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Schematic representation of the secondary endosymbiont hypothesis of diatom evolution. The upper panel shows the conventional primary endosymbiosis at the origin of green and red algae and Glaucophytes. By contrast, diatoms are now believed to be derived from a serial secondary endosymbiosis (lower panel) in which a heterotrophic host cell (exosymbiont) combined first with a green alga and subsequently with a red alga (Moustafa et al., 2009). EGT, endosymbiotic gene transfer. 

Schematic representation of the secondary endosymbiont hypothesis of diatom evolution. The upper panel shows the conventional primary endosymbiosis at the origin of green and red algae and Glaucophytes. By contrast, diatoms are now believed to be derived from a serial secondary endosymbiosis (lower panel) in which a heterotrophic host cell (exosymbiont) combined first with a green alga and subsequently with a red alga (Moustafa et al., 2009). EGT, endosymbiotic gene transfer. 

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Diatoms are unicellular, mainly photosynthetic, eukaryotes living within elaborate silicified cell walls and believed to be responsible for around 40% of global primary productivity in the oceans. Their abundance in aquatic ecosystems is such that they have on different occasions been described as the insects, the weeds, or the cancer cells of the...

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... are eukaryotic unicellular organisms inhabiting aquatic and other humid ecosystems. Most diatom species are photosynthetic, and because they represent a significant component of both planktonic and benthic ecosystems in the contemporary ocean they are believed to be responsible for about 20% of primary productivity on Earth (Falkowski et al. , 1998; Field et al. , 1998) and to produce around 40% of marine organic carbon (Nelson et al. , 1995). Another well-known characteristic of diatoms is their ornate cell wall constructed of amorphous silica, which makes the cells heavy and susceptible to sinking when they die or when they are grazed. By generating oxygen through photosynthesis and sequestering atmospheric carbon into the ocean in- terior, they are therefore likely to have influenced significantly the Earth’s atmosphere and climate (Brzezinski et al. , 2002). The reasons underlying the evolutionary and ecological success of diatoms are largely unknown, but the availability of whole genome sequences from two divergent diatom species (Armbrust et al. , 2004; Bowler et al. , 2008) has provided a genetic context for exploring their evolutionary trajectory and for predicting their biochemical potential. Studies that have exploited these genome sequences and the enabling resources that allow their dissection suggest unorthodox interactions between diatom plastids and mitochondria. The results have implications for understanding the basics of diatom cell physiology and their response to environmental change, as well as for exploiting these organisms in applied applications such as nanotechnology and for biofuels (Dismukes et al. , 2008; Kro ̈ ger and Poulsen, 2008). These recent results have been reviewed here and their potential evolutionary and metabolic significance is discussed. Based on evidence from the fossil record and from molecular clocks, diatoms are believed to have appeared after the Permian–Triassic mass extinctions (250 million years ago), and the first reliable fossils date to around 180 million years ago (Sims et al. , 2006; Kooistra et al. , 2007; Armbrust, 2009). The two major diatom divisions that are now recognized based on their symmetry, the centrics (radially symmetrical) and pennates (bilaterally symmetrical), diverged during the Cretaceous around 90 million years ago and their populations expanded and diversified enormously around 30 million years ago at the Eocene–Oligocene boundary, from where we can trace back the appearance of many modern diatoms (Bowler et al. , 2010). It is now believed that there may be as many as 100 000 extant species, comprising two groups each within the centric (radial and bi/multipolar) and pennate (raphid and araphid) lineages. But from where did diatoms arise and what do we know about their origins? Plants and algae are believed to have originated through a process where a non-photosynthetic eukaryote engulfed (or was invaded by) a cyanobacterium, thereby acquiring a photosynthetic apparatus that became housed within an organelle surrounded by two membranes (Fig. 1). This event, known as a primary endosymbiosis, is believed to have occurred around 1.8 billion years ago, and it conveniently explains the monophyletic origins of all plastids within eukaryotic cells (Gould et al. , 2008; Keeling, 2010). The host cell can be termed the exosymbiont (Hamm and Smetacek, 2007), whereas the cyanobacterium in known as an endosymbiont. This initial endosymbiotic event gave rise to the green and red algal lineages, as well as to the glaucophytes (Fig. 1). Land plants arose following the evolution of multicellularity within the green algal lineage. The endosymbiotic process also involved the transfer of thousands of genes from the cyanobacterial genome to the host eukaryotic nucleus (Martin et al. , 2002), whereas the genome within the chloroplast (a photosynthetic plastid) became reduced to only a few hundred genes. In contrast to the small genome of the chloroplast, this organelle contains a large number of plastid proteins, probably between 2000 and 5000 (van Wijk and Baginsky, 2011), the majority of which are nuclear encoded, synthesized on cytosolic ribosomes, and targeted to the plastid using amino-terminal targeting peptides (Soll and Schleiff, 2004). Interestingly, dual protein targeting to mitochondria and plastids is also quite a common phenom- enon and, in some cases, these plastid proteins do not even have targeting sequences (Jarvis, 2004; Jarvis and Robinson, 2004; Millar et al. , 2006; Radhamony and Theg, 2006) By contrast with the evolution of land plants and green algae, the evolutionary history of diatoms is believed to have followed a rather different path (Fig. 1). Specifically, diatoms and their relatives are thought to have originated when a second non-photosynthetic eukaryote engulfed a photosynthetic eukaryote about 1.4 billion years ago (Yoon et al. , 2002). This is known as a secondary endosymbiosis, and a single event is currently believed to be at the origin of the whole Chromalveolata supergroup, which comprises heterokonts (also known as stramenopiles, and to which the diatoms belong), alveolates, haptophytes, cryptophytes, and perhaps also rhizaria (Bhattacharya et al. , 2007; Cavalier-Smith, 1999; Keeling, 2010). Impor- tant evidence for the secondary endosymbiosis is that the plastids in many of these organisms are surrounded by four rather than two membranes, corresponding to (from outside to inside) the exosymbiont endomembrane, the plasma membrane of the engulfed alga, and the two membranes of the primary plastid. These nested cellular compartments provide clues about the evolutionary history of these organisms. For example, a vestige of the nuclear genome of the endosymbiont (known as a nucleomorph) can some- times be found between the inner two and the outer two membranes surrounding the plastid (Ben Ali et al. , 2001), albeit not in diatoms. The nucleomorphs of cryptophytes still encode 18S rRNA, and it has been shown that the endosymbiont was most probably related to red algae (Van de Peer et al. , 1996). By extension, it would therefore appear that the chromalveolate secondary endosymbiosis involved a red alga (Yoon et al. , 2002). This further supports earlier molecular phylogenetic studies, which place the plastids of heterokonts as close relatives to those of red algae and cryptophytes (as reviewed in Keeling, 2010; Green, 2011). Diatom chloroplasts are typical secondary plastids surrounded by four membranes (Fig. 2). The outer envelope is termed the chloroplast endoplasmic reticulum (CER) and is continuous with the nuclear envelope. Diatom plastids are also characterized by a ‘girdle lamella’ that runs in parallel with the four membranes that surround them (Fig. 2D). The girdle lamella and the thylakoids are always found in bundles of three but are never partitioned between stacked and unstacked grana, as in some green algae and higher plants. A further contrast with green algae is that all the algae within the chromalveolate grouping have chlorophyll a and c , whereas green algae contain chlorophyll a and b (Delwiche, 1999; Green, 2011). Furthermore, diatoms do not use state 1/state 2 transitions to balance absorbed excitation energy distribution between Photosystem I (PSI) and Photosystem II (PSII) (Owens, 1986), most likely because the photosystems are not distributed between stacked and unstacked grana (Pfannschmidt et al. , 2009). The ultrastructure of red algal thylakoids is the simplest among eukaryotes ( 48292/Algae.html’’>Algae-Prokaryotic Algae), with single thylakoids that are not stacked. They use chlorophyll a and phycobilins, and the phycobilisomes that house them are attached to the stromal surface of the thylakoids (http:// science.jrank.org/pages/48292/Algae.html’’>Algae-Prokaryotic Algae). Phycobiliproteins have been lost in diatoms but they are still present in cryptophytes (Delwiche et al. , 1995; Gibbs, 1981). Evidence for the derivation of diatoms and other chlorophyll c -containing algae from the red lineage is therefore somewhat anecdotal, but molecular phylogenetic analyses are consistent with this hypothesis (Van de Peer et al. , 1996; Delwiche et al. , 1995). The light-harvesting peripheral antennae of the diatom photosynthetic machinery are composed of fucoxanthin chlorophyll a/c binding proteins (FCPs) structured into oligomeric complexes (Bu ̈chel, 2003; Beer et al. , 2006). These complexes possess a large number of carotenoids only found within photosynthetic ...
