 1). The cryptomonad endosymbiont is derived from a red alga, while that of chlorarachniophytes is derived from a green alga. Their genomes encode very few genes, and most of them are housekeeping genes for replication, transcription and protein folding and degradation [7, 8]. A handful of proteins related to plastid function have also been retained, however, they are relatively few [7, 9, 10]. The periplastidial space (equivalent to the cytosol of the engulfed alga) itself has specific metabolic processes, such as starch synthesis in cryptomonads, but most of the proteins for these pathways are missing from the nucleomorph genome [7] and are anticipated to be found in the nuclear genome, as has been shown for a few examples [11].

Endosymbiotic events that gave rise to cryptomonads and chlorarachniophytes.

The nucleomorph is often thought of as an anomaly, a rare occurrence, since it is known only in cryptomonads and chlorarachniophytes, but if one considers 'loss or gain' rather than 'presence or absence' then it is perhaps not so anomalous. All lineages that are known to contain secondary plastids (haptophytes, heterokonts, cryptomonads, dinoflagellates, apicomplexans, euglenids and chlorarachniophytes) have ancestors that contained a nucleomorph. Depending on the number of secondary endosymbiotic events that took place, which is still contentious [3, 12–14], the number of nucleomorph losses and gains differs. The balance of molecular evidence points to two events involving green algae [15, 16] and one involving a red alga [17–19]. With respect to green algae this means one lineage lost its nucleomorph and one retained it. With respect to red algae, this means a single nucleomorph gain (if one accepts the chromalveolate hypothesis [20]) and perhaps only one loss, if cryptomonads are the deepest branch of chromalveolates, or perhaps two if they diverged later. Overall, lineages retaining nucleomorphs may be as common as lineages that lost them, or at least the proportions are very similar. Whatever the case, nucleomorphs existed in the common ancestors of a great deal of algal diversity, so the study of the lineages in which they remain may help us understand the process of secondary (and higher order) endosymbiotic events, especially the reduction and subsequent loss of the enslaved genome.

Cryptomonads and chlorarachniophytes arose from separate endosymbiotic events, and neither host cell nor endosymbiont are very closely related. Yet the nucleomorph genomes of the cryptomonad, Guillardia theta [7] and the chlorarachniophyte, Bigelowiella natans [8–10] share several characteristics. Both nucleomorph genomes have undergone substantial gene loss and are ultra-compact compared to their free-living relatives in the red and green algae. Some of these features, such as overlapping genes, short intergenic regions, a reduction in elements like transposons, and the presence of multigene transcripts have been found in other compact eukaryotic genomes such as microsporidia [21, 22]. Compact genomes and many of these features are common to endosymbionts in general, however, until the sequences of the G. theta and B. natans, nucleomorph genomes were completed, all known endosymbiont genomes have been of prokaryotic origin. The best examples of prokaryotic endosymbiont genomes are those of the mitochondrion, once a free-living alpha-proteobacterium, and the chloroplast, once a free-living cyanobacterium [1]. Also well described, although not organellar, are the bacterial endosymbionts of insects, of these there are several complete genomes for example, Wolbachia [23–25], Buchnera [26], Wigglesworthia [27] and Blochmania [28], the features of which have been compared and defined [29–31]. These bacteria reside within a range of diverse insects but, while they retain certain distinct genes that can be linked to the physiology of their host, they show similar patterns of genome reduction, strong mutational AT bias and strict amino acid bias at high expression genes [32] an effect of selection against mutation driven amino acid changes [31, 33]. The AT mutational pressure in endosymbionts, is sometimes very extreme estimated to be a remarkable 90% GC->AT in Buchnera [34]. A universal AT mutational bias, has been suggested because many types of spontaneous mutations (e.g. the deamination of cytosine) cause GC to AT changes [35]. The effects of this mutational bias may be more pronounced and gene loss more rapid in small, endosymbiont genomes because they are deficient in at least one DNA repair mechanism, experience strong genetic drift and have experienced a relaxation of selection in the intracellular environment in comparison to free-living existence [31, 33].

There is less chromosomal information for eukaryotic obligate intracellular parasites, however certain alveolate and microsporidian genomes show some similar characteristics such as genome compaction [22], AT bias [7, 36, 37], codon bias [38, 39] and extreme divergence. A summary of the features of organelle-, obligate-intracellular- and nucleomorph-genomes is given in Table 1. These features are important to consider as measure of how unusual, or not, nucleomorph genomes are.

