Endosymbiosis, gene transfer and algal cell evolution Shinichiro Maruyama and John M Archibald
Shinichiro Maruyama and John M Archibald
Plastids, specifically chloroplasts, originated from prokaryotic endosymbionts akin to modern cyanobacteria, as proposed by the endosymbiont hypothesis This theory suggests that these prokaryotes were initially engulfed by a phagotrophic eukaryote and retained rather than digested Over time, the relationship evolved, leading to the transfer of genetic material from the endosymbionts to the host, ultimately resulting in the endosymbionts becoming fully dependent and transforming into primary plastids Additionally, some eukaryotes with primary plastids were later engulfed by other phagotrophic eukaryotes, a phenomenon known as secondary endosymbiosis, which contributed to the emergence of various distinct algal lineages It is widely accepted that primary endosymbiotic events occurred once in eukaryotic history, while secondary endosymbiosis is believed to have happened at least three times However, there is ongoing debate among researchers regarding these events, and despite the growing number of complete algal genome sequences, the relationships between modern algal plastids remain a contentious topic in eukaryotic evolution.
The endosymbiont hypothesis offers a compelling explanation for the evolution of algal cells and the acquisition of oxygenic photosynthesis by eukaryotes Researchers are keen to identify the specific types of cells involved in this process, but the diverse nature of eukaryotic phototrophs and the ancient endosymbiotic events complicate this inquiry Algal cells possess three genome-bearing organelles: the nucleus, plastid, and mitochondrion, making their evolution a composite of these distinct lineages Various scenarios illustrate how primary plastid-bearing eukaryotes may have evolved, highlighting the complex interplay between the phylogenies of plastids and algal nuclei Considering secondary endosymbiosis adds another layer of complexity, requiring additional phylogenetic signals from the secondary endosymbiont's nucleus While genomic data aids in unraveling this intricate history, it also reveals that even the most straightforward models of plastid origin and evolution may be overly simplistic.
A B C D plastid origin single multiple single multiple host lineages single clade single clade multi-clades multi-clades plastid bearers monophyletic ? ‘paraphyletic’ polyphyletic
Four competing scenarios explain the origins of primary plastids The first scenario suggests that a derived eukaryote acquired primary plastids through a single event of primary endosymbiosis The second scenario posits that multiple primary endosymbioses occurred within a single lineage of eukaryotes The third scenario indicates that, after a single primary endosymbiosis, some lineages retained primary plastids while others lost them Lastly, the fourth scenario proposes that primary endosymbionts were independently acquired in different lineages, evolving into plastids multiple times, with some lineages losing plastids secondarily.
2nd rank classifi cation Organism Secondary plastids
Chloroplast sensu stricto green algae and land plants euglenophytes, chlorarachniophytes, the dinofl agellate Lepidodinium
Rhodoplast red algae cryptophytes, haptophytes, stramenopiles, dinofl agellates, chromerids, apicomplexans 2 Cyanelle (Muroplast) 1 glaucophytes
1 See text for discussion on the terminology
2 The red versus green origin of ‘ apicoplasts ’ in apicomplexans is still contentious (Cai et al 2003; Funes et al 2004; Lau et al 2009; Obornik et al 2009; Janouskovec et al 2010)
Endosymbiosis, gene transfer and algal cell evolution 23
Endosymbiotic gene transfer (EGT) significantly influences the genetic structure of algal nuclear genomes, as it involves the transfer of genetic material from endosymbionts to their hosts Modern plastid genomes have limited coding capacity, with most plastid proteins in photosynthetic eukaryotes encoded by nuclear genes that are targeted to the organelle However, distinguishing between nuclear genes from organelles, transient endosymbionts, or ingested prey remains challenging yet crucial This chapter explores algal cell evolution through phylogenetics and comparative genomics, highlighting advancements made possible by extensive genomic data Nonetheless, debates continue regarding the circumstances under which we can confidently infer past endosymbiotic events.
The primary endosymbiotic origin of plastid s
Extensive phylogenetic, biochemical, and morphological evidence indicates that modern cyanobacteria and plastids share a common ancestor (McFadden 2001; Archibald 2009b) However, significant differences exist, particularly in genome size; plastid genomes are typically only 10-20% the size of the smallest sequenced cyanobacterial genomes, such as the 1.66 Mb genome of Prochlorococcus sp strain MED4 (Rocap et al 2003) and the 1.44 Mb genome of the uncultured marine cyanobacterium UCYN-A (Tripp et al 2010) This notable discrepancy in size and gene content implies that a substantial reduction in plastid genome size occurred in the ancestors of primary plastid-bearing eukaryotes.
The loss of genes from plastid genomes follows a non-random pattern, with only 46 protein-encoding genes commonly retained across all sequenced plastid genomes, primarily related to photosynthesis and ribosomal functions (Race et al 1999) Non-photosynthetic plastids are even more reduced but still maintain essential genes such as tRNA and ribosomal proteins (Krause 2008) Interestingly, some non-photosynthetic plastids, like those in Euglena longa and Cryptomonas paramecium, retain genes associated with photosynthesis, including the rbcL gene for RuBisCO, which plays a crucial role in carbon fixation (Gockel and Hachtel 2000; Donaher et al 2009) Furthermore, RuBisCO has been implicated in lipid biosynthesis within developmentally non-photosynthetic plastids found in land plant seeds (Schwender et al.).
2004), its function in the secondarily non-photosynthetic plastids of unicellular algae remains unclear (Krause 2008)
Which cyanobacterial lineage is most closely related to the plastid progenitor ?
Genome reduction and endosymbiotic gene transfer (EGT) complicate the understanding of plastid origins, as significant genetic information has moved from plastids to the nucleus Identifying which nuclear genes originated from the cyanobacterial ancestor of plastids poses challenges Researchers typically utilize nuclear genes with strong cyanobacterial signatures in phylogenetic analyses, but caution is essential to avoid incorrectly inferring plastid phylogeny from genes not derived from the organelle.
Current studies have yet to determine which lineage of existing cyanobacteria closely resembles the ancestor of plastids Traditional phylogenetic analyses using the 16S ribosomal RNA gene suggest that plastid sequences are either positioned near the root of the cyanobacterial lineage or are closely related to nitrogen-fixing unicellular cyanobacteria In contrast, phylogenomic analyses indicate a basal branching of plastids, rather than a direct affiliation with a specific cyanobacterial lineage Recent research points to the possibility that the plastid progenitor could resemble heterocyst-forming nitrogen-fixing filamentous cyanobacteria, such as Anabaena or Nostoc However, a significant limitation of these analyses is the restricted number of taxa available for whole-genome comparison, leaving the evidence still inconclusive.
To gain a clearer understanding of the relationship between plastids and cyanobacteria, it is essential to increase the number of sequenced plastid genomes, which currently represent only a limited selection of algal lineages Expanding sampling within major algal clades and including unidentified taxa at the base of the cyanobacterial tree could provide significant insights However, existing data analysis has revealed that plastid genomes exhibit mixed ancestry, complicating the determination of plastid origins in contemporary plants and algae.
How heterogeneous was the ancestral plastid genome ?
A non -cyanobacterial RuBisCO operon in red algae
Inferring the evolution of plastids presents significant challenges, as their genomes are not merely reduced versions of cyanobacterial genomes A key example of plastid genome heterogeneity is the discovery that red algal and red algal-derived plastids possess distinct types of RuBisCO large (rbcL) and small (rbcS) subunit genes, which are more closely related to those found in proteobacteria than in cyanobacteria, green plants, or glaucophyte plastids This complexity is further heightened by the shorter length of rbcS genes compared to rbcL, and the presence of rbcS in the nuclear genomes of green plants and glaucophytes, unlike the rbcLS operon found in red algal plastid genomes.
Endosymbiosis and gene transfer play crucial roles in algal cell evolution, particularly concerning the 25 distinct proteobacterial lineages The specific relationships of red algal rbcLS genes to these lineages remain unclear To prevent confusion, we will refer to these red algal rbcLS genes as ‘non-cyanobacterial’ type genes.
The rbcL gene serves as a widely utilized phylogenetic marker, having been sequenced across various lineages Its incongruence with other plastid genes, such as 16S and 23S rRNA, underscores the complex nature of plastid genomes To explain the rbcL phylogeny, two extreme scenarios have been proposed: one involves lateral gene transfer (LGT) from a proteobacterial lineage to the plastid genome of red algae, while the other suggests ancestral gene duplication before the divergence of primary plastid-bearing eukaryotes, followed by subsequent gene losses.
The debate regarding the presence of non-cyanobacterial rbcL genes in green algae, plants, and glaucophytes remains unresolved, as no eukaryotes have been identified with both cyanobacterial and non-cyanobacterial rbcLS genes Maier et al investigated this by examining the cbbX gene family, which often forms an operon with rbcLS in certain red algal and prokaryotic plastids Their research on the cryptophyte alga Guillardia theta revealed that its cbbX genes are found in both the red alga-derived plastid and the nucleomorph, and these genes are orthologous to those in prokaryotes with non-cyanobacterial RuBisCO This was supported by Fujita et al., who confirmed the orthology of cbbX genes in red algal nuclei and plastids, suggesting they regulate the RuBisCO operon in the unicellular red alga Cyanidioschyzon merolae Additionally, Maier et al proposed that the ancestor of plastids may have possessed both cyanobacterial and non-cyanobacterial rbcL-S-cbbX operons, with subsequent differential loss in the lineages of green plants, red algae, and glaucophytes However, the phylogenetic origin of the Oryza sativa cbbX homolog is still undetermined, leaving the evolutionary history of non-cyanobacterial rbcL-S-cbbX operons to be further explored.
‘ Chimeric ’ origin s of the menaquinone/phylloquinone biosynthesis gene cluster
Gross et al (2008) conducted phylogenetic analyses of plastid and nuclear men gene clusters, revealing significant insights into the evolution of plastid genomes The men cluster, which is highly conserved across prokaryotes and eukaryotes, encodes enzymes essential for the biosynthesis of vitamin K, including menaquinone and phylloquinone Their research indicated that this gene cluster is exclusively found in phototrophic eukaryotes, with most men genes located within the plastid genomes of the acidothermophilic red algal group Cyanidiales In contrast, green plants and diatoms contain nuclear genes, including the menF-D-C-H fusion gene known as PHYLLO.
Chapter 2 reveals that many nuclear genes associated with plastid-localized proteins, particularly those from the Cyanidiales, show a close relation to sequences from non-cyanobacterial prokaryotes Notable differences in phylogenetic affiliations between red algal and green plant genes are evident; for example, Cyanidiales have a gammaproteobacterial type plastid-encoded MenA, alongside a Chlorobi/gammaproteobacterial type MenE and a nuclear-encoded MenG In contrast, green plants exhibit cyanobacterial-type MenA and MenG, with MenE originating from deltaproteobacteria Gross et al (2008) argued that the complex phylogenetic patterns indicate evolutionary 'chimerism' in the plastid ancestor's genome, potentially resulting from the incorporation of extracellular DNA facilitated by viruses like cyanophages.