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... Algae), with single thylakoids that are not stacked. They use chlorophyll a and phycobilins, and the phycobilisomes that house them are attached to the stromal surface of the thylakoids (http:// science.jrank.org/pages/48292/Algae.html’’>Algae-Prokaryotic Algae). Phycobiliproteins have been lost in diatoms but they are still present in cryptophytes (Delwiche et al. , 1995; Gibbs, 1981). Evidence for the derivation of diatoms and other chlorophyll c -containing algae from the red lineage is therefore somewhat anecdotal, but molecular phylogenetic analyses are consistent with this hypothesis (Van de Peer et al. , 1996; Delwiche et al. , 1995). The light-harvesting peripheral antennae of the diatom photosynthetic machinery are composed of fucoxanthin chlorophyll a/c binding proteins (FCPs) structured into oligomeric complexes (Bu ̈chel, 2003; Beer et al. , 2006). These complexes possess a large number of carotenoids only found within photosynthetic heterokonts and haptophytes, such as fucoxanthin (Fx), as well as diadinoxanthin (Ddx) and diatoxanthin (Dtx) pigments that are involved in their unique xanthophyll cycle (Lepetit et al. , 2011). Besides the FCP proteins, three other antenna protein families have been found: Lhcf (the classical light-harvesting proteins), Lhcr (red algal-related proteins), and the less abundant (Westermann and Rhiel, 2005) Lhcx proteins (previously known as LHCSR and Li818) (Eppard et al. , 2000; Green, 2007; Koziol et al. , 2007; Lepetit et al. , 2011). Diatoms also have a PSI-specific antenna (Veith and Bu ̈chel, 2007; Veith et al. , 2009; Lepetit et al. , 2011) that has a higher amount of Ddx and Fx than the main FCP proteins (Lepetit et al. , 2011). Diatom thylakoid membranes contain the same classes of lipids as higher plants and green algae (Goss and Wilhelm, 2009; Lepetit et al. , 2011), although in contrast to plants and green algae which have mostly neutral galactolipids, diatom thylakoid galactolipids are mainly negatively charged (Vieler et al. , 2007 a , b ; Goss et al. , 2009; Lepetit et al. , 2011). In higher plants the most abundant galactolipids are MGDG (monogalactosyldiacylglycerol), while in diatoms the main lipid is the anionic SQDG (sulphoquino- vosyldiacylglycerol) (Goss et al. , 2009). Another difference is that diatom thylakoid membranes contain the phospho- lipid phosphatidylcholine (PC), while in plants this lipid is not present in thylakoids (Lepetit et al. , 2011). As mentioned above, only about 2% of the original plastid genome is retained in the chloroplast, while most of the other genes have either been lost or have become incorporated into the nucleus of the host. This was pre- sumably advantageous for avoiding Muller’s ratchet, the accumulation of deleterious mutations when population sizes are small (Muller, 1932). Furthermore, the plastid genome may be subject to higher mutation rates due to increased oxidative stress as a result of the high levels of reduced oxygen species (ROS) that can be generated from the photosynthetic apparatus (Allen and Raven, 1996). It has been argued that the large number of plastid genomes per cell favours net gene transfer from plastid to the nucleus, simply by a ‘diffusion gradient’ argument, compared with the less probable transfer from a single copy nuclear genome to multiple copies of the plastid genome (Martin, 2003). These factors perhaps combined to provide a selective advantage to moving genes from the plastid to the nucleus. Although only a small percentage of the original plastid genome remained, the fact that it did remain signifies that it has an important role. According to Puthiyaveetil et al. (2010) plastid-encoded genes are required for redox regulation within the organelle, while the genes encoding ribosomal proteins and RNAs support the primary redox regulatory control of photosynthesis (Allen, 2003; Puthiyaveetil et al. , 2010). Like other eukaryotes, diatom cells contain mitochondria evolved from a single primary endosymbiotic event involving an a -proteobacterium. No trace of mitochondria remain in the secondary endosymbiont, and so it is believed that diatom mitochondria are derived from the exosymbiont. In support of this, heterokont, haptophyte, and dinoflagellate mitochondria are all characterized by tubular cristae, as in animals, whereas green and red algae (as well as cryptophytes) all contain flattened cristae ( Algae.html’’>Algae-Prokaryotic Algae). The functional significance of this difference is unclear (Frey and Mannella, 2000), but given that the cristae contain and organize the respiratory electron transport chain and the proton-motive ATP synthase of oxidative phosphorylation, the issue warrants further investigation. Following secondary endosymbiosis, the different genomes of the exosymbiont and endosymbiont are predicted to have combined to form a novel and unique set of genes (Falkowski et al. , 2004) dispersed within the nuclear, mitochondrial, and chloroplast genomes (Fig. 1). Consider- ing that such a fusion is thought to involve two nuclear genomes, two mitochondrial genomes, and one plastid genome, the process must have been highly complex and, because it happened so long ago, reconstructing its history has proven extremely difficult. The following section will address how the availability of completed diatom genome sequences has been able to contribute to addressing this fundamental question. The first diatom species whose genome was fully sequenced, Thalassiosira pseudonana , belongs to the bi/multipolar centric family of diatoms known as Mediophyceae. Armbrust et al. (2004) found that this diatom has a 34 Mb nuclear genome, a 129 kb plastid genome, and a 44 kb mitochondrial genome. In total, 11 242 protein-coding genes are predicted in the nuclear genome, 127 in the plastid, and 34 genes in the mitochondria. Following the centric diatom T. pseudonana , a raphid pennate diatom species (Bacillariophyceae) Phaeodactylum tricornutum was sequenced, revealing more information about diatom adaptation to the varied aquatic environments which they inhabit. P. tricornutum has a smaller nuclear genome, of about 27.4 Mb, a chloroplast genome of 117.4 kb, and a mitochondrial genome of 77.4 kb, predicted to have 10 402, 130, and 34 genes, respectively (Oudot-Le Secq et al. , 2007; Bowler et al. , 2008; Oudot-Le Secq and Green, 2011). The two aforementioned groups of diatoms diverged about 90 million years ago (Sims et al. , 2006; Kooistra et al. , 2007), and so significant differences are expected between their genomes. It is interesting to note that the divergence is so large between these two types of diatoms that it can be compared with the difference between Homo sapiens and Takifugu rubripes (puffer fish), which diverged around 550 million years ago. This comparison indicates a high rate of diatom gene modification, losses and gains of genes and introns, and gene exchanges with other organisms, all of which probably contributed to high diatom diversification rates. Notwithstanding, about 57% of genes are shared between T. pseudonana and P. tricornutum . The secondary endosymbiont hypothesis posits that diatoms acquired genes from both non-photosynthetic and photosynthetic ancestors, therefore gaining a chimeric genome from a varied origin. Further studies of the T. pseudonana genome provided strong support for this hypothesis. Of particular interest, in a comparison with animals ( Mus musculus ) and green plants ( Arabidopsis thaliana ), 806 proteins homologous to sequences found only in the animal were discovered, whereas 865 proteins matched sequences found in the plant but not in the mouse. It was therefore proposed that these two sets of sequences were derived from the exo- and endosymbionts at the origin of diatom evolution (and by extrapolation all chromalveolates) (Armbrust et al. , 2004). In spite of the large number of sequences that can be traced with confidence to Arabidopsis , it was noted with surprise that the T. pseudonana genome contained relatively few genes of red algal origin. At the time this was attributed to the poor taxon sampling of the red lineage, because the only whole genome sequence available was that of Cyanidioschyzon merolae (Matsuzaki et al. , 2004), which is not particularly represen- tative of the red lineage because it is known to be highly derived due to its extremophile lifestyle. In a subsequent comparison of the P. tricornutum genome with the red algal genome, Bowler et al. found just 171 genes of red algal origin, 108 of which were also found in T. pseudonana (Bowler et al. , 2008). A high number of these, specifically 74 genes (43%), encode plastid-related functions, and 11 genes are also shared with oomycetes, non-photosynthetic heterokonts which are also believed to be derived from the same secondary endosymbiotic event with a red alga, but which subsequently lost photosynthesis. By contrast, when the diatom sequences are compared with those in a cyanobacterium ( Nostoc sp. PCC 7120), numerous proteins are found to be shared with photosynthetic clusters found in both green and red lineages. As mentioned earlier, diatom plastids are surrounded by four membranes, and the outer one is contiguous with the endoplasmic reticulum (ER) that surrounds the nucleus (Fig. 2G). This suggests that diatoms must have developed a special way of transferring proteins from the ER into the chloroplast. Analysis of nuclear-encoded chloroplast targeted proteins in diatoms indeed shows the presence of ER signal sequences in addition to the more conventional chloroplast targeting transit peptides found in plants (Kilian and Kroth, 2005). The functionality of these dual targeting sequences has also been verified experimentally to the extent that it is now possible to predict whether a nuclear-encoded protein in diatoms is likely to be plastid targeted (Kroth, 2002). The incorrectly folded proteins in the ER that cannot be repaired must be relocated ...
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... are eukaryotic unicellular organisms inhabiting aquatic and other humid ecosystems. Most diatom species are photosynthetic, and because they represent a significant component of both planktonic and benthic ecosystems in the contemporary ocean they are believed to be responsible for about 20% of primary productivity on Earth (Falkowski et al. , 1998; Field et al. , 1998) and to produce around 40% of marine organic carbon (Nelson et al. , 1995). Another well-known characteristic of diatoms is their ornate cell wall constructed of amorphous silica, which makes the cells heavy and susceptible to sinking when they die or when they are grazed. By generating oxygen through photosynthesis and sequestering atmospheric carbon into the ocean in- terior, they are therefore likely to have influenced significantly the Earth’s atmosphere and climate (Brzezinski et al. , 2002). The reasons underlying the evolutionary and ecological success of diatoms are largely unknown, but the availability of whole genome sequences from two divergent diatom species (Armbrust et al. , 2004; Bowler et al. , 2008) has provided a genetic context for exploring their evolutionary trajectory and for predicting their biochemical potential. Studies that have exploited these genome sequences and the enabling resources that allow their dissection suggest unorthodox interactions between diatom plastids and mitochondria. The results have implications for understanding the basics of diatom cell physiology and their response to environmental change, as well as for exploiting these organisms in applied applications such as nanotechnology and for biofuels (Dismukes et al. , 2008; Kro ̈ ger and Poulsen, 2008). These recent results have been reviewed here and their potential evolutionary and metabolic significance is discussed. Based on evidence from the fossil record and from molecular clocks, diatoms are believed to have appeared after the Permian–Triassic mass extinctions (250 million years ago), and the first reliable fossils date to around 180 million years ago (Sims et al. , 2006; Kooistra et al. , 2007; Armbrust, 2009). The two major diatom divisions that are now recognized based on their symmetry, the centrics (radially symmetrical) and pennates (bilaterally symmetrical), diverged during the Cretaceous around 90 million years ago and their populations expanded and diversified enormously around 30 million years ago at the Eocene–Oligocene boundary, from where we can trace back the appearance of many modern diatoms (Bowler et al. , 2010). It is now believed that there may be as many as 100 000 extant species, comprising two groups each within the centric (radial and bi/multipolar) and pennate (raphid and araphid) lineages. But from where did diatoms arise and what do we know about their origins? Plants and algae are believed to have originated through a process where a non-photosynthetic eukaryote engulfed (or was invaded by) a cyanobacterium, thereby acquiring a photosynthetic apparatus that became housed within an organelle surrounded by two membranes (Fig. 1). This event, known as a primary endosymbiosis, is believed to have occurred around 1.8 billion years ago, and it conveniently explains the monophyletic origins of all plastids within eukaryotic cells (Gould et al. , 2008; Keeling, 2010). The host cell can be termed the exosymbiont (Hamm and Smetacek, 2007), whereas the cyanobacterium in known as an endosymbiont. This initial endosymbiotic event gave rise to the green and red algal lineages, as well as to the glaucophytes (Fig. 1). Land plants arose following the evolution of multicellularity within the green algal lineage. The endosymbiotic process also involved the transfer of thousands of genes from the cyanobacterial genome to the host eukaryotic nucleus (Martin et al. , 2002), whereas the genome within the chloroplast (a photosynthetic plastid) became reduced to only a few hundred genes. In contrast to the small genome of the chloroplast, this organelle contains a large number of plastid proteins, probably between 2000 and 5000 (van Wijk and Baginsky, 2011), the majority of which are nuclear encoded, synthesized on cytosolic ribosomes, and targeted to the plastid using amino-terminal targeting peptides (Soll and Schleiff, 2004). Interestingly, dual protein targeting to mitochondria and plastids is also quite a common phenom- enon and, in some cases, these plastid proteins do not even have targeting sequences (Jarvis, 2004; Jarvis and Robinson, 2004; Millar et al. , 2006; Radhamony and Theg, 2006) By contrast with the evolution of land plants and green algae, the evolutionary history of diatoms is believed to have followed a rather different path (Fig. 1). Specifically, diatoms and their relatives are thought to have originated when a second non-photosynthetic eukaryote engulfed a photosynthetic eukaryote about 1.4 billion years ago (Yoon et al. , 2002). This is known as a secondary endosymbiosis, and a single event is currently believed to be at the origin of the whole Chromalveolata supergroup, which comprises heterokonts (also known as stramenopiles, and to which the diatoms belong), alveolates, haptophytes, cryptophytes, and perhaps also rhizaria (Bhattacharya et al. , 2007; Cavalier-Smith, 1999; Keeling, 2010). Impor- tant evidence for the secondary endosymbiosis is that the plastids in many of these organisms are surrounded by four rather than two membranes, corresponding to (from outside to inside) the exosymbiont endomembrane, the plasma membrane of the engulfed alga, and the two membranes of the primary plastid. These nested cellular compartments provide clues about the evolutionary history of these organisms. For example, a vestige of the nuclear genome of the endosymbiont (known as a nucleomorph) can some- times be found between the inner two and the outer two membranes surrounding the plastid (Ben Ali et al. , 2001), albeit not in diatoms. The nucleomorphs of cryptophytes still encode 18S rRNA, and it has been shown that the endosymbiont was most probably related to red algae (Van de Peer et al. , 1996). By extension, it would therefore appear that the chromalveolate secondary endosymbiosis involved a red alga (Yoon et al. , 2002). This further supports earlier molecular phylogenetic studies, which place the plastids of heterokonts as close relatives to those of red algae and cryptophytes (as reviewed in Keeling, 2010; Green, 2011). Diatom chloroplasts are typical secondary plastids surrounded by four membranes (Fig. 2). The outer envelope is termed the chloroplast endoplasmic reticulum (CER) and is continuous with the nuclear envelope. Diatom plastids are also characterized by a ‘girdle lamella’ that runs in parallel with the four membranes that surround them (Fig. 2D). The girdle lamella and the thylakoids are always found in bundles of three but are never partitioned between stacked and unstacked grana, as in some green algae and higher plants. A further contrast with green algae is that all the algae within the chromalveolate grouping have chlorophyll a and c , whereas green algae contain chlorophyll a and b (Delwiche, 1999; Green, 2011). Furthermore, diatoms do not use state 1/state 2 transitions to balance absorbed excitation energy distribution between Photosystem I (PSI) and Photosystem II (PSII) (Owens, 1986), most likely because the photosystems are not distributed between stacked and unstacked grana (Pfannschmidt et al. , 2009). The ultrastructure of red algal thylakoids is the simplest among eukaryotes ( 48292/Algae.html’’>Algae-Prokaryotic Algae), with single thylakoids that are not stacked. They use chlorophyll a and phycobilins, and the phycobilisomes that house them are attached to the stromal surface of the thylakoids (http:// science.jrank.org/pages/48292/Algae.html’’>Algae-Prokaryotic Algae). Phycobiliproteins have been lost in diatoms but they are still present in cryptophytes (Delwiche et al. , 1995; Gibbs, 1981). Evidence for the derivation of diatoms and other chlorophyll c -containing algae from the red ...
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... does indicate more similarity with red plastids than with green plastids (Fig. 3) (Allen JF et al. , 2011). Furthermore, Chloroplast Sensor Kinase (CSK), a nuclear-encoded bacterial-type sensor kinase that plays a major role in transcriptional control of plastid genes, is of clear red algal origin in diatoms (Puthiyaveetil et al. , 2010). Diatom mitochondria are considered to have been derived from the exosymbiont. The mitochondrial genomes from both diatoms (as well as a third species Synedra acus ) were found to display almost the same gene composition as in the mitochondrial genomes of haptophytes and cryptophytes (Oudot-Le Secq and Green, 2011). While there is evidence of significant gene transfer from the plastid and mitochondrial genomes to the nucleus in higher plants (Martin, 2003) and dinoflagellates (Hackett et al. , 2004), in the diatoms no proof of such gene transfers from the mitochondria to the nucleus were found. There are no red algal mitochondrial genes found in the T. pseudonana or P. tricornutum nuclear genomes, which strengthens the conclusion that the red algal mitochondrion was lost and that only the exosymbiont mitochondria was retained during the evolutionary process. The general properties of diatom mitochondrial genomes are indeed more similar to animal than to plant mitochondrial genomes (Oudot-Le Secq and Green, 2011). Furthermore, recent studies have highlighted the novel metabolisms within diatom mitochondria, that are quite unlike those of green algae and higher plants, such as a urea cycle (see later). Besides providing evidence for the ancient secondary endosymbiotic event at the origin of diatoms (and perhaps all chromalveolates), it was found that diatom genomes also contain a large number of genes (587 in P. tricornutum ) proposed to be derived from bacteria by horizontal gene transfer (Bowler et al. , 2008). These genes were not found in any other photosynthetic eukaryotes (other than other heterokonts), and it is believed that they have provided diatoms with increased flexibility in their regulatory and metabolic networks that may have contributed to their evolutionary success. For example, diatoms probably acquired genes enabling novel metabolic offshoots from the urea cycle through such processes (see later). Equally striking are a bacterial glutamine synthetase targeted to the mitochondria, and a bacterial NAD(P)H nitrite reductase (Allen et al. , 2006). Such observa- tions hint that nitrogen metabolism has been configured in a unique manner in diatoms. As mentioned above, although multiple evidence indicates that diatoms and other chromalveolates gained a plastid of red algal origin through secondary endosymbiosis, the initial analysis of whole genome sequences did not provide incontrovertible evidence about the origin of diatom plastids (Armbrust et al. , 2004; Bowler et al. , 2008). The subject was reinvestigated by Moustafa et al. (2009), who used a phylogenomic analysis pipeline based on the wholesale generation of phylogenetic trees from each diatom protein sequence encoded by the two diatom nuclear genomes. Using this approach, in T. pseudonana 2423 genes were identified as being of red or green algal origin, while in P. tricornutum 2533 such genes were found. Subsequent analysis revealed that more than 70% of these sequences were more similar to green algal proteins than to red algal proteins, contrasting with the prediction of the chromalveolate hypothesis (Cavalier-Smith, 1999). The >1700 identified ‘green’ genes comprise around 16% of the diatom genome, in contrast to the ‘red’ genes which only represented around 3% of the nuclear genome. Some green proteins known to be encoded in the nucleus of green algae and higher plants, such as naphthoate synthase, haem oxygenase, pyruvate dehydrogenase, and GUN4, can similarly be found in the diatom nucleus even though these genes are encoded in the plastids of red algae. Rather than being of red algal origin and present in the plastid genome, they are therefore absent in the red algal-derived plastid of diatoms and are instead of green algal origin and encoded in the nucleus. Another impressive example of green gene acquisition is phytoene desaturase, which catalyses one of the early steps in carotenoid biosynthesis, as well as many other genes encoding enzymes of this pathway. This is of particular significance because diatoms are known to contain a diatom-specific xanthophyll cycle involved in photoprotection (Lohr and Wilhelm, 1999; Coesel et al. , 2008). It would therefore appear that this innovation was derived from genes originally encoded in green algae. The results from Frommolt et al. (2008) indicated for the first time that the cryptic green alga might have been a Prasinophyte, a primitive group of green algae. The conclusion from the phylogenomic studies of Moustafa et al. (2009) was, therefore, that a cryptic green alga was involved in the secondary endosymbiotic event, in addition to the red alga (Fig. 1). The fact that diatom plastids have clear biochemical and genetic affiliations with red algal plastids was interpreted as meaning that the green algal endosymbiont was acquired first, and that the red alga followed in a serial secondary endoymbiotic event. In such a scenario, the data would imply that the genes derived from the green algal nucleus were largely retained and that the majority of red algal nuclear genes were lost because they were not required due to the availability of green algal nucleus-derived orthologues already present in the host nucleus. By contrast, the data in Fig. 3 indicate that the genes already present within the plastid of the red algal endosymbiont were largely retained. The same analytical pipeline, when used to interrogate the genome sequences available from other heterokonts and alveolates (as well as the haptophyte Emiliania huxleyi , whose phylogeny is uncertain with respect to the heterokonts and alveolates), indicated similar overall patterns, suggesting that these same serial secondary endosymbiotic events were at the origin of all the chromalveolates (Moustafa et al. , 2009). Such data therefore confirm the phylogenetic affiliation of the chromalveolates (Steinko ̈ tter et al. , 1994; Petersen et al. , 2006; Frommolt et al. , 2008; Reyes-Prieto et al. , 2008), although the implication of a third partner in the secondary endosymbiotic event was a major surprise. A further question that was addressed by Moustafa et al. (2009) was what kind of green alga was party to the serial secondary endosymbiosis. Among the green lineages of the Viridiplantae, several unicellular members have been studied at the whole genome level, in particular within the Chlor- ophyta and Streptophyta clades (Tirichine and Bowler, 2011). The green genes from the two diatoms were found to share most similarity with those present in prasinophytes, which lie within the Streptophyta and constitute a primitive group of green algae most commonly found in marine environments (Derelle et al. , 2006). It was therefore proposed that a related alga was most likely to have been the source of the green genes in diatoms. In summary then, the evolutionary trajectory of diatoms has brought together a highly unorthodox combination of genes derived by endosymbiotic gene transfer from two secondary endosymbionts to the exosymbiont nucleus, as well as by horizontal gene transfer that permitted numerous additional acquisitions from bacteria and Archaea. Con- versely, exosymbiont-derived mitochondria gained the op- portunity to work alongside a red-algal-derived plastid that was powered largely by green algal genes. It can therefore be predicted that diatoms display novel biochemical pathways that drive physiological processes that are unknown in plants, animals, and fungi. The following section reveals that this is indeed the case. Interorganellar co-ordination of metabolism has been studied in green algae and higher plants, for example, regarding the exchange of metabolites between chloroplasts, peroxisomes, and mitochondria during photorespiration (Raghavendra and Padmasree, 2003; Noctor et al. , 2007; Parker et al. , 2008). However, the preceding discussion has presented evidence that diatom chloroplasts and mitochondria both have unusual characteristics with respect to those in better studied experimental organisms. An additional curiosity is that these two organelles are often found in very close proximity within the diatom cell (Fig. 2A–E). This juxtaposition suggests some important metabolic interactions that perhaps go beyond those in the green lineage. Some possibilities are discussed below. Photosynthesis occurs by the light-dependent generation of energy in the chloroplast through a process known as linear electron flow (LEF), where electrons are transferred from water to NADP via three major complexes: Photosystem II (PS II), the cytochrome b 6 f complex (cyt b 6 f ) and Photosystem I (PS I). The produced NADPH is used in the Calvin– Benson–Bassham cycle, where carbon dioxide is fixed to produce organic compounds. Optimized functioning of photosynthesis requires fine-tuning between conversion of light into chemical energy as NADPH and ATP, and its use by metabolic reactions such as carbon fixation. The metabolic demand for ATP and NADPH varies under different physiological and environmental conditions, so their relative abundances have to be finely controlled. In green algae and higher plants, the water–water cycle (WWC; also known as chlororespiration or pseudo-cyclic electron flow) and cyclic electron flow around PS I (CEF) play physiologically important roles in both the regulation of photosynthesis and the alleviation of photoinhibition by consuming excess electrons and maintaining an appropriate NADPH/ATP ratio (Grossman et al. , 2010; Wilhelm and Selmar, 2011). In Arabidopsis and Chlamydomonas , CEF appears to be particularly important for balancing light absorption with carbon ...
Context 5
... are eukaryotic unicellular organisms inhabiting aquatic and other humid ecosystems. Most diatom species are photosynthetic, and because they represent a significant component of both planktonic and benthic ecosystems in the contemporary ocean they are believed to be responsible for about 20% of primary productivity on Earth (Falkowski et al. , 1998; Field et al. , 1998) and to produce around 40% of marine organic carbon (Nelson et al. , 1995). Another well-known characteristic of diatoms is their ornate cell wall constructed of amorphous silica, which makes the cells heavy and susceptible to sinking when they die or when they are grazed. By generating oxygen through photosynthesis and sequestering atmospheric carbon into the ocean in- terior, they are therefore likely to have influenced significantly the Earth’s atmosphere and climate (Brzezinski et al. , 2002). The reasons underlying the evolutionary and ecological success of diatoms are largely unknown, but the availability of whole genome sequences from two divergent diatom species (Armbrust et al. , 2004; Bowler et al. , 2008) has provided a genetic context for exploring their evolutionary trajectory and for predicting their biochemical potential. Studies that have exploited these genome sequences and the enabling resources that allow their dissection suggest unorthodox interactions between diatom plastids and mitochondria. The results have implications for understanding the basics of diatom cell physiology and their response to environmental change, as well as for exploiting these organisms in applied applications such as nanotechnology and for biofuels (Dismukes et al. , 2008; Kro ̈ ger and Poulsen, 2008). These recent results have been reviewed here and their potential evolutionary and metabolic significance is discussed. Based on evidence from the fossil record and from molecular clocks, diatoms are believed to have appeared after the Permian–Triassic mass extinctions (250 million years ago), and the first reliable fossils date to around 180 million years ago (Sims et al. , 2006; Kooistra et al. , 2007; Armbrust, 2009). The two major diatom divisions that are now recognized based on their symmetry, the centrics (radially symmetrical) and pennates (bilaterally symmetrical), diverged during the Cretaceous around 90 million years ago and their populations expanded and diversified enormously around 30 million years ago at the Eocene–Oligocene boundary, from where we can trace back the appearance of many modern diatoms (Bowler et al. , 2010). It is now believed that there may be as many as 100 000 extant species, comprising two groups each within the centric (radial and bi/multipolar) and pennate (raphid and araphid) lineages. But from where did diatoms arise and what do we know about their origins? Plants and algae are believed to have originated through a process where a non-photosynthetic eukaryote engulfed (or was invaded by) a cyanobacterium, thereby acquiring a photosynthetic apparatus that became housed within an organelle surrounded by two membranes (Fig. 1). This event, known as a primary endosymbiosis, is believed to have occurred around 1.8 billion years ago, and it conveniently explains the monophyletic origins of all plastids within eukaryotic cells (Gould et al. , 2008; Keeling, 2010). The host cell can be termed the exosymbiont (Hamm and Smetacek, 2007), whereas the cyanobacterium in known as an endosymbiont. This initial endosymbiotic event gave rise to the green and red algal lineages, as well as to the glaucophytes (Fig. 1). Land plants arose following the evolution of multicellularity within the green algal lineage. The endosymbiotic process also involved the transfer of thousands of genes from the cyanobacterial genome to the host eukaryotic nucleus (Martin et al. , 2002), whereas the genome within the chloroplast (a photosynthetic plastid) became reduced to only a few hundred genes. In contrast to the small genome of the chloroplast, this organelle contains a large number of plastid proteins, probably between 2000 and 5000 (van Wijk and Baginsky, 2011), the majority of which are nuclear encoded, synthesized on cytosolic ribosomes, and targeted to the plastid using amino-terminal targeting peptides (Soll and Schleiff, 2004). Interestingly, dual protein targeting to mitochondria and plastids is also quite a common phenom- enon and, in some cases, these plastid proteins do not even have targeting sequences (Jarvis, 2004; Jarvis and Robinson, 2004; Millar et al. , 2006; Radhamony and Theg, 2006) By contrast with the evolution of land plants and green algae, the evolutionary history of diatoms is believed to have followed a rather different path (Fig. 1). Specifically, diatoms and their relatives are thought to have originated when a second non-photosynthetic eukaryote engulfed a photosynthetic eukaryote about 1.4 billion years ago (Yoon et al. , 2002). This is known as a secondary endosymbiosis, and a single event is currently believed to be at the origin of the whole Chromalveolata supergroup, which comprises heterokonts (also known as stramenopiles, and to which the diatoms belong), alveolates, haptophytes, cryptophytes, and perhaps also rhizaria (Bhattacharya et al. , 2007; Cavalier-Smith, 1999; Keeling, 2010). Impor- tant evidence for the secondary endosymbiosis is that the plastids in many of these organisms are surrounded by four rather than two membranes, corresponding to (from outside to inside) the exosymbiont endomembrane, the plasma membrane of the engulfed alga, and the two membranes of the primary plastid. These nested cellular compartments provide clues about the evolutionary history of these organisms. For example, a vestige of the nuclear genome of the endosymbiont (known as a nucleomorph) can some- times be found between the inner two and the outer two membranes surrounding the plastid (Ben Ali et al. , 2001), albeit not in diatoms. The nucleomorphs of cryptophytes still encode 18S rRNA, and it has been shown that the endosymbiont was most probably related to red algae (Van de Peer et al. , 1996). By extension, it would therefore appear that the chromalveolate secondary endosymbiosis involved a red alga (Yoon et al. , 2002). This further supports earlier molecular phylogenetic studies, which place the plastids of heterokonts as close relatives to those of red algae and cryptophytes (as reviewed in Keeling, 2010; Green, 2011). Diatom chloroplasts are typical secondary plastids surrounded by four membranes (Fig. 2). The outer envelope is termed the chloroplast endoplasmic reticulum (CER) and is continuous with the nuclear envelope. Diatom plastids are also characterized by a ‘girdle lamella’ that runs in parallel with the four membranes that surround them (Fig. 2D). The girdle lamella and the thylakoids are always found in bundles of three but are never partitioned between stacked and unstacked grana, as in some green algae and higher plants. A further contrast with green algae is that all the algae within the chromalveolate grouping have chlorophyll a and c , whereas green algae contain chlorophyll a and b (Delwiche, 1999; Green, 2011). Furthermore, diatoms do not use state 1/state 2 transitions to balance absorbed excitation energy distribution between Photosystem I (PSI) and Photosystem II (PSII) (Owens, 1986), most likely because the photosystems are not distributed between stacked and unstacked grana (Pfannschmidt et al. , 2009). The ultrastructure of red algal thylakoids is the simplest among eukaryotes ( 48292/Algae.html’’>Algae-Prokaryotic Algae), with single thylakoids that are not stacked. They use chlorophyll a and phycobilins, and the phycobilisomes that house them are attached to the stromal surface of the thylakoids (http:// science.jrank.org/pages/48292/Algae.html’’>Algae-Prokaryotic Algae). Phycobiliproteins have been lost in diatoms but they are still present in cryptophytes (Delwiche et al. , 1995; Gibbs, 1981). Evidence for the derivation of diatoms and other chlorophyll c -containing algae from the red lineage is therefore somewhat anecdotal, but molecular phylogenetic analyses are consistent with this hypothesis (Van de Peer et al. , 1996; Delwiche et al. , 1995). The light-harvesting peripheral antennae of the diatom photosynthetic machinery are composed of fucoxanthin chlorophyll a/c binding proteins (FCPs) structured into oligomeric complexes (Bu ̈chel, 2003; Beer et al. , 2006). These complexes possess a large number of carotenoids only found within photosynthetic heterokonts and haptophytes, such as fucoxanthin (Fx), as well as diadinoxanthin (Ddx) and diatoxanthin (Dtx) pigments that are involved in their unique xanthophyll cycle (Lepetit et al. , 2011). Besides the FCP proteins, three other antenna protein families have been found: Lhcf (the classical light-harvesting proteins), Lhcr (red algal-related proteins), and the less abundant (Westermann and Rhiel, 2005) Lhcx proteins (previously known as LHCSR and Li818) (Eppard et al. , 2000; Green, 2007; Koziol et al. , 2007; Lepetit et al. , 2011). Diatoms also have a PSI-specific antenna (Veith and Bu ̈chel, 2007; Veith et al. , 2009; Lepetit et al. , 2011) that has a higher amount of Ddx and Fx than the main FCP proteins (Lepetit et al. , 2011). Diatom thylakoid membranes contain the same classes of lipids as higher plants and green algae (Goss and Wilhelm, 2009; Lepetit et al. , 2011), although in contrast to plants and green algae which have mostly neutral galactolipids, diatom thylakoid galactolipids are mainly negatively charged (Vieler et al. , 2007 a , b ; Goss et al. , 2009; Lepetit et al. , 2011). In higher plants the most abundant ...

Citations

... Flori et al. (2017) observed physical contact between mitochondria and chloroplasts in P. tricornutum using focused ion beam scanning electron microscopy (FIB-SEM). This and the existence of genes encoding malate shuttle transporters (Prihoda et al., 2012), may allow the energetic exchange between these two organelles (Bailleul et al., 2015). Thus, we propose that malate produced in the mitochondria might be transported into the plastid via malate shuttle transporters or through physical interactions between the two organelles. ...
Article
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Photosynthetic carbon fixation is often limited by CO2 availability, which led to the evolution of CO2 concentrating mechanisms (CCMs). Some diatoms possess CCMs that employ biochemical fixation of bicarbonate, similar to C4 plants, but it is controversially discussed whether biochemical CCMs are a commonly found in diatoms. In the diatom Phaeodactylum tricornutum, Phosphoenolpyruvate Carboxylase (PEPC) is present in two isoforms, PEPC1 in the plastids and PEPC2 in the mitochondria. We used real‐time quantitative PCR, western blots, and enzymatic assays to examine PEPC expression and PEPC activities, under low and high concentrations of dissolved inorganic carbon (DIC). We generated and analyzed individual knockout cell lines of PEPC1 and PEPC2, as well as a PEPC1/2 double‐knockout strain. While we could not detect an altered phenotype in the PEPC1 knockout strains at ambient, low or high DIC concentrations, PEPC2 and the double‐knockout strains grown under ambient air or lower DIC availability, showed reduced growth and photosynthetic affinity to DIC, while behaving similarly as WT cells at high DIC concentrations. These mutants furthermore exhibited significantly lower 13C/12C ratios compared to WT. Our data implies that in P. tricornutum at least parts of the CCM relies on biochemical bicarbonate fixation catalyzed by the mitochondrial PEPC2.
... Diatoms are ancient organisms that appeared due to secondary endosymbiosis involving green and red algae and heterotrophic eukaryotes (Prihoda et al., 2012). As a result of endosymbiosis involving several organisms and their genomes, diatoms have inherited many of the metabolic features of their ancestors (Gruber and Haferkamp, 2019). ...
Article
A new strain of benthic diatom Cylindrotheca fusiformis producing fucoxanthin (Fx) and polyunsaturated fatty acids (PUFAs) proved to be promising for biotechnology. Identification of Fx was carried out from the analysis of the ultraviolet and visible (UV-VIS) absorption spectra, electrospray ionization mass spectra (ESI MS) and proton magnetic resonance spectra (¹H NMR). The specific growth rate of the culture was 0.52 1/day, and the maximum productivity 1.56 g/(L × day). The accumulation rates of eicosapentaenoic and arachidonic acids in the stationary growth phase were 4.5 and 3.2 mg/(L × day), respectively, and that of Fx was 6 mg/(L × day). The accumulation of PUFAs in the biomass reached 4.68% of dry weight. The Fx content in the biomass reached 21.4 mg/g. The strain settles to the photobioreactor bottom in the absence of mixing, which property simplifies the biomass harvesting.
... MBE Ochrophyta homologs have been replaced by plastidtargeted ones. This observation can be rationalized by metabolic and genetic redundancy kept in the last common ancestor of Actinophryidae and Ochrophyta, redundancy which has been eliminated in the current plastids of Ochrophyta (Kroth et al. 2008;Prihoda et al. 2012). A similar assumption was previously made for the plastid evolution in Archaeplastida and Picozoa (Schön et al. 2021). ...
Article
Ochrophyta is an algal group belonging to the Stramenopiles and comprises diverse lineages of algae which contribute significantly to the oceanic ecosystems as primary producers. However, early evolution of the plastid organelle in Ochrophyta is not fully understood. In this study, we provide a well-supported tree of the Stramenopiles inferred by the large-scale phylogenomic analysis that unveils the eukaryvorous (non-photosynthetic) protist Actinophrys sol (Actinophryidae) is closely related to Ochrophyta. We used genomic and transcriptomic data generated from A. sol to detect molecular traits of its plastid and we found no evidence of plastid genome and plastid-mediated biosynthesis, consistent with previous ultrastructural studies that did not identify any plastids in Actinophryidae. Moreover, our phylogenetic analyses of particular biosynthetic pathways provide no evidence of a current and past plastid in A. sol. However, we found more than a dozen organellar aminoacyl-tRNA synthases (aaRS) that are of algal origin. Close relationships between aaRS from A. sol and their ochrophyte homologs document gene transfer of algal genes that happened prior to the divergence of Actinophryidae and Ochrophyta lineages. We further showed experimentally that organellar aaRSs of A. sol are targeted exclusively to mitochondria, although organellar aaRSs in Ochrophyta are dually-targeted to mitochondria and plastids. Together, our findings suggested that the last common ancestor of Actinophryidae and Ochrophyta had not yet completed the establishment of host-plastid partnership as seen in the current Ochrophyta species, but acquired at least certain nuclear-encoded genes for the plastid functions.
... Overall, these data raise the question of how the function of this protein is regulated in diatoms. The KEA3 protein is predicted to contain a peculiar EF hand domain in P. tricornutum, similarly to other proteins involved in cell energetic metabolism (Prihoda et al., 2012). This Ca 2+ binding domain is located close to the RCK domain (Fig. S6), i.e. in a position where it could modulate the activity of the antiporter (Wang et al., 2017;Galvis et al., 2020). ...
Article
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Diatoms are successful phytoplankton clades able to acclimate to changing environmental conditions, including e.g. variable light intensity. Diatoms are outstanding at dissipating light energy exceeding the maximum photosynthetic electron transfer (PET) capacity via the Non Photochemical Quenching (NPQ) process. While the molecular effectors of NPQ as well as the involvement of the Proton Motive Force (PMF) in its regulation are known, the regulators of the PET/PMF relationship remain unidentified in diatoms. We generated mutants of the H+/K+ antiporter KEA3 in the model diatom Phaeodactylum tricornutum. Loss of KEA3 activity affects the PET/PMF coupling and NPQ responses at the onset of illumination, during transients and in steady‐state conditions. Thus, this antiporter is a main regulator of the PET/PMF coupling. Consistent with this conclusion, a parsimonious model including only two free components, KEA3 and the diadinoxanthin de‐epoxidase, describes most of the feedback loops between PET and NPQ. This simple regulatory system allows for efficient responses to fast (minutes) or slow (e.g. diel) changes in light environment, thanks to the presence of a regulatory Ca2+‐binding domain in KEA3 modulating its activity. This circuit is likely tuned by the NPQ‐effector proteins, LHCXs, providing diatoms with the required flexibility to thrive in different ocean provinces.
... Metabolite antiporters and two isoenzymes for MDH and amino AAT are involved (Table 2, Figure 6, Table S8). In diatoms, the malate shunt has been proposed to connect the chloroplast with the mitochondria (Bailleul et al., 2015;Prihoda et al., 2012). In P. tricornutum, both MDH1 and MDH2 are targeted to the mitochondrion (Ewe et al., 2018), but in T. pseudonana, MDH2 is predicted to be targeted to the chloroplast (Smith et al., 2012). ...
... In diatoms, the interaction between the chloroplast and mitochondria is expected to be multifaceted, possibly with direct exchange of ATP/ADP (Bailleul et al., 2015) and indirect exchange of NAD(P)H via the ornithine/glutamate shunt (Broddrick et al., 2019;Levering et al., 2016) and the malate/aspartate shunt (Bailleul et al., 2015;Prihoda et al., 2012). Some support for the spatial interconnectedness between chloroplast and mitochondria in diatoms has been reported recently (Flori et al., 2017). ...
Article
Full-text available
Diatoms are one of the most successful phytoplankton groups in our oceans, being responsible for over 20% of the Earth's photosynthetic productivity. Their chimeric genomes have genes derived from red algae, green algae, bacteria, and heterotrophs, resulting in multiple isoenzymes targeted to different cellular compartments with the potential for differential regulation under nutrient limitation. The resulting interactions between metabolic pathways are not yet fully understood. We previously showed how acclimation to Cu limitation enhanced susceptibility to overreduction of the photosynthetic electron transport chain and its reorganization to favor photoprotection over light harvesting in the oceanic diatom Thalassiosira oceanica (Hippmann et al., 2017, 10.1371/journal.pone.0181753). In order to gain a better understanding of the overall metabolic changes that help alleviate the stress of Cu limitation, we have further analyzed the comprehensive proteomic datasets generated in that study to identify differentially expressed proteins involved in carbon, nitrogen, and oxidative stress‐related metabolic pathways. Metabolic pathway analysis showed integrated responses to Cu limitation. The upregulation of ferredoxin (Fdx) was correlated with upregulation of plastidial Fdx‐dependent isoenzymes involved in nitrogen assimilation as well as enzymes involved in glutathione synthesis, thus suggesting an integration of nitrogen uptake and metabolism with photosynthesis and oxidative stress resistance. The differential expression of glycolytic isoenzymes located in the chloroplast and mitochondria may enable them to channel both excess electrons and/or ATP between these compartments. An additional support for chloroplast–mitochondrial cross‐talk is the increased expression of chloroplast and mitochondrial proteins involved in the proposed malate shunt under Cu limitation.
... The "just-in-time" strategy requires a higher FtsH:PsbA ratio than the 'warehouse' strategy. Furthermore, PSII repair continues in the dark in diatoms (Li et al. 2016), which we hypothesize is driven by tight integration of chloroplastic and mitochondrial metabolism to fuel the chloroplastic ATP requirements for FtsH, RNA transcription, and translation (Prihoda et al. 2012;Bailleul et al. 2015). This capacity for dark repair of previously photoinactivated PSII allows for temporal offsets between episodes of net photoinactivation under high light with transient accumulation of [PSII] inactive and subsequent counteracting repair in low light or darkness, and could thereby contribute to the success of diatoms in environments of fluctuating light. ...
... Overall these data raise the question of how the function of this protein is regulated in diatoms. The KEA3 gene has a peculiar EF hand domain in P. tricornutum, similarly to other genes involved in cell energetic metabolism (Prihoda et al., 2012). ...
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Diatoms are amongst the most successful clades of oceanic phytoplankton, significantly contributing to photosynthesis on Earth. Their ecological success likely stems from their ability to acclimate to changing environmental conditions, including e.g. variable light intensity. Diatoms are outstanding at dissipating light energy exceeding the maximum photosynthetic electron transfer (PET) capacity of via Non Photochemical Quenching (NPQ). While the molecular effectors of this process, as well as the role of the Proton Motive Force (PMF) in its regulation are known, the putative regulators of the PET/PMF relationship in diatoms remain unidentified. Here, we demonstrate that the H ⁺ /K ⁺ antiporter KEA3 is the main regulator of the coupling between PMF and PET in the model diatom Phaeodactylum tricornutum . By controlling the PMF, it modulates NPQ responses at the onset of illumination, during transients and in steady state conditions. Under intermittent light KEA3 absence results in reduced fitness. Using a parsimonious model including only two components, KEA3 and the diadinoxanthin de-epoxidase, we can describe most of the feedback loops observed between PET and NPQ. This two-components regulatory system allows for efficient responses to fast (minutes) or slow (e.g. diel) changes in light environment, thanks to the presence of a regulatory Ca ²⁺ -binding domain in KEA3 that controls its activity. This circuit is likely finely tuned by the NPQ effector proteins LHCX, providing diatoms with the required flexibility to thrive in different ocean provinces. One sentence summary The author(s) responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors ( https://academic.oup.com/plcell/pages/General-Instructions ) is Giovanni Finazzi.
... In diatoms, it has been suggested that the chloroplast-mitochondrion energetic coupling could be favoured by an intracellular placing of the mitochondrial network in close proximity to the single chloroplast (Prihoda et al., 2012;Flori et al., 2017). It was recently shown that the extent of chloroplast-mitochondrion physical interaction varies greatly among phytoplanktonic species of different lineages, being high in the diatom P. tricornutum and low in Symbiodinium sp. or Nannochloropsis sp. ...
Article
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The coupling between mitochondrial respiration and photosynthesis plays an important role in the energetic physiology of green plants and some secondary‐red photosynthetic eukaryotes (diatoms), allowing an efficient CO2 assimilation and optimal growth. ●Using the flagellate Euglena gracilis, we first tested if photosynthesis‐respiration coupling occurs in this species harbouring secondary green plastids (i.e. originated from an endosymbiosis between a green alga and a phagotrophic euglenozoan). Second, we tested how the trophic state (mixotrophy and photoautotrophy) of the cell alters the mechanisms involved in the photosynthesis‐respiration coupling. ●Energetic coupling between photosynthesis and respiration was determined by testing the effect of respiratory inhibitors on photosynthesis, and measuring the simultaneous variation of photosynthesis and respiration rates as a function of temperature (i.e. thermal response curves). The mechanism involved in the photosynthesis‐respiration coupling was assessed by combining proteomics, biophysical, and cytological analyses. ●Our work shows that there is photosynthesis‐respiration coupling and membrane contacts between mitochondria and chloroplasts in E. gracilis. However, whereas in mixotrophy adjustment of the chloroplast ATP/NADPH ratio drives the interaction, in photoautotrophy the coupling is conditioned by CO2 limitation and photorespiration. This indicates that maintenance of photosynthesis‐respiration coupling, through plastic metabolic responses, is key to E. gracilis functioning under changing environmental conditions.
... However, the origin of the chloroplast is still a matter of discussion. Other hypotheses suggest that the chloroplast originated from a single ancestral secondary endosymbiosis involving a Rhodophyta algae (Keeling, 2010) or serial endosymbiosis events, where a green algal endosymbiont was succeeded by a Rhodophyta endosymbiont (Armbrust, 2009;Dorrell et al., 2017;Prihoda et al., 2012). ...
Article
Full-text available
Diatoms are unicellular organisms containing red algal‐derived plastids that probably originated as result of serial endosymbioses between an ancestral heterotrophic organism and a red alga or cryptophyte algae from which has only the chloroplast left. Diatom mitochondria are thus believed to derive from the exosymbiont. Unlike animals and fungi, diatoms seem to contain ancestral respiratory chains. In support of this, genes encoding gamma type carbonic anhydrases whose products were shown to be intrinsic complex I subunits in plants, Euglena and Achantamoeba were found in diatoms, a representative of Stramenopiles. In this work, we experimentally show that mitochondrial complex I in diatoms is a large complex containing gamma type carbonic anhydrase subunits, supporting an ancestral origin. By using a bioinformatic approach, a complex I integrated CA domain with heterotrimeric subunit composition is proposed.
... In contrast, comprehension of cellular processes from the marine diatom Phaeodactylum tricornutum is still limited. P. tricornutum is an unicellular Stramenopile believed to have arisen via a serial endosymbiotic event in which a red microalga were engulfed by a heterotroph (Moustafa et al., 2009;Bowler et al., 2010;Prihoda et al., 2012), thus generating specific genomic features and metabolic pathways (Bowler et al., 2008;Keeling and Palmer, 2008). Indeed, a recent investigation of P. tricornutum genome revealed that a total of 3,170 genes (26%) are unique and specific to this organism (Rastogi et al., 2018). ...
Article
Full-text available
The diatom Phaeodactylum tricornutum is a marine unicellular microalga that exists under three main morphotypes: oval, fusiform, and triradiate. Previous works have demonstrated that the oval morphotype of P. tricornutum Pt3 strain presents specific metabolic features. Here, we compared the cellular organization of the main morphotypes of the diatom P. tricornutum Pt3 strain through transmission electron and advanced light microscopies. The three morphotypes share similarities including spectral characteristics of the plastid, the location of the nucleus, the organization of mitochondria around the plastid as well as the existence of both a F-actin cortex, and an intracellular network of F-actin. In contrast, compared to fusiform and triradiate cells, oval cells spontaneously release proteins more rapidly. In addition, comparison of whole transcriptomes of oval versus fusiform or triradiate cells revealed numerous differential expression of positive and negative regulators belonging to the complex dynamic secretory machinery. This study highlights the specificities occurring within the oval morphotype underlying that the oval cells secrete proteins more rapidly.