Genome analysis and its significance in four unicellular algae, Cyanidioshyzon merolae, Ostreococcus tauri, Chlamydomonas reinhardtii, and Thalassiosira pseudonana

Misumi, Osami; Yoshida, Yamato; Nishida, Keiji; Fujiwara, Takayuki; Sakajiri, Takayuki; Hirooka, Syunsuke; Nishimura, Yoshiki; Kuroiwa, Tsuneyoshi

doi:10.1007/s10265-007-0133-9

Cited by 32 publications

(17 citation statements)

References 92 publications

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“…Homology search in the available genomic databases revealed that such bi-domain GPDHs only exist in green alga, but not in higher plants or other species, such as yeasts and animals. Green algae live in diverse and variable environments and can acclimate to different environmental stresses (Osami et al 2008). Analysis of green algae genomes revealed interesting features of gene amplification and diversification, which pointed toward novel mechanisms for survival in the diverse and fluctuating environments (Merchant et al 2007;Graham 2008).…”

Section: Discussionmentioning

confidence: 99%

Cloning and characterization of two novel chloroplastic glycerol-3-phosphate dehydrogenases from Dunaliella viridis

Meng

Fan

et al. 2009

Plant Mol Biol

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Dunaliella, a unicellular green alga, has the unusual ability to survive dramatic osmotic stress by accumulating high concentrations of intracellular glycerol as a compatible solute. The chloroplastic glycerol-3-phosphate dehydrogenase (GPDH) has been considered to be the key enzyme that produces glycerol for osmoregulation in Dunaliella. In this study, we cloned the two most prominent GPDH cDNAs (DvGPDH1 and DvGPDH2) from Dunaliella viridis, which encode two polypeptides of 695 and 701 amino acids, respectively. Unlike higher plant GPDHs, both proteins contained extra phosphoserine phosphatase (SerB) domains at their N-termini in addition to C-terminal GPDH domains. Such bi-domain GPDHs represent a novel type of GPDH and are found exclusively in the chlorophyte lineage. Transient expression of EGFP fusion proteins in tobacco leaf cells demonstrated that both DvGPDH1 and DvGPDH2 are localized in the chloroplast. Overexpression of DvGPDH1 or DvGPDH2 could complement a yeast GPDH mutant (gpd1Delta), but not a yeast SerB mutant (ser2Delta). In vitro assays with purified DvGPDH1 and DvGPDH2 also showed apparent GPDH activity for both, but no SerB activity was detected. Surprisingly, unlike chloroplastic GPDHs from plants, DvGPDH1 and DvGPDH2 could utilize both NADH and NADPH as coenzymes and exhibited significantly higher GPDH activities when NADH was used as the coenzyme. Q-PCR analysis revealed that both genes exhibited transient transcriptional induction of gene expression upon hypersalinity shock, followed by a negative feedback of gene expression. These results shed light on the regulation of glycerol synthesis during salt stress in Dunaliella.

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Section: Discussionmentioning

confidence: 99%

Cloning and characterization of two novel chloroplastic glycerol-3-phosphate dehydrogenases from Dunaliella viridis

Meng

Fan

et al. 2009

Plant Mol Biol

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“…In our opinion, however, this is unlikely to remove the green genes altogether or to reduce the number significantly, as the C. merolae genome appears to have retained most of the genes shared by red algae and chromalveolates; even including sequences from P. cruentum and C. tuberculosum, only approximately 750 candidate red genes are identifiable from chromalveolates (19). Furthermore, while the C. merolae genome is extremely reduced, it contains greater proportions of some genes, e.g., those involved in translation, DNA replication, and protein and amino acid biosynthesis, than other sequenced photosynthetic eukaryotes (73,78), yet we could visually identify a consistently green signal even in these relatively unreduced functional gene families across both species (Table 1). We consider that even in a most extreme scenario, a consistent and strong green signal should still emerge.…”

Section: Going Green-evidence For Ancient Green Ancestorsmentioning

confidence: 99%

Do Red and Green Make Brown?: Perspectives on Plastid Acquisitions within Chromalveolates

2011

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The chromalveolate "supergroup" is of key interest in contemporary phycology, as it contains the overwhelming majority of extant algal species, including several phyla of key importance to oceanic net primary productivity such as diatoms, kelps, and dinoflagellates. There is also intense current interest in the exploitation of these algae for industrial purposes, such as biodiesel production. However, the evolution of the constituent species, and in particular the origin and radiation of the chloroplast genomes, remains poorly understood. In this review, we discuss current theories of the origins of the extant red alga-derived chloroplast lineages in the chromalveolates and the potential ramifications of the recent discovery of large numbers of green algal genes in chromalveolate genomes. We consider that the best explanation for this is that chromalveolates historically possessed a cryptic green algal endosymbiont that was subsequently replaced by a red algal chloroplast. We consider how changing selective pressures acting on ancient chromalveolate lineages may have selectively favored the serial endosymbioses of green and red algae and whether a complex endosymbiotic history facilitated the rise of chromalveolates to their current position of ecological prominence.Algae are emerging as being of key interest in contemporary biological research. As the principal primary producers in oceanic and freshwater communities, algae support the development of complex food webs and biodiverse communities and are responsible for the net flux of nearly 2 gigatons of carbon per year from the atmosphere to the lithosphere, an amount equivalent to or higher than that of tropical rainforests (24,68,122). Understanding why specific algal lineages are more ecologically prominent than others may provide valuable insight into the stability of these ecosystems, particularly as some of the most important taxa are believed to be sensitive to changes in atmospheric and oceanic climates (42, 49), so that phytoplankton community composition is predicted to change considerably in response to current and future climate (28,31,44). In addition, algae are morphologically and physiologically diverse, ranging from microscopic single-celled diatoms and prasinophytes smaller than some bacteria to forests of giant kelps, and differing in their photosynthetic pigments, hence red, green, and brown algae, among others (Fig. 1). The enormous array of biological and biochemical characteristics presented by algae offers great opportunities for exploitation across a wide range of technologies, for example, in the production of biodiesel, industrial chemicals, and even nanotechnologies such as microchips (58,71). This variety offers challenges too, and a much better understanding of the biochemical properties of different algal groups and their chloroplast lineages, which are intimately related to their evolutionary histories, will be required to aid in the identification and culturing of candidate species.In this review, we explore the evolutionary hist...

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“…This organism belongs to the Prasi-nophyceae class (12), potentially the most ancient species in the green lineage that diverged from the ancestor of all green plants and algae (13)(14)(15). O. tauri has a single starch granule and the full set of genes present in higher plants for polysaccharide metabolism (16).…”

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confidence: 99%

Ostreococcus tauri ADP-glucose Pyrophosphorylase Reveals Alternative Paths for the Evolution of Subunit Roles

Kuhn¹,

Falaschetti²,

Ballícora

2009

Journal of Biological Chemistry

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ADP-glucose pyrophosphorylase controls starch synthesis in plants and is an interesting case to study the evolution and differentiation of roles in heteromeric enzymes. It includes two homologous subunits, small (S) and large (L), that originated from a common photosynthetic eukaryotic ancestor. In present day organisms, these subunits became complementary after loss of certain roles in a process described as subfunctionalization. For instance, the potato tuber enzyme has a noncatalytic L subunit that complements an S subunit with suboptimal allosteric properties. To understand the evolution of catalysis and regulation in this family, we artificially synthesized both subunit genes from the unicellular alga Ostreococcus tauri. This is among the most ancient species in the green lineage that diverged from the ancestor of all green plants and algae. After heterologous gene expression, we purified and characterized the proteins. The O. tauri enzyme was not redox-regulated, suggesting that redox regulation of ADP-glucose pyrophosphorylases appeared later in evolution. The S subunit had a typical low apparent affinity for the activator 3-phosphoglycerate, but it was atypically defective in the catalytic efficiency (V max /K m ) for the substrate Glc-1-P. The L subunit needed the S subunit for soluble expression. In the presence of a mutated S subunit (to avoid interference), the L subunit had a high apparent affinity for 3-phosphoglycerate and substrates suggesting a leading role in catalysis. Therefore, the subfunctionalization of the O. tauri enzyme was different from previously described cases. To the best of our knowledge, this is the first biochemical description of a system with alternative subfunctionalization paths.Starch synthesis in photosynthetic eukaryotes such as higher plants and unicellular algae is controlled by a heterotetrameric ADP-glucose pyrophosphorylase (ADP-Glc PPase, 4 EC 2.7.7.27). This enzyme catalyzes the reaction of ATP and Glc-1-P to form ADP-glucose (ADP-Glc) and PP i , and it is primarily activated by 3-phosphoglycerate (3-PGA) and inhibited by P i . In photosynthetic eukaryotes the enzyme includes two distinct S and L homologous subunits (S 2 L 2 or ␣ 2 ␤ 2 ), but in photosynthetic bacteria the enzyme is a homotetramer (␣ 4 ). There has been debate regarding the role of the different subunits of ADP-Glc PPase. The S subunit homotetramer from potato (Solanum tuberosum) tuber (StuS), Arabidopsis thaliana (APS1), and barley (Hordeum vulgare) endosperm have a catalytic function with defective regulatory properties (1-3). It is not clear if there is a set of universal roles for the L subunit in plants. The L subunit from potato tuber (StuL) is catalytically deficient and plays more of a regulatory role by modifying the apparent affinity of the S subunit toward allosteric regulators (1, 4). On the other hand, the Arabidopsis APL1 and APL2 isoforms have both catalytic and regulatory functions, whereas the APL3 and APL4 isoforms behave like StuL (2, 5). The maize (Zea mays) endosperm L subunit...

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Genome analysis and its significance in four unicellular algae, Cyanidioshyzon merolae, Ostreococcus tauri, Chlamydomonas reinhardtii, and Thalassiosira pseudonana

Cited by 32 publications

References 92 publications

Cloning and characterization of two novel chloroplastic glycerol-3-phosphate dehydrogenases from Dunaliella viridis

Cloning and characterization of two novel chloroplastic glycerol-3-phosphate dehydrogenases from Dunaliella viridis

Do Red and Green Make Brown?: Perspectives on Plastid Acquisitions within Chromalveolates

Ostreococcus tauri ADP-glucose Pyrophosphorylase Reveals Alternative Paths for the Evolution of Subunit Roles

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