Carbohydrate Metabolism

Menon, Ram K.; Sperling, Martin

doi:10.1007/978-3-030-92499-7_17

Cited by 6 publications

(4 citation statements)

References 160 publications

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“…Genome‐enabled exploration of Phaeodactylum tricorutum has also revealed important features of diatom nutrient metabolism (Coale et al., 2022; Kroth & Matsuda, 2022; Smith & Allen, 2022). Examples include the discovery of a functional urea cycle involved in the metabolism optimization under nitrogen limitation (Allen et al., 2011), or the role of the nitrate reductase in controlling the balance between nitrate transport and assimilation, and the distribution of carbon flux (Levitan et al., 2015; McCarthy et al., 2017).…”

Section: Insight Into the Biology Of Diatomsmentioning

confidence: 99%

Phaeodactylum tricornutum: An established model species for diatom molecular research and an emerging chassis for algal synthetic biology

Russo,

Rogato,

Jaubert

et al. 2023

Journal of Phycology

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Diatoms are prominent and highly diverse microalgae in aquatic environments. Compared with other diatom species, Phaeodactylum tricornutum is an “atypical diatom” displaying three different morphotypes and lacking the usual silica shell. Despite being of limited ecological relevance, its ease of growth in the laboratory and well‐known physiology, alongside the steady increase in genome‐enabled information coupled with effective tools for manipulating gene expression, have meant it has gained increased recognition as a powerful experimental model for molecular research on diatoms. We here present a brief overview of how over the last 25 years P. tricornutum has contributed to the unveiling of fundamental aspects of diatom biology, while also emerging as a new tool for algal process engineering and synthetic biology.

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Section: Insight Into the Biology Of Diatomsmentioning

confidence: 99%

Phaeodactylum tricornutum: An established model species for diatom molecular research and an emerging chassis for algal synthetic biology

Russo,

Rogato,

Jaubert

et al. 2023

Journal of Phycology

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“…In addition, it has been used for studies of various processes with biogeochemical implications such as photosynthesis [22][23][24][25][26], cell morphology control [21] and nutrient deprivation responses [27,28]. It is worth mentioning that most of the scientific discoveries in P. tricornutum were based studies using Pt1.…”

Section: Introductionmentioning

confidence: 99%

A removable and cosmopolitan dsRNA Toti-like virus causes latent infection in a model diatom strain

Zhang,

Li,

Xiong

et al. 2024

Preprint

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Diatoms contribute to 20% of global primary productivity. Although some diatom viruses have been identified, the molecular mechanisms underlying their interactions with the host remain poorly understood. In this study, we report the discovery of an RNA molecule in the DNA extracts of the Phaeodactylum tricornutum strain Pt1, which possesses a well-annotated genome and has been used as a diatom model system since 1956. We confirmed this molecule to be a double-stranded linear RNA molecule and, through sequencing, demonstrated it to be a virus in the Totiviridae family that is prevalent among marine stramenopiles. We also detected this virus in Phaeodactylum tricornutum strain Pt3, which was collected in 1930s from a similar geographic location to Pt1, suggesting its prevalence within the region. By employing various inhibitors of the viral RNA-dependent RNA polymerase, we successfully generated a virus-free line isogenic to Pt1, establishing a model system to investigate the impact of RNA viruses on diatom physiology. The virus-free lines did not display obvious growth advantages or defects, indicating a tendency of the virus towards latent infection. Furthermore, we generated a robust antibody against the coat protein of this virus. By performing immunoprecipitation coupled with mass spectrometry, we found that translation-related proteins are enriched as potential interacting partners of the coat protein. Our results suggest that potential viral impacts in molecular research should be considered when Pt1 and Pt3 are used for studying translation-related processes. Additionally, our study unveiled a temperate mode of interaction between viruses and marine algal hosts that differs from the commonly-reported virulent, lytic infections.

