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1. In vivo localization of iron starvation induced proteins under variable iron supplementation regimes in Phaeodactylum tricornutum

   https://doi.org/10.1002/pld3.472  

   Kazamia, Elena ; Mach, Jan ; McQuaid, Jeffrey B. ; Gao, Xia ; Coale, Tyler H. ; Malych, Ronald ; Camadro, Jean‐Michel ; Lesuisse, Emmanuel ; Allen, Andrew E. ; Bowler, Chris ; et al ( December 2022 , Plant Direct)

   The model pennate diatomPhaeodactylum tricornutumis able to assimilate a range of iron sources. It therefore provides a platform to study different mechanisms of iron processing concomitantly in the same cell. In this study, we follow the localization of three iron starvation induced proteins (ISIPs) in vivo, driven by their native promoters and tagged by fluorophores in an engineered line ofP. tricornutum. We find that the localization patterns of ISIPs are dynamic and variable depending on the overall iron status of the cell and the source of iron it is exposed to. Notwithstanding, a shared destination of the three ISIPs both under ferric iron and siderophore‐bound iron supplementation is a globular compartment in the vicinity of the chloroplast. In a proteomic analysis, we identify that the cell engages endocytosis machinery involved in the vesicular trafficking as a response to siderophore molecules, even when these are not bound to iron. Our results suggest that there may be a direct vesicle traffic connection between the diatom cell membrane and the periplastidial compartment (PPC) that co‐opts clathrin‐mediated endocytosis and the “cytoplasm to vacuole” (Cvt) pathway, for proteins involved in iron assimilation.

   Proteomics data are available via ProteomeXchange with identifier PXD021172.

   The marine diatomP. tricornutumengages a vesicular network to traffic siderophores and phytotransferrin from the cell membrane directly to a putative iron processing site in the vicinity of the chloroplast.

    

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2. Subcellular proteomics for determining iron‐limited remodeling of plastids in the model diatom Thalassiosira pseudonana (Bacillariophyta)

   https://doi.org/10.1111/jpy.13379  

   Gomes, Kristofer M. ; Nunn, Brook L. ; Chappell, P. Dreux ; Jenkins, Bethany D. ( August 2023 , Journal of Phycology)

   Diatoms are important primary producers in the world's oceans, yet their growth is constrained in large regions by low bioavailable iron (Fe). Low‐Fe stress‐induced limitation of primary production is due to requirements for Fe in components of essential metabolic pathways including photosynthesis and other chloroplast plastid functions. Studies have shown that under low‐Fe stress, diatoms alter plastid‐specific processes, including components of electron transport. These physiological changes suggest changes of protein content and in protein abundances within the diatom plastid. While in silico predictions provide putative information on plastid‐localized proteins, knowledge of diatom plastid proteins remains limited in comparison to well‐studied model photosynthetic organisms. To address this, we employed shotgun proteomics to investigate the proteome of subcellular plastid‐enriched fractions fromThalassiosira pseudonanato gain a better understanding of how the plastid proteome is remodeled in response to Fe limitation. Using mass spectrometry‐based peptide identification and quantification, we analyzedT. pseudonanagrown under Fe‐replete and ‐limiting conditions. Through these analyses, we inferred the relative quantities of each protein, revealing that Fe limitation regulates major metabolic pathways in the plastid, including the Calvin cycle. Additionally, we observed changes in the expression of light‐harvesting proteins. In silico localization predictions of proteins identified in this plastid‐enriched proteome allowed for an in‐depth comparison of theoretical versus observed plastid‐localization, providing evidence for the potential of additional protein import pathways into the diatom plastid.

    

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3. Reduction-dependent siderophore assimilation in a model pennate diatom

   https://doi.org/10.1073/pnas.1907234116  

   Coale, Tyler H. ; Moosburner, Mark ; Horák, Aleš ; Oborník, Miroslav ; Barbeau, Katherine A. ; Allen, Andrew E. ( November 2019 , Proceedings of the National Academy of Sciences)

   Iron uptake by diatoms is a biochemical process with global biogeochemical implications. In large regions of the surface ocean diatoms are both responsible for the majority of primary production and frequently experiencing iron limitation of growth. The strategies used by these phytoplankton to extract iron from seawater constrain carbon flux into higher trophic levels and sequestration into sediments. In this study we use reverse genetic techniques to target putative iron-acquisition genes in the model pennate diatom Phaeodactylum tricornutum . We describe components of a reduction-dependent siderophore acquisition pathway that relies on a bacterial-derived receptor protein and provides a viable alternative to inorganic iron uptake under certain conditions. This form of iron uptake entails a close association between diatoms and siderophore-producing organisms during low-iron conditions. Homologs of these proteins are found distributed across diatom lineages, suggesting the significance of siderophore utilization by diatoms in the marine environment. Evaluation of specific proteins enables us to confirm independent iron-acquisition pathways in diatoms and characterize their preferred substrates. These findings refine our mechanistic understanding of the multiple iron-uptake systems used by diatoms and help us better predict the influence of iron speciation on taxa-specific iron bioavailability. 

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4. Widespread use of proton-pumping rhodopsin in Antarctic phytoplankton

   https://doi.org/10.1073/pnas.2307638120  

   Andrew, Sarah M. ; Moreno, Carly M. ; Plumb, Kaylie ; Hassanzadeh, Babak ; Gomez-Consarnau, Laura ; Smith, Stephanie N. ; Schofield, Oscar ; Yoshizawa, Susumu ; Fujiwara, Takayoshi ; Sunda, William G. ; et al ( September 2023 , Proceedings of the National Academy of Sciences)

   Photosynthetic carbon (C) fixation by phytoplankton in the Southern Ocean (SO) plays a critical role in regulating air–sea exchange of carbon dioxide and thus global climate. In the SO, photosynthesis (PS) is often constrained by low iron, low temperatures, and low but highly variable light intensities. Recently, proton-pumping rhodopsins (PPRs) were identified in marine phytoplankton, providing an alternate iron-free, light-driven source of cellular energy. These proteins pump protons across cellular membranes through light absorption by the chromophore retinal, and the resulting pH energy gradient can then be used for active membrane transport or for synthesis of adenosine triphosphate. Here, we show that PPR is pervasive in Antarctic phytoplankton, especially in iron-limited regions. In a model SO diatom, we found that it was localized to the vacuolar membrane, making the vacuole a putative alternative phototrophic organelle for light-driven production of cellular energy. Unlike photosynthetic C fixation, which decreases substantially at colder temperatures, the proton transport activity of PPR was unaffected by decreasing temperature. Cellular PPR levels in cultured SO diatoms increased with decreasing iron concentrations and energy production from PPR photochemistry could substantially augment that of PS, especially under high light intensities, where PS is often photoinhibited. PPR gene expression and high retinal concentrations in phytoplankton in SO waters support its widespread use in polar environments. PPRs are an important adaptation of SO phytoplankton to growth and survival in their cold, iron-limited, and variable light environment.

    

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5. Heterotrophic carbon metabolism and energy acquisition in Candidatus Thioglobus singularis strain PS1, a member of the SUP05 clade of marine Gammaproteobacteria

   https://doi.org/10.1111/1462-2920.14623  

   Spietz, Rachel L. ; Lundeen, Rachel A. ; Zhao, Xiaowei ; Nicastro, Daniela ; Ingalls, Anitra E. ; Morris, Robert M. ( April 2019 , Environmental Microbiology)

   A hallmark of the SUP05 clade of marineGammaproteobacteriais the ability to use energy obtained from reduced inorganic sulfur to fuel autotrophic fixation of carbon using RuBisCo. However, some SUP05 also have the genetic potential for heterotrophic growth, raising questions about the roles of SUP05 in the marine carbon cycle. We used genomic reconstructions, physiological growth experiments and proteomics to characterize central carbon and energy metabolism inCandidatusThioglobus singularis strain PS1, a representative from the SUP05 clade that has the genetic potential for autotrophy and heterotrophy. Here, we show that the addition of individual organic compounds and 0.2 μm filtered diatom lysate significantly enhanced the growth of this bacterium. This positive growth response to organic substrates, combined with expression of a complete TCA cycle, heterotrophic pathways for carbon assimilation, and methylotrophic pathways for energy conversion demonstrate strain PS1's capacity for heterotrophic growth. Further, our inability to verify the expression of RuBisCO suggests that carbon fixation was not critical for growth. These results highlight the metabolic diversity of the SUP05 clade that harbours both primary producers and consumers of organic carbon in the oceans and expand our understanding of specific pathways of organic matter oxidation by the heterotrophic SUP05.

    

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