With the recent availability of red algal [40] and green algal [41] genomic data we are for the first time in a position to do comparative genomics between nucleomorphs of both cryptomonads and chlorarachniophytes and examples of their free-living relatives, with the plant Arabidopsis thaliana serving as an outgroup. Here we test whether the phylogenetically distinct nucleomorph genomes of G. theta and B. natans have experienced similar evolutionary pressures that influenced genome-wide variation in predictable ways and with the same severity and whether these effects are in common to those described in other enslaved nuclei. Proteins from both nucleomorph genomes have been observed to reside on long branches of phylogenetic trees indicating that they are poorly conserved [42–45], however this has never been investigated at the genomic level. It is also assumed that nucleomorph genes are highly derived because the proteins function within a sub-cellular compartment, the periplastidial space, where selection is relaxed due to reduced interactions with other proteins. However, both the G. theta and B. natans nucleomorphs encode proteins that are directed to the plastid. Proteins that function in the plastid are presumably subject to similar selection pressures in organisms with nucleomorphs as they are in other algae. We have therefore used plastid proteins encoded in the plastid genome, the nucleomorph, or the nucleus, to examine differences in rates of evolution in the different genomes to determine whether the nucleomorph is evolving at a dissimilar rate to the plastid and nuclear genomes. We also investigate the overall variability of evolutionary rates of nucleomorph-encoded proteins and their homologues in other species to determine if the proteins still encoded within these genomes are generally well conserved, and whether this can shed light on their retention in the nucleomorph. By comparing proteins from the nucleomorph of two cryptomonads, G. theta and Rhodomonas salina, we also investigate whether cryptomonad nucleomorph genomes are diverging at the same rate as their nuclear genomes.


Mitochondria (singular = mitochondrion) are often called the “powerhouses” or “energy factories” of a cell because they are responsible for making adenosine triphosphate (ATP), the cell’s main energy-carrying molecule. The formation of ATP from the breakdown of glucose is known as cellular respiration. Mitochondria are oval-shaped, double-membrane organelles (Figure 1) that have their own ribosomes and DNA. Each membrane is a phospholipid bilayer embedded with proteins. The inner layer has folds called cristae, which increase the surface area of the inner membrane. The area surrounded by the folds is called the mitochondrial matrix. The cristae and the matrix have different roles in cellular respiration.

In keeping with our theme of form following function, it is important to point out that muscle cells have a very high concentration of mitochondria because muscle cells need a lot of energy to contract.

Figure 1 This transmission electron micrograph shows a mitochondrion as viewed with an electron microscope. Notice the inner and outer membranes, the cristae, and the mitochondrial matrix. (credit: modification of work by Matthew Britton scale-bar data from Matt Russell)

Like mitochondria, chloroplasts also have their own DNA and ribosomes. Chloroplasts function in photosynthesis and can be found in eukaryotic cells such as plants and algae. Carbon dioxide (CO2), water, and light energy are used to make glucose and oxygen in photosynthesis. This is the major difference between plants and animals: Plants (autotrophs) are able to make their own food, like glucose, whereas animals (heterotrophs) must rely on other organisms for their organic compounds or food source.

Like mitochondria, chloroplasts have outer and inner membranes, but within the space enclosed by a chloroplast’s inner membrane is a set of interconnected and stacked, fluid-filled membrane sacs called thylakoids (Figure 2). Each stack of thylakoids is called a granum (plural = grana). The fluid enclosed by the inner membrane and surrounding the grana is called the stroma.

Figure 2 This simplified diagram of a chloroplast shows the outer membrane, inner membrane, thylakoids, grana, and stroma.

The chloroplasts contain a green pigment called chlorophyll, which captures the energy of sunlight for photosynthesis. Like plant cells, photosynthetic protists also have chloroplasts. Some bacteria also perform photosynthesis, but they do not have chloroplasts. Their photosynthetic pigments are located in the thylakoid membrane within the cell itself.

Theory of Endosymbiosis

We have mentioned that both mitochondria and chloroplasts contain DNA and ribosomes. Have you wondered why? Strong evidence points to endosymbiosis as the explanation.

Symbiosis is a relationship in which organisms from two separate species live in close association and typically exhibit specific adaptations to each other. Endosymbiosis (endo-= within) is a relationship in which one organism lives inside the other. Endosymbiotic relationships abound in nature. Microbes that produce vitamin K live inside the human gut. This relationship is beneficial for us because we are unable to synthesize vitamin K. It is also beneficial for the microbes because they are protected from other organisms and are provided a stable habitat and abundant food by living within the large intestine.

Scientists have long noticed that bacteria, mitochondria, and chloroplasts are similar in size. We also know that mitochondria and chloroplasts have DNA and ribosomes, just as bacteria do. Scientists believe that host cells and bacteria formed a mutually beneficial endosymbiotic relationship when the host cells ingested aerobic bacteria and cyanobacteria but did not destroy them. Through evolution, these ingested bacteria became more specialized in their functions, with the aerobic bacteria becoming mitochondria and the photosynthetic bacteria becoming chloroplasts.