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“…tricornutum have distinct origins and arose from endosymbiotic red algae, stramenopile host cells, or diatom-specific bacterial gene transfer (Allen et al, 2011;Nonoyama et al, 2019;Kroth and Matsuda, 2022). In the other words, the pyrenoids of diatoms and green algae may have convergently evolved similar functions from a different set of proteins.…”

Section: Introductionmentioning

confidence: 99%

“…In addition to Rubisco, this pyrenoid contains β-type CAs (Tachibana et al, 2011), fructose 1,6-bisphosphate aldolases (FBAs) (Allen et al, 2011), and a θ-type CA specifically localized in the lumen of the thylakoids at the center of the pyrenoid (Kikutani et al, 2016; Shimakawa et al, 2023). Although these observations strongly suggest that diatom pyrenoids increase CO 2 concentration around Rubisco in a similar fashion to green algae, the pyrenoid components in P. tricornutum have distinct origins and arose from endosymbiotic red algae, stramenopile host cells, or diatom-specific bacterial gene transfer (Allen et al, 2011; Nonoyama et al, 2019; Kroth and Matsuda, 2022). In the other words, the pyrenoids of diatoms and green algae may have convergently evolved similar functions from a different set of proteins.…”

Section: Introductionmentioning

confidence: 99%

Diatom pyrenoids are encased in a protein shell that enables efficient CO₂fixation

Shimakawa,

Demulder,

Flori

et al. 2023

Preprint

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Pyrenoids are subcompartments of algal chloroplasts that concentrate Rubisco enzymes and their CO2 substrate, thereby increasing the efficiency of carbon fixation. Diatoms perform up to 20% of global CO2 fixation, but their pyrenoids remain poorly characterized at a molecular level. Here, we used in vivo photo-crosslinking to catalogue components of diatom pyrenoids and identified a pyrenoid shell (PyShell) protein, which we localized to the pyrenoid periphery of both the pennate diatom, Pheaodactylum tricornutum, and the centric diatom, Thalassiosira pseudonana. In situ cryo-electron tomography (cryo-ET) revealed that the pyrenoids of both diatom species are encased in a lattice-like protein sheath. Disruption of PyShell expression in T. pseudonana resulted in the absence of this protein sheath, altered pyrenoid morphology, and a high-CO2 requiring phenotype, with impaired growth and reduced carbon fixation efficiency under standard atmospheric conditions. Pyrenoids in mutant cells were fragmented and lacked the thylakoid membranes that normally traverse the Rubisco matrix, demonstrating how the PyShell plays a guiding role in establishing pyrenoid architecture. Recombinant PyShell proteins self-assembled into helical tubes, enabling us to determine a 3.0 Å-resolution PyShell structure. We then fit this in vitro structure into an in situ subtomogram average of the pyrenoid's protein sheath, yielding a putative atomic model of the PyShell within diatom cells. The structure and function of the diatom PyShell provides a new molecular view of how CO2 is assimilated in the ocean, a crucial biome that is on the front lines of climate change.

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Carbohydrate Metabolism

Cited by 6 publications

References 160 publications

Phaeodactylum tricornutum: An established model species for diatom molecular research and an emerging chassis for algal synthetic biology

Phaeodactylum tricornutum: An established model species for diatom molecular research and an emerging chassis for algal synthetic biology

A removable and cosmopolitan dsRNA Toti-like virus causes latent infection in a model diatom strain

Diatom pyrenoids are encased in a protein shell that enables efficient CO₂fixation

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Carbohydrate Metabolism

Cited by 6 publications

References 160 publications

Phaeodactylum tricornutum: An established model species for diatom molecular research and an emerging chassis for algal synthetic biology

Phaeodactylum tricornutum: An established model species for diatom molecular research and an emerging chassis for algal synthetic biology

A removable and cosmopolitan dsRNA Toti-like virus causes latent infection in a model diatom strain

Diatom pyrenoids are encased in a protein shell that enables efficient CO2fixation

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Diatom pyrenoids are encased in a protein shell that enables efficient CO₂fixation