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Dyhrman ST. Putting together the polyphosphate puzzle for microalgae. JOURNAL OF PHYCOLOGY 2024; 60:621-623. [PMID: 38858859 DOI: 10.1111/jpy.13460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Affiliation(s)
- Sonya T Dyhrman
- Department of Earth and Environmental Science, Columbia University, New York, New York, USA
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York, USA
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2
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Lapointe A, Kocademir M, Bergman P, Ragupathy IC, Laumann M, Underwood GJC, Zumbusch A, Spiteller D, Kroth PG. Characterization of polyphosphate dynamics in the widespread freshwater diatom Achnanthidium minutissimum under varying phosphorus supplies. JOURNAL OF PHYCOLOGY 2024; 60:624-638. [PMID: 38163284 DOI: 10.1111/jpy.13423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 11/11/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024]
Abstract
Polyphosphates (polyP) are ubiquitous biomolecules that play a multitude of physiological roles in many cells. We have studied the presence and role of polyP in a unicellular alga, the freshwater diatom Achnanthidium minutissimum. This diatom stores up to 2.0 pg·cell-1 of polyP, with chain lengths ranging from 130 to 500 inorganic phosphate units (Pi). We applied energy dispersive X-ray spectroscopy, Raman/fluorescence microscopy, and biochemical assays to localize and characterize the intracellular polyP granules that were present in large apical vacuoles. We investigated the fate of polyP in axenic A. minutissimum cells grown under phosphorus (P), replete (P(+)), or P deplete (P(-)) cultivation conditions and observed that in the absence of exogenous P, A. minutissimum rapidly utilizes their internal polyP reserves, maintaining their intrinsic growth rates for up to 8 days. PolyP-depleted A. minutissimum cells rapidly took up exogenous P a few hours after Pi resupply and generated polyP three times faster than cells that were not initially subjected to P limitation. Accordingly, we propose that A. minutissimum deploys a succession of acclimation strategies regarding polyP dynamics where the production or consumption of polyP plays a central role in the homeostasis of the diatom.
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Affiliation(s)
- Adrien Lapointe
- Department of Biology, University of Konstanz, Konstanz, Germany
| | | | - Paavo Bergman
- Electron-Microscopy Centre, University of Konstanz, Konstanz, Germany
| | | | - Michael Laumann
- Electron-Microscopy Centre, University of Konstanz, Konstanz, Germany
| | | | - Andreas Zumbusch
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - Dieter Spiteller
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Peter G Kroth
- Department of Biology, University of Konstanz, Konstanz, Germany
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3
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Keroack CD, Elsworth B, Tennessen JA, Paul AS, Hua R, Ramirez-Ramirez L, Ye S, Moreira CK, Meyers MJ, Zarringhalam K, Duraisingh MT. Comparative chemical genomics in Babesia species identifies the alkaline phosphatase PhoD as a determinant of antiparasitic resistance. Proc Natl Acad Sci U S A 2024; 121:e2312987121. [PMID: 38377214 PMCID: PMC10907312 DOI: 10.1073/pnas.2312987121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/09/2024] [Indexed: 02/22/2024] Open
Abstract
Babesiosis is an emerging zoonosis and widely distributed veterinary infection caused by 100+ species of Babesia parasites. The diversity of Babesia parasites and the lack of specific drugs necessitate the discovery of broadly effective antibabesials. Here, we describe a comparative chemogenomics (CCG) pipeline for the identification of conserved targets. CCG relies on parallel in vitro evolution of resistance in independent populations of Babesia spp. (B. bovis and B. divergens). We identified a potent antibabesial, MMV019266, from the Malaria Box, and selected for resistance in two species of Babesia. After sequencing of multiple independently derived lines in the two species, we identified mutations in a membrane-bound metallodependent phosphatase (phoD). In both species, the mutations were found in the phoD-like phosphatase domain. Using reverse genetics, we validated that mutations in bdphoD confer resistance to MMV019266 in B. divergens. We have also demonstrated that BdPhoD localizes to the endomembrane system and partially with the apicoplast. Finally, conditional knockdown and constitutive overexpression of BdPhoD alter the sensitivity to MMV019266 in the parasite. Overexpression of BdPhoD results in increased sensitivity to the compound, while knockdown increases resistance, suggesting BdPhoD is a pro-susceptibility factor. Together, we have generated a robust pipeline for identification of resistance loci and identified BdPhoD as a resistance mechanism in Babesia species.
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Affiliation(s)
- Caroline D. Keroack
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Brendan Elsworth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Jacob A. Tennessen
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Aditya S. Paul
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Renee Hua
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Luz Ramirez-Ramirez
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Sida Ye
- Department of Mathematics, University of Massachusetts, Boston, MA02125
- Center for Personalized Cancer Therapy, University of Massachusetts, Boston, MA02125
| | - Cristina K. Moreira
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Marvin J. Meyers
- Department of Chemistry, Saint Louis University, St. Louis, MO63103
| | - Kourosh Zarringhalam
- Department of Mathematics, University of Massachusetts, Boston, MA02125
- Center for Personalized Cancer Therapy, University of Massachusetts, Boston, MA02125
| | - Manoj T. Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
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Santin A, Russo MT, de Los Ríos LM, Chiurazzi M, d'Alcalà MR, Lacombe B, Ferrante MI, Rogato A. The tonoplast localized protein PtNPF1 participates in the regulation of nitrogen response in diatoms. THE NEW PHYTOLOGIST 2024; 241:1592-1604. [PMID: 38084038 DOI: 10.1111/nph.19461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 11/21/2023] [Indexed: 01/26/2024]
Abstract
Diatoms are a highly successful group of phytoplankton, well adapted also to oligotrophic environments and capable of handling nutrient fluctuations in the ocean, particularly nitrate. The presence of a large vacuole is an important trait contributing to their adaptive features. It confers diatoms the ability to accumulate and store nutrients, such as nitrate, when they are abundant outside and then to reallocate them into the cytosol to meet deficiencies, in a process called luxury uptake. The molecular mechanisms that regulate these nitrate fluxes are still not known in diatoms. In this work, we provide new insights into the function of Phaeodactylum tricornutum NPF1, a putative low-affinity nitrate transporter. To accomplish this, we generated overexpressing strains and CRISPR/Cas9 loss-of-function mutants. Microscopy observations confirmed predictions that PtNPF1 is localized on the vacuole membrane. Furthermore, functional characterizations performed on knock-out mutants revealed a transient growth delay phenotype linked to altered nitrate uptake. Together, these results allowed us to hypothesize that PtNPF1 is presumably involved in modulating intracellular nitrogen fluxes, managing intracellular nutrient availability. This ability might allow diatoms to fine-tune the assimilation, storage and reallocation of nitrate, conferring them a strong advantage in oligotrophic environments.
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Affiliation(s)
- Anna Santin
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
| | | | - Laura Morales de Los Ríos
- Institute for Plant Science of Montpellier (IPSiM), University of Montpellier, CNRS, INRAE, Montpellier SupAgro, Place Pierre Viala 2, Montpellier, 34060, France
| | - Maurizio Chiurazzi
- Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, Naples, 80131, Italy
| | | | - Benoît Lacombe
- Institute for Plant Science of Montpellier (IPSiM), University of Montpellier, CNRS, INRAE, Montpellier SupAgro, Place Pierre Viala 2, Montpellier, 34060, France
| | - Maria Immacolata Ferrante
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
- National Institute of Oceanography and Applied Geophysics, Trieste, 34010, Italy
| | - Alessandra Rogato
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
- Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, Naples, 80131, Italy
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5
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Matsui H, Harada H, Maeda K, Sugiyama T, Fukuchi Y, Kimura N, Nawaly H, Tsuji Y, Matsuda Y. Coordinated phosphate uptake by extracellular alkaline phosphatase and solute carrier transporters in marine diatoms. THE NEW PHYTOLOGIST 2024; 241:1210-1221. [PMID: 38013640 DOI: 10.1111/nph.19410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/31/2023] [Indexed: 11/29/2023]
Abstract
Marine diatoms express genes encoding potential phosphate transporter and alkaline phosphatase (APase) under phosphate-limited (-P) condition. This indicates that diatoms use high-affinity phosphate uptake system with organic phosphate hydration. The function of molecules playing roles for Pi uptake was determined in this study. Pi uptake and APase activity of two marine diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana, were monitored during acclimation to -P condition. The transcript levels of Pi transporter were analyzed, and Pi transporters were localized with GFP tagging in diatom cells. KO mutants of plasma membrane solute carrier proteins (SLC34s) or APase were established, and their phenotype was evaluated. Some Na+ /Pi transporter candidates, SLC34s in P. tricornutum and T. pseudonana, increased transcript under -P condition. Whole-cell Pi transport was specifically stimulated by sodium ion but independent of potassium, lithium, or proton. Genome-editing KO of PtSLC34-5 and APase (Pt49678) in P. tricornutum was highly inhibitory for Pi uptake, and KO of TpSLC34-2 was also highly inhibitory for Pi uptake in T. pseudonana. SLC34s and APase were co-expressed under -P conditions in marine diatoms. SLC34s play a major role in the initial acclimation stage of diatom cells to -P condition and APase plays an increasing role in the prolonged Pi-starved condition.
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Affiliation(s)
- Hiroaki Matsui
- Department of Bioscience, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Hyogo, Japan
| | - Hisashi Harada
- Department of Chemistry and Biotechnology, Tottori University, Tottori, 680-8550, Japan
| | - Kanako Maeda
- Department of Bioscience, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Hyogo, Japan
| | - Toshiki Sugiyama
- Department of Bioscience, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Hyogo, Japan
| | - Yohei Fukuchi
- Department of Bioscience, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Hyogo, Japan
| | - Nanae Kimura
- Department of Bioscience, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Hyogo, Japan
| | - Hermanus Nawaly
- Department of Bioscience, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Hyogo, Japan
| | - Yoshinori Tsuji
- Department of Bioscience, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Hyogo, Japan
| | - Yusuke Matsuda
- Department of Bioscience, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Hyogo, Japan
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6
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Setta SP, Lerch S, Jenkins BD, Dyhrman ST, Rynearson TA. Oligotrophic waters of the Northwest Atlantic support taxonomically diverse diatom communities that are distinct from coastal waters. JOURNAL OF PHYCOLOGY 2023; 59:1202-1216. [PMID: 37737069 DOI: 10.1111/jpy.13388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/23/2023] [Accepted: 08/09/2023] [Indexed: 09/23/2023]
Abstract
Diatoms are important components of the marine food web and one of the most species-rich groups of phytoplankton. The diversity and composition of diatoms in eutrophic nearshore habitats have been well documented due to the outsized influence of diatoms on coastal ecosystem functioning. In contrast, patterns of both diatom diversity and community composition in offshore oligotrophic regions where diatom biomass is low have been poorly resolved. To compare the diatom diversity and community composition in oligotrophic and eutrophic waters, diatom communities were sampled along a 1,250 km transect from the oligotrophic Sargasso Sea to the coastal waters of the northeast US shelf. Diatom community composition was determined by amplifying and sequencing the 18S rDNA V4 region. Of the 301 amplicon sequence variants (ASVs) identified along the transect, the majority (70%) were sampled exclusively from oligotrophic waters of the Gulf Stream and Sargasso Sea and included the genera Bacteriastrum, Haslea, Hemiaulus, Pseudo-nitzschia, and Nitzschia. Diatom ASV richness did not vary along the transect, indicating that the oligotrophic Sargasso Sea and Gulf Stream are occupied by a diverse diatom community. Although ASV richness was similar between oligotrophic and coastal waters, diatom community composition in these regions differed significantly and was correlated with temperature and phosphate, two environmental variables known to influence diatom metabolism and geographic distribution. In sum, oligotrophic waters of the western North Atlantic harbor diverse diatom assemblages that are distinct from coastal regions, and these open ocean diatoms warrant additional study, as they may play critical roles in oligotrophic ecosystems.
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Affiliation(s)
- Samantha P Setta
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
| | - Sarah Lerch
- College of the Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Bethany D Jenkins
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
- College of the Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Sonya T Dyhrman
- Department of Earth and Environmental Sciences, Columbia University, Palisades, New York, USA
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York, USA
| | - Tatiana A Rynearson
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
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7
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Wolfram-Schauerte M, Pozhydaieva N, Grawenhoff J, Welp LM, Silbern I, Wulf A, Billau FA, Glatter T, Urlaub H, Jäschke A, Höfer K. A viral ADP-ribosyltransferase attaches RNA chains to host proteins. Nature 2023; 620:1054-1062. [PMID: 37587340 PMCID: PMC10468400 DOI: 10.1038/s41586-023-06429-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/12/2023] [Indexed: 08/18/2023]
Abstract
The mechanisms by which viruses hijack the genetic machinery of the cells they infect are of current interest. When bacteriophage T4 infects Escherichia coli, it uses three different adenosine diphosphate (ADP)-ribosyltransferases (ARTs) to reprogram the transcriptional and translational apparatus of the host by ADP-ribosylation using nicotinamide adenine dinucleotide (NAD) as a substrate1,2. NAD has previously been identified as a 5' modification of cellular RNAs3-5. Here we report that the T4 ART ModB accepts not only NAD but also NAD-capped RNA (NAD-RNA) as a substrate and attaches entire RNA chains to acceptor proteins in an 'RNAylation' reaction. ModB specifically RNAylates the ribosomal proteins rS1 and rL2 at defined Arg residues, and selected E. coli and T4 phage RNAs are linked to rS1 in vivo. T4 phages that express an inactive mutant of ModB have a decreased burst size and slowed lysis of E. coli. Our findings reveal a distinct biological role for NAD-RNA, namely the activation of the RNA for enzymatic transfer to proteins. The attachment of specific RNAs to ribosomal proteins might provide a strategy for the phage to modulate the host's translation machinery. This work reveals a direct connection between RNA modification and post-translational protein modification. ARTs have important roles far beyond viral infections6, so RNAylation may have far-reaching implications.
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Affiliation(s)
- Maik Wolfram-Schauerte
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | | | - Julia Grawenhoff
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Luisa M Welp
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center, Göttingen, Germany
| | - Ivan Silbern
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center, Göttingen, Germany
| | - Alexander Wulf
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Franziska A Billau
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Timo Glatter
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Georg-August-University, Göttingen, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
| | - Katharina Höfer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany.
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8
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Keroack CD, Elsworth B, Tennessen JA, Paul AS, Hua R, Ramirez-Ramirez L, Ye S, Moreira CM, Meyers MJ, Zarringhalam K, Duraisingh MT. Comparative chemical genomics in Babesia species identifies the alkaline phosphatase phoD as a novel determinant of resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544849. [PMID: 37398106 PMCID: PMC10312741 DOI: 10.1101/2023.06.13.544849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Babesiosis is an emerging zoonosis and widely distributed veterinary infection caused by 100+ species of Babesia parasites. The diversity of Babesia parasites, coupled with the lack of potent inhibitors necessitates the discovery of novel conserved druggable targets for the generation of broadly effective antibabesials. Here, we describe a comparative chemogenomics (CCG) pipeline for the identification of novel and conserved targets. CCG relies on parallel in vitro evolution of resistance in independent populations of evolutionarily-related Babesia spp. ( B. bovis and B. divergens ). We identified a potent antibabesial inhibitor from the Malaria Box, MMV019266. We were able to select for resistance to this compound in two species of Babesia, achieving 10-fold or greater resistance after ten weeks of intermittent selection. After sequencing of multiple independently derived lines in the two species, we identified mutations in a single conserved gene in both species: a membrane-bound metallodependent phosphatase (putatively named PhoD). In both species, the mutations were found in the phoD-like phosphatase domain, proximal to the predicted ligand binding site. Using reverse genetics, we validated that mutations in PhoD confer resistance to MMV019266. We have also demonstrated that PhoD localizes to the endomembrane system and partially with the apicoplast. Finally, conditional knockdown and constitutive overexpression of PhoD alter the sensitivity to MMV019266 in the parasite: overexpression of PhoD results in increased sensitivity to the compound, while knockdown increases resistance, suggesting PhoD is a resistance mechanism. Together, we have generated a robust pipeline for identification of resistance loci, and identified PhoD as a novel determinant of resistance in Babesia species. Highlights Use of two species for in vitro evolution identifies a high confidence locus associated with resistance Resistance mutation in phoD was validated using reverse genetics in B. divergens Perturbation of phoD using function genetics results in changes in the level of resistance to MMV019266Epitope tagging reveals localization to the ER/apicoplast, a conserved localization with a similar protein in diatoms Together, phoD is a novel resistance determinant in multiple Babesia spp .
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9
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Chandran R, K Singh R, Singh A, Ganesan K, Thipramalai Thangappan AK, K Lal K, Mohindra V. Evaluating the influence of environmental variables on the length-weight relationship and prediction modelling in flathead grey mullet, Mugil cephalus Linnaeus, 1758. PeerJ 2023; 11:e14884. [PMID: 36860765 PMCID: PMC9969857 DOI: 10.7717/peerj.14884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/22/2023] [Indexed: 03/03/2023] Open
Abstract
Fish stocks that are grown under diverse environmental conditions have different biometric relationships and growth patterns. The biometric length-weight relationship (LWR) is an essential fishery assessment tool, as fish growth is continuous and depends on genetic and environmental factors. The present study attempts to understand the LWR of the flathead grey mullet, Mugil cephalus Linnaeus, 1758, from different locations. The study area encompassed its distribution in the wild across freshwater location (one), coastal habitats (eight locations), and estuaries (six locations) in India to determine the relationship between various environmental parameters. Specimens (n = 476) of M. cephalus were collected from commercial catches and the length and weight of individual specimens were recorded. Monthly data from the study locations were extracted for nine environmental variables from the datasets downloaded from the Physical Oceanography Distributed Active Archive Center (PO.DAAC) and the Copernicus Marine Environment Monitoring Service (CMEMS) over 16 years (2002 to 2017) on the Geographical Information System platform. The parameters of the LWR, intercept 'a' and slope or regression coefficient 'b', varied from 0.005321 to 0.22182 and 2.235 to 3.173, respectively. The condition factor ranged from 0.92 to 1.41. The partial least squares (PLS) score scatter plot matrix indicated differences in the environmental variables between the locations. PLS analysis of the regression coefficient and environment parameters revealed that certain environment variables viz., sea surface temperature, salinity, dissolved oxygen, nitrate, and phosphate, played a positive role. However, chlorophyll, pH, silicate, and iron played a negative role in influencing weight growth across various locations. The results revealed that the M. cephalus specimens from three locations, Mandapam, Karwar, and Ratnagiri, possessed significantly higher fitness to their environment than those from the other six locations. The PLS model can be used to predict weight growth under the various environmental conditions of different ecosystems. The three identified locations are useful sites for the mariculture of this species considering their growth performance, the environmental variables, and their interactions. The results of this study will improve the management and conservation of exploited stocks in regions affected by climate change. Our results will also aid in making environment clearance decisions for coastal development projects and will improve the efficiency of mariculture systems.
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Affiliation(s)
- Rejani Chandran
- Fish Conservation Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India
| | - Rajeev K Singh
- Fish Conservation Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India
| | - Achal Singh
- Fish Conservation Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India
| | - Kantharajan Ganesan
- Fish Conservation Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India
| | | | - Kuldeep K Lal
- Fish Conservation Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India,ICAR-Central Institute of Brackishwater Aquaculture (CIBA), Chennai, Tamil Nadu, India
| | - Vindhya Mohindra
- Fish Conservation Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India
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10
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Brownlee C, Helliwell KE, Meeda Y, McLachlan D, Murphy EA, Wheeler GL. Regulation and integration of membrane transport in marine diatoms. Semin Cell Dev Biol 2023; 134:79-89. [PMID: 35305902 DOI: 10.1016/j.semcdb.2022.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/18/2022] [Accepted: 03/04/2022] [Indexed: 12/27/2022]
Abstract
Diatoms represent one of the most successful groups of marine phytoplankton and are major contributors to ocean biogeochemical cycling. They have colonized marine, freshwater and ice environments and inhabit all regions of the World's oceans, from poles to tropics. Their success is underpinned by a remarkable ability to regulate their growth and metabolism during nutrient limitation and to respond rapidly when nutrients are available. This requires precise regulation of membrane transport and nutrient acquisition mechanisms, integration of nutrient sensing mechanisms and coordination of different transport pathways. This review outlines transport mechanisms involved in acquisition of key nutrients (N, C, P, Si, Fe) by marine diatoms, illustrating their complexity, sophistication and multiple levels of control.
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Affiliation(s)
- Colin Brownlee
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK; School of Ocean and Earth Sciences, University of Southampton, Southampton SO14 3ZH, UK
| | - Katherine E Helliwell
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK; Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Yasmin Meeda
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Deirdre McLachlan
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK; School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Eleanor A Murphy
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Glen L Wheeler
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
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11
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Li J, Zhang K, Li L, Wang Y, Lin S. Unsuspected functions of alkaline phosphatase PhoD in the diatom Phaeodactylum tricornutum. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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12
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Liu S, Storti M, Finazzi G, Bowler C, Dorrell RG. A metabolic, phylogenomic and environmental atlas of diatom plastid transporters from the model species Phaeodactylum. FRONTIERS IN PLANT SCIENCE 2022; 13:950467. [PMID: 36212359 PMCID: PMC9546453 DOI: 10.3389/fpls.2022.950467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Diatoms are an important group of algae, contributing nearly 40% of total marine photosynthetic activity. However, the specific molecular agents and transporters underpinning the metabolic efficiency of the diatom plastid remain to be revealed. We performed in silico analyses of 70 predicted plastid transporters identified by genome-wide searches of Phaeodactylum tricornutum. We considered similarity with Arabidopsis thaliana plastid transporters, transcriptional co-regulation with genes encoding core plastid metabolic pathways and with genes encoded in the mitochondrial genomes, inferred evolutionary histories using single-gene phylogeny, and environmental expression trends using Tara Oceans meta-transcriptomics and meta-genomes data. Our data reveal diatoms conserve some of the ion, nucleotide and sugar plastid transporters associated with plants, such as non-specific triose phosphate transporters implicated in the transport of phosphorylated sugars, NTP/NDP and cation exchange transporters. However, our data also highlight the presence of diatom-specific transporter functions, such as carbon and amino acid transporters implicated in intricate plastid-mitochondria crosstalk events. These confirm previous observations that substrate non-specific triose phosphate transporters (TPT) may exist as principal transporters of phosphorylated sugars into and out of the diatom plastid, alongside suggesting probable agents of NTP exchange. Carbon and amino acid transport may be related to intricate metabolic plastid-mitochondria crosstalk. We additionally provide evidence from environmental meta-transcriptomic/meta- genomic data that plastid transporters may underpin diatom sensitivity to ocean warming, and identify a diatom plastid transporter (J43171) whose expression may be positively correlated with temperature.
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Affiliation(s)
- Shun Liu
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National De La Recherche Scientifique (CNRS), Institut National De La Santé Et De La Recherche Médicale (INSERM), Université Paris Sciences et Lettres (PSL), Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, Paris, France
| | - Mattia Storti
- Univ. Grenoble Alpes (UGA), Centre National Recherche Scientifique (CNRS), Commissariat Energie Atomique Energies Alternatives (CEA), Institut National Recherche Agriculture Alimentation Environnement (INRAE), Interdisciplinary Research Institute of Grenoble (IRIG), Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Grenoble, France
| | - Giovanni Finazzi
- Univ. Grenoble Alpes (UGA), Centre National Recherche Scientifique (CNRS), Commissariat Energie Atomique Energies Alternatives (CEA), Institut National Recherche Agriculture Alimentation Environnement (INRAE), Interdisciplinary Research Institute of Grenoble (IRIG), Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Grenoble, France
| | - Chris Bowler
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National De La Recherche Scientifique (CNRS), Institut National De La Santé Et De La Recherche Médicale (INSERM), Université Paris Sciences et Lettres (PSL), Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, Paris, France
| | - Richard G. Dorrell
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National De La Recherche Scientifique (CNRS), Institut National De La Santé Et De La Recherche Médicale (INSERM), Université Paris Sciences et Lettres (PSL), Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, Paris, France
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13
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Krämer LC, Wasser D, Haitz F, Sabel B, Büchel C. Heterologous expression of HUP1 glucose transporter enables low-light mediated growth on glucose in Phaeodactylum tricornutum. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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14
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Kamikawa R, Mochizuki T, Sakamoto M, Tanizawa Y, Nakayama T, Onuma R, Cenci U, Moog D, Speak S, Sarkozi K, Toseland A, van Oosterhout C, Oyama K, Kato M, Kume K, Kayama M, Azuma T, Ishii KI, Miyashita H, Henrissat B, Lombard V, Win J, Kamoun S, Kashiyama Y, Mayama S, Miyagishima SY, Tanifuji G, Mock T, Nakamura Y. Genome evolution of a nonparasitic secondary heterotroph, the diatom Nitzschia putrida. SCIENCE ADVANCES 2022; 8:eabi5075. [PMID: 35486731 PMCID: PMC9054022 DOI: 10.1126/sciadv.abi5075] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Secondary loss of photosynthesis is observed across almost all plastid-bearing branches of the eukaryotic tree of life. However, genome-based insights into the transition from a phototroph into a secondary heterotroph have so far only been revealed for parasitic species. Free-living organisms can yield unique insights into the evolutionary consequence of the loss of photosynthesis, as the parasitic lifestyle requires specific adaptations to host environments. Here, we report on the diploid genome of the free-living diatom Nitzschia putrida (35 Mbp), a nonphotosynthetic osmotroph whose photosynthetic relatives contribute ca. 40% of net oceanic primary production. Comparative analyses with photosynthetic diatoms and heterotrophic algae with parasitic lifestyle revealed that a combination of gene loss, the accumulation of genes involved in organic carbon degradation, a unique secretome, and the rapid divergence of conserved gene families involved in cell wall and extracellular metabolism appear to have facilitated the lifestyle of a free-living secondary heterotroph.
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Affiliation(s)
- Ryoma Kamikawa
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takako Mochizuki
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
| | - Mika Sakamoto
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
| | - Takuro Nakayama
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Ryo Onuma
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Ugo Cenci
- Université de Lille, CNRS, UMR 8576 – UGSF – Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Daniel Moog
- Laboratory for Cell Biology, Philipps University Marburg, Karl-von-Frisch-Str. 8
- SYNMIKRO Research Center, Hans-Meerwein-Str. 6, 35032, Marburg, Germany
| | - Samuel Speak
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Krisztina Sarkozi
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrew Toseland
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Kaori Oyama
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Misako Kato
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Keitaro Kume
- Department of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Motoki Kayama
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Tomonori Azuma
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Ken-ichiro Ishii
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Hideaki Miyashita
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288 Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288 Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Joe Win
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yuichiro Kashiyama
- Graduate School of Engineering, Fukui University of Technology, Fukui, Japan
| | - Shigeki Mayama
- Advanced Support Center for Science Teachers, Tokyo Gakugei University, Koganei, Tokyo, Japan
| | - Shin-ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Goro Tanifuji
- Department of Zoology, National Museum of Nature and Science, Tsukuba 305-0005, Japan
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yasukazu Nakamura
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
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15
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Slattery SS, Giguere DJ, Stuckless EE, Shrestha A, Briere LAK, Galbraith A, Reaume S, Boyko X, Say HH, Browne TS, Frederick MI, Lant JT, Heinemann IU, O'Donoghue P, Dsouza L, Martin S, Howard P, Jedeszko C, Ali K, Styba G, Flatley M, Karas BJ, Gloor GB, Edgell DR. Phosphate-regulated expression of the SARS-CoV-2 receptor-binding domain in the diatom Phaeodactylum tricornutum for pandemic diagnostics. Sci Rep 2022; 12:7010. [PMID: 35487958 PMCID: PMC9051505 DOI: 10.1038/s41598-022-11053-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/18/2022] [Indexed: 12/22/2022] Open
Abstract
The worldwide COVID-19 pandemic caused by the SARS-CoV-2 betacoronavirus has highlighted the need for a synthetic biology approach to create reliable and scalable sources of viral antigen for uses in diagnostics, therapeutics and basic biomedical research. Here, we adapt plasmid-based systems in the eukaryotic microalgae Phaeodactylum tricornutum to develop an inducible overexpression system for SARS-CoV-2 proteins. Limiting phosphate and iron in growth media induced expression of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein from the P. tricornutum HASP1 promoter in the wild-type strain and in a histidine auxotrophic strain that alleviates the requirement for antibiotic selection of expression plasmids. The RBD was purified from whole cell extracts (algae-RBD) with yield compromised by the finding that 90-95% of expressed RBD lacked the genetically encoded C-terminal 6X-histidine tag. Constructs that lacked the TEV protease site between the RBD and C-terminal 6X-histidine tag retained the tag, increasing yield. Purified algae-RBD was found to be N-linked glycosylated by treatment with endoglycosidases, was cross-reactive with anti-RBD polyclonal antibodies, and inhibited binding of recombinant RBD purified from mammalian cell lines to the human ACE2 receptor. We also show that the algae-RBD can be used in a lateral flow assay device to detect SARS-CoV-2 specific IgG antibodies from donor serum at sensitivity equivalent to assays performed with RBD made in mammalian cell lines. Our study shows that P. tricornutum is a scalable system with minimal biocontainment requirements for the inducible production of SARS-CoV-2 or other coronavirus antigens for pandemic diagnostics.
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Affiliation(s)
- Samuel S Slattery
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Daniel J Giguere
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Emily E Stuckless
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Arina Shrestha
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Lee-Ann K Briere
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Alexa Galbraith
- Lambton College, 1457 London Rd, Sarnia, ON, N7S 6K4, Canada
| | - Stephen Reaume
- Lambton College, 1457 London Rd, Sarnia, ON, N7S 6K4, Canada
| | - Xenia Boyko
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Henry H Say
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Tyler S Browne
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Mallory I Frederick
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Jeremy T Lant
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Ilka U Heinemann
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Patrick O'Donoghue
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
- Department of Chemistry, Western University, London, ON, N6A 3K7, Canada
| | - Liann Dsouza
- Pond Technologies Inc., Markham, ON, L3R 9W7, Canada
| | - Steven Martin
- Pond Technologies Inc., Markham, ON, L3R 9W7, Canada
| | - Peter Howard
- Pond Technologies Inc., Markham, ON, L3R 9W7, Canada
| | - Christopher Jedeszko
- International Point of Care Inc., 135 The West Mall Unit 9, Toronto, ON, M9C 1C2, Canada
| | - Kinza Ali
- International Point of Care Inc., 135 The West Mall Unit 9, Toronto, ON, M9C 1C2, Canada
| | - Garth Styba
- International Point of Care Inc., 135 The West Mall Unit 9, Toronto, ON, M9C 1C2, Canada
| | - Martin Flatley
- Suncor Energy Inc., Sarnia Refinery, 1900 River Road, Sarnia, ON, N7T 7J3, Canada
| | - Bogumil J Karas
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Gregory B Gloor
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada.
| | - David R Edgell
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada.
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16
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Zhang K, Li J, Wang J, Lin X, Li L, You Y, Wu X, Zhou Z, Lin S. Functional differentiation and complementation of alkaline phosphatases and choreography of DOP scavenging in a marine diatom. Mol Ecol 2022; 31:3389-3399. [PMID: 35445467 DOI: 10.1111/mec.16475] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 11/29/2022]
Abstract
Facing phosphate deficiency, phytoplankton use alkaline phosphatase (AP) to scavenge dissolved organophosphate (DOP). AP is a multi-type (e.g. PhoA, PhoD) family of hydrolases and is known as a promiscuous enzyme with broad DOP substrate compatibility. Yet whether the multiple types differentiate on substrates and collaborate to provide physiological flexibility remain elusive. Here we identify PhoA and PhoDs and document the functional differentiation between PhoA and a PhoD (PhoD_45757) in Phaeodactylum tricornutum. CRISPR/Cas9-based mutations and physiological analyses reveal that 1) PhoA is a secreted enzyme and contributes the majority of total AP activity whereas PhoD_45757 is intracellular and contributes a minor fraction of the total AP activity; 2) AP gene expression compensates for each other after one is disrupted; 3) the DOP→PhoA→phosphate_uptake and the DOP_uptake→PhoD→phosphate pathways function interchangeably for some DOP substrates. These findings shed light on the underpinning of AP's multiformity and have important implications in phytoplankton phosphorus-nutrient niche differentiation, physiological plasticity, and competitive strategy.
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Affiliation(s)
- Kaidian Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China.,Department of Marine Sciences, University of Connecticut, Groton, CT, USA.,State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, China
| | - Jiashun Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Jierui Wang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Yanchun You
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xiaomei Wu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Zhi Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China.,Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao, Shandong, China.,Department of Marine Sciences, University of Connecticut, Groton, CT, USA
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17
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Phytate as a phosphorus nutrient with impacts on iron stress-related gene expression for phytoplankton: insights from diatom Phaeodactylum tricornutum. Appl Environ Microbiol 2021; 88:e0209721. [PMID: 34757820 DOI: 10.1128/aem.02097-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phytoplankton have evolved a capability to acquire phosphorus (P) from dissolved organic phosphorus (DOP) since the preferred form, dissolved inorganic phosphate (DIP, or Pi), is often limited in parts of the ocean. Phytic acid (PA) is abundantly synthesized in plants and rich in excreta of animals, potentially enriching the DOP pool in coastal oceans. However, whether and how PA may be used by phytoplankton are poorly understood. Here, we investigated PA utilization and underlying metabolic pathways in the diatom model Phaeodactylum tricornutum. The physiological results showed that P. tricornutum could utilize PA as a sole source of P nutrient to support growth. Meanwhile, the replacement of PA for DIP also caused changes in multiple cellular processes such as inositol phosphate metabolism, photosynthesis, and signal transduction. These results suggest that PA is bioavailable to P. tricornutum and can directly participate the metabolic pathways of PA-grown cells. However, our data showed that the utilization of PA was markedly less efficient than that of DIP, and PA-grown cells exhibited P and iron (Fe) nutrient stress signals. Implicated in these findings is the potential of complicated responses of phytoplankton to an ambient DOP species, which calls for more systematic investigation. IMPORTANCE PA is abundant in plