Complex origins of chloroplast membranes with photosynthetic machineries: multiple transfers of genes from divergent organisms at different times or a single endosymbiotic event?

Evolution of light-dependent functions of GIGANTEA

GIGANTEA (GI) is a multifaceted plant-specific protein that originated in a streptophyte ancestor. The current known functions of GI include circadian clock control, light signalling, flowering time regulation, stomata response, chloroplast biogenesis, accumulation of anthocyanin, chlorophyll, and starch, phytohormone signalling, senescence, and response to drought, salt, and oxidative stress. Six decades since its discovery, no functional domains have been defined, and its mechanism of action is still not well characterized. In this review, we explore the functional evolution of GI to distinguish between ancestral and more recently acquired roles. GI integrated itself into various existing signalling pathways of the circadian clock, blue light, photoperiod, and osmotic and oxidative stress response. It also evolved parallelly to acquire new functions for chloroplast accumulation, red light signalling, and anthocyanin production. In this review, we have encapsulated the known mechanisms of various biological functions of GI, and cast light on the evolution of GI in the plant lineage.

Genomic and biochemical analyses of lipid biosynthesis in Cyanophora paradoxa: limited role of the chloroplast in fatty acid synthesis

Archaeplastida, a group of photosynthetic organisms with primary plastids, consists of green algae (plus land plants), red algae, and glaucophytes. In contrast to green and red algae, information on lipids and lipid biosynthesis is still incomplete in the glaucophytes. The chloroplast is the site of photosynthesis and fatty acid synthesis in all photosynthetic organisms known to date. However, the genomic data of the glaucophyte Cyanophora paradoxa indicated the lack of acetyl-CoA carboxylase and most components of fatty acid synthase in the chloroplast. Instead, multifunctional fatty acid synthase and acetyl-CoA carboxylase are likely to reside in the cytosol. To examine this hypothesis, we measured fatty acid synthesis in isolated chloroplasts and whole cells using stable isotope labeling. The chloroplasts had very low fatty acid synthesis activity, if any. Most processes of fatty acid synthesis, including elongation and desaturation, must be performed within the cytosol, and the fatty acids imported into the chloroplasts are assembled into the chloroplast lipids by the enzymes common to other algae and plants. Cyanophora paradoxa is a rare organism in which fatty acid synthesis and photosynthesis are not tightly linked. This could question the common origin of these two biosynthetic processes in Archaeplastida.

On the origin of fatty acid biosynthesis in Archaeplastida

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Sato N, Ikemura E, Uemura M, Awai K. 2025. Genomic and biochemical analyses of lipid biosynthesis in Cyanophora paradoxa: limited role of the chloroplast in fatty acid synthesis. Journal of Experimental Botany 76, 532–545. https://doi.org/10.1093/jxb/erae420

Chloroplasts with clefts and holes: a reassessment of the chloroplast shape using 3D FE-SEM cellular reconstruction of two species of Chlamydomonas

Chloroplasts are usually considered spheroid organelles, but this is not the only shape of chloroplasts. The chloroplast of Chlamydomonas has been typically described as cup-shaped. However, in old studies, it was also modeled as a complex shape with "perforations" or windows. Here, we reconstructed the cellular architecture of Chlamydomonas reinhardtii and C. applanata using an array tomography system installed on a field emission scanning electron microscope. C. reinhardtii chloroplasts resembled a baseball glove or a cup without a side, featuring numerous large and small holes that may facilitate the transport of metabolites and proteins produced in the Golgi apparatus fitted in the holes. In a lipid-accumulating, high-light condition, the chloroplast volume increased by filling the side cleft with an entire wall. Many accumulated large lipid droplets were accommodated within the chloroplast holes, which could have been considered as "chloroplast lipid droplets." Mitochondrial meshworks surrounded the chloroplast. C. applanata chloroplasts appeared like a folded starfish or a cup with many side clefts and a few holes. There was a single mitochondrion or two that branched in a complex form. Tight contacts of various organelles were also found in C. applanata. These reconstructions illustrate the complexity of chloroplast shape, which necessitates a revised understanding of the localization of lipid droplets and the evolution of chloroplasts: The prevailing image of the spheroid chloroplasts that reminds us of the similarity between chloroplasts and cyanobacteria is no longer tenable.

Acyl-turnover of acylplastoquinol enhances recovery of photodamaged PSII in Synechocystis

Photosynthetic electron transport is carried out by the electron carrier, plastoquinone (PQ). Recently, another form of PQ, acylplastoquinol (APQ), was discovered in Synechocystis sp. PCC 6803 (Synechocystis), but its physiological function in photosynthesis is unclear. In the present study, we identified a lipase encoded in sll0482 gene in Synechocystis that deacylates APQ and releases a free fatty acid and a reduced PQ (plastoquinol, PQH2), which we named acylplastoquinol lipase (APL). Disruption of apl gene increased APQ content, and recovery of photodamaged PSII under low light (LL) after the exposure to very high light (vHL) at 2500 μmol photons m-2 sec-1 without aeration (vHL) for 60 min, was suppressed in the Δapl cells. Δapl cells also show the slow rate of de novo synthesis of D1, a reaction center of PSII under such condition. Under high light, the cellular growth of Δapl was inhibited; however, disruption of apl gene did not affect the photosynthetic activity or photoinhibition of PSII. In wild-type cells, APQ content increased under vHL condition. Also, APQ was converted to PQH2 after transfer to LL with aeration by ambient air. Such striking changes in APQ were not observed in Δapl cells. The deacylation of APQ by APL may help repair PSII when PSII cannot drive photosynthetic electron transport efficiently.

Evolutionary implications from lipids in membrane bilayers and photosynthetic complexes in cyanobacteria and chloroplasts

In biomembranes, lipids form bilayer structures that serve as the fluid matrix for membrane proteins and other hydrophobic compounds. Additionally, lipid molecules associate with membrane proteins and impact their structures and functions. In both cyanobacteria and the chloroplasts of plants and algae, the lipid bilayer of the thylakoid membrane consists of four distinct glycerolipid classes: monogalactosyldiacylglycerol, digalactosyldiacylglycerol, sulfoquinovosyldiacylglycerol, and phosphatidylglycerol. These lipids are also integral components of photosynthetic complexes such as photosystem II and photosystem I. The lipid-binding sites within the photosystems, as well as the lipid composition in the thylakoid membrane, are highly conserved between cyanobacteria and photosynthetic eukaryotes, and each lipid class has specific roles in oxygenic photosynthesis. This review aims to shed light on the potential evolutionary implications of lipid utilization in membrane lipid bilayers and photosynthetic complexes in oxygenic photosynthetic organisms.

Chloroplast genome assembly of Serjania erecta Raldk: comparative analysis reveals gene number variation and selection in protein-coding plastid genes of Sapindaceae

Serjania erecta Raldk is an essential genetic resource due to its anti-inflammatory, gastric protection, and anti-Alzheimer properties. However, the genetic and evolutionary aspects of the species remain poorly known. Here, we sequenced and assembled the complete chloroplast genome of S. erecta and used it in a comparative analysis within the Sapindaceae family. S. erecta has a chloroplast genome (cpDNA) of 159,297 bp, divided into a Large Single Copy region (LSC) of 84,556 bp and a Small Single Copy region (SSC) of 18,057 bp that are surrounded by two Inverted Repeat regions (IRa and IRb) of 28,342 bp. Among the 12 species used in the comparative analysis, S. erecta has the fewest long and microsatellite repeats. The genome structure of Sapindaceae species is relatively conserved; the number of genes varies from 128 to 132 genes, and this variation is associated with three main factors: (1) Expansion and retraction events in the size of the IRs, resulting in variations in the number of rpl22, rps19, and rps3 genes; (2) Pseudogenization of the rps2 gene; and (3) Loss or duplication of genes encoding tRNAs, associated with the duplication of trnH-GUG in X. sorbifolium and the absence of trnT-CGU in the Dodonaeoideae subfamily. We identified 10 and 11 mutational hotspots for Sapindaceae and Sapindoideae, respectively, and identified six highly diverse regions (tRNA-Lys - rps16, ndhC - tRNA-Val, petA - psbJ, ndhF, rpl32 - ccsA, and ycf1) are found in both groups, which show potential for the development of DNA barcode markers for molecular taxonomic identification of Serjania. We identified that the psaI gene evolves under neutrality in Sapindaceae, while all other chloroplast genes are under strong negative selection. However, local positive selection exists in the ndhF, rpoC2, ycf1, and ycf2 genes. The genes ndhF and ycf1 also present high nucleotide diversity and local positive selection, demonstrating significant potential as markers. Our findings include providing the first chloroplast genome of a member of the Paullinieae tribe. Furthermore, we identified patterns in variations in the number of genes and selection in genes possibly associated with the family's evolutionary history.

The Chloroplast Envelope of Angiosperms Contains a Peptidoglycan Layer

Plastids in plants are assumed to have evolved from cyanobacteria as they have maintained several bacterial features. Recently, peptidoglycans, as bacterial cell wall components, have been shown to exist in the envelopes of moss chloroplasts. Phylogenomic comparisons of bacterial and plant genomes have raised the question of whether such structures are also part of chloroplasts in angiosperms. To address this question, we visualized canonical amino acids of peptidoglycan around chloroplasts of Arabidopsis and Nicotiana via click chemistry and fluorescence microscopy. Additional detection by different peptidoglycan-binding proteins from bacteria and animals supported this observation. Further Arabidopsis experiments with D-cycloserine and AtMurE knock-out lines, both affecting putative peptidoglycan biosynthesis, revealed a central role of this pathway in plastid genesis and division. Taken together, these results indicate that peptidoglycans are integral parts of plastids in the whole plant lineage. Elucidating their biosynthesis and further roles in the function of these organelles is yet to be achieved.

Acyl plastoquinol is a major cyanobacterial substance that co-migrates with triacylglycerol in thin-layer chromatography

Various studies have suggested the presence of triacylglycerol in cyanobacteria, but no convincing evidence exists. We purified a substance co-migrating with triacylglycerol in thin-layer chromatography and determined its structure using mass spectrometry, gas chromatography, and ¹H and ¹³C NMR. The major components were palmitoyl and stearoyl plastoquinols (acyl plastoquinol). Acyl plastoquinol has never been described before, although acyloxy derivative of plastoquione has been described as plastoquinone B. The level of acyl plastoquinol was 0.4% of the total lipids. We still do not have clear evidence for the presence of triacylglycerol. If present, the maximum triacylglycerol level must be at most 10% of acyl plastoquinol. The Synechocystis Slr2103 protein was suggested to synthesize triacylglycerol, but the product could be acyl plastoquinol. The possible roles of this novel compound in photosynthesis should be a new focus of research.

Position of Algae on the Tree of Life

Issues related to evolution of algal chloroplasts are considered. The position of algae on the Tree of Life is discussed. Algae are now included in five of the monophyletic eukaryotic supergroups: Archaeplastida (Glaucocystophyta, Rhodophyta, Prasinodermophyta, Chlorophyta, and Charophyta), TSAR (Ochrophyta; Dinophyta; Chlorarachniophyta; and photosynthetic species of the genera Chromera, Vetrella, and Paulinella), Haptista (Prymnesiophyta and Rappemonads), Cryptista (Cryptophyta), and Discoba (Euglenophyta). The algal divisions and the respective supergroups are characterized in brief.

Euglena, a Gravitactic Flagellate of Multiple Usages

Human exploration of space and other celestial bodies bears a multitude of challenges. The Earth-bound supply of material and food is restricted, and in situ resource utilisation (ISRU) is a prerequisite. Excellent candidates for delivering several services are unicellular algae, such as the space-approved flagellate Euglena gracilis. This review summarizes the main characteristics of this unicellular organism. Euglena has been exposed on various platforms that alter the impact of gravity to analyse its corresponding gravity-dependent physiological and molecular genetic responses. The sensory transduction chain of gravitaxis in E. gracilis has been identified. The molecular gravi-(mechano-)receptors are mechanosensory calcium channels (TRP channels). The inward gated calcium binds specifically to one of several calmodulins (CaM.2), which, in turn, activates an adenylyl cyclase. This enzyme uses ATP to produce cAMP, which induces protein kinase A, followed by the phosphorylation of a motor protein in the flagellum, initiating a course correction, and, finally, resulting in gravitaxis. During long space missions, a considerable amount of food, oxygen, and water has to be carried, and the exhaled carbon dioxide has to be removed. In this context, E. gracilis is an excellent candidate for biological life support systems, since it produces oxygen by photosynthesis, takes up carbon dioxide, and is even edible. Various species and mutants of Euglena are utilized as a producer of commercial food items, as well as a source of medicines, as it produces a number of vitamins, contains numerous trace elements, and synthesizes dietary proteins, lipids, and the reserve molecule paramylon. Euglena has anti-inflammatory, -oxidant, and -obesity properties.

Ghost lineages can invalidate or even reverse findings regarding gene flow

Introgression, endosymbiosis, and gene transfer, i.e., horizontal gene flow (HGF), are primordial sources of innovation in all domains of life. Our knowledge on HGF relies on detection methods that exploit some of its signatures left on extant genomes. One of them is the effect of HGF on branch lengths of constructed phylogenies. This signature has been formalized in statistical tests for HGF detection and used for example to detect massive adaptive gene flows in malaria vectors or to order evolutionary events involved in eukaryogenesis. However, these studies rely on the assumption that ghost lineages (all unsampled extant and extinct taxa) have little influence. We demonstrate here with simulations and data reanalysis that when considering the more realistic condition that unsampled taxa are legion compared to sampled ones, the conclusion of these studies become unfounded or even reversed. This illustrates the necessity to recognize the existence of ghosts in evolutionary studies.

Lipids in photosynthetic protein complexes in the thylakoid membrane of plants, algae, and cyanobacteria

In the thylakoid membrane of cyanobacteria and chloroplasts, many proteins involved in photosynthesis are associated with or integrated into the fluid bilayer matrix formed by four unique glycerolipid classes, monogalactosyldiacylglycerol, digalactosyldiacylglycerol, sulfoquinovosyldiacylglycerol, and phosphatidylglycerol. Biochemical and molecular genetic studies have revealed that these glycerolipids play essential roles not only in the formation of thylakoid lipid bilayers but also in the assembly and functions of photosynthetic complexes. Moreover, considerable advances in structural biology have identified a number of lipid molecules within the photosynthetic complexes such as PSI and PSII. These data have provided important insights into the association of lipids with protein subunits in photosynthetic complexes and the distribution of lipids in the thylakoid membrane. Here, we summarize recent high-resolution observations of lipid molecules in the structures of photosynthetic complexes from plants, algae, and cyanobacteria, and evaluate the distribution of lipids among photosynthetic protein complexes and thylakoid lipid bilayers. By integrating the structural information into the findings from biochemical and molecular genetic studies, we highlight the conserved and differentiated roles of lipids in the assembly and functions of photosynthetic complexes among plants, algae, and cyanobacteria.

Are Cyanobacteria an Ancestor of Chloroplasts or Just One of the Gene Donors for Plants and Algae?

Chloroplasts of plants and algae are currently believed to originate from a cyanobacterial endosymbiont, mainly based on the shared proteins involved in the oxygenic photosynthesis and gene expression system. The phylogenetic relationship between the chloroplast and cyanobacterial genomes was important evidence for the notion that chloroplasts originated from cyanobacterial endosymbiosis. However, studies in the post-genomic era revealed that various substances (glycolipids, peptidoglycan, etc.) shared by cyanobacteria and chloroplasts are synthesized by different pathways or phylogenetically unrelated enzymes. Membranes and genomes are essential components of a cell (or an organelle), but the origins of these turned out to be different. Besides, phylogenetic trees of chloroplast-encoded genes suggest an alternative possibility that chloroplast genes could be acquired from at least three different lineages of cyanobacteria. We have to seriously examine that the chloroplast genome might be chimeric due to various independent gene flows from cyanobacteria. Chloroplast formation could be more complex than a single event of cyanobacterial endosymbiosis. I present the “host-directed chloroplast formation” hypothesis, in which the eukaryotic host cell that had acquired glycolipid synthesis genes as an adaptation to phosphate limitation facilitated chloroplast formation by providing glycolipid-based membranes (pre-adaptation). The origins of the membranes and the genome could be different, and the origin of the genome could be complex.

Microbial driven genetic variation in holobionts

Genetic variation in holobionts, (host and microbiome), occurring by changes in both host and microbiome genomes, can be observed from two perspectives: observable variations and the processes that bring about the variation. The observable includes the enormous genetic diversity of prokaryotes, which gave rise to eukaryotic organisms. Holobionts then evolved a rich microbiome with a stable core containing essential genes, less so common taxa, and a more diverse non-core enabling considerable genetic variation. The result being that, the human gut microbiome, for example, contains 1,000 times more unique genes than are present in the human genome. Microbial driven genetic variation processes in holobionts include: (1) Acquisition of novel microbes from the environment, which bring in multiple genes in one step, (2) amplification/reduction of certain microbes in the microbiome, that contribute to holobiont` s adaptation to changing conditions, (3) horizontal gene transfer between microbes and between microbes and host, (4) mutation, which plays an important role in optimizing interactions between different microbiota and between microbiota and host. We suggest that invertebrates and plants, where microbes can live intracellularly, have a greater chance of genetic exchange between microbiota and host, thus a greater chance of vertical transmission and a greater effect of microbiome on evolution of host than vertebrates. However, even in vertebrates the microbiome can aid in environmental fluctuations by amplification/reduction and by acquisition of novel microorganisms.

AP2/ERF transcription factors regulate salt-induced chloroplast division in the moss Physcomitrella patens

Chloroplast division is a critical process for the maintenance of appropriate chloroplast number in plant cells. It is known that in some plant species and cell types, environmental stresses can affect chloroplast division, differentiation and morphology, however the significance and regulation of these processes are largely unknown. Here we investigated the regulation of salt stress-induced chloroplast division in protonemal cells of the moss, Physcomitrella patens, and found that, salt stress as one of the major abiotic stresses, induced chloroplast division and resulted in increased chloroplast numbers. We further identified three APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factors (TFs) that were responsible for this regulation. These AP2/ERF genes were up-regulated under salt stress, and amino acid sequences and phylogenetic analyses indicated that all TFs possess only one conserved AP2 domain and likely belong to the same subgroup of ERF-B3 in the AP2/ERF superfamily. Overexpression of these TFs significantly increased the chloroplast number even in the absence of NaCl stress. On the contrary, inducible overexpression of the dominant repressor form of these TFs suppressed salt stress-induced chloroplast division. Thus, our results suggest that salt stress induced-chloroplast division is regulated through members of the AP2/ERF TF superfamily.

Characterization and Biosynthesis of Lipids in Paulinella micropora MYN1: Evidence for Efficient Integration of Chromatophores into Cellular Lipid Metabolism

The chromatophores found in the cells of photosynthetic Paulinella species, once believed to be endosymbiotic cyanobacteria, are photosynthetic organelles that are distinct from chloroplasts. The chromatophore genome is similar to the genomes of α-cyanobacteria and encodes about 1,000 genes. Therefore, the chromatophore is an intriguing model of organelle formation. In this study, we analyzed the lipids of Paulinella micropora MYN1 to verify that this organism is a composite of cyanobacterial descendants and a heterotrophic protist. We detected glycolipids and phospholipids, as well as a betaine lipid diacylglyceryl-3-O-carboxyhydroxymethylcholine, previously detected in many marine algae. Cholesterol was the only sterol component detected, suggesting that the host cell is similar to animal cells. The glycolipids, presumably present in the chromatophores, contained mainly C16 fatty acids, whereas other classes of lipids, presumably present in the other compartments, were abundant in C20 and C22 polyunsaturated fatty acids. This suggests that chromatophores are metabolically distinct from the rest of the cell. Metabolic studies using isotopically labeled substrates showed that different fatty acids are synthesized in the chromatophore and the cytosol, which is consistent with the presence of both type I and type II fatty acid synthases, supposedly present in the cytosol and the chromatophore, respectively. Nevertheless, rapid labeling of the fatty acids in triacylglycerol and phosphatidylcholine by photosynthetically fixed carbon suggested that the chromatophores efficiently provide metabolites to the host. The metabolic and ultrastructural evidence suggests that chromatophores are tightly integrated into the whole cellular metabolism.

The Peptidoglycan Biosynthesis Gene murC in Frankia: Actinorhizal vs. Plant Type

Nitrogen-fixing Actinobacteria of the genus Frankia can be subdivided into four phylogenetically distinct clades; members of clusters one to three engage in nitrogen-fixing root nodule symbioses with actinorhizal plants. Mur enzymes are responsible for the biosynthesis of the peptidoglycan layer of bacteria. The four Mur ligases,MurC, MurD, MurE, and MurF, catalyse the addition of a short polypeptide to UDP-N-acetylmuramic acid. Frankia strains of cluster-2 and cluster-3 contain two copies of murC, while the strains of cluster-1 and cluster-4 contain only one. Phylogenetically, the protein encoded by the murC gene shared only by cluster-2 and cluster-3, termed MurC1, groups with MurC proteins of other Actinobacteria. The protein encoded by the murC gene found in all Frankia strains, MurC2, shows a higher similarity to the MurC proteins of plants than of Actinobacteria. MurC2 could have been either acquired via horizontal gene transfer or via gene duplication and convergent evolution, while murC1 was subsequently lost in the cluster-1 and cluster-4 strains. In the nodules induced by the cluster-2 strains, the expression levels of murC2 were significantly higher than those of murC1. Thus, there is clear sequence divergence between both types of Frankia MurC, and Frankia murC1 is in the process of being replaced by murC2, indicating selection in favour of murC2. Nevertheless, protein modelling showed no major structural differences between the MurCs from any phylogenetic group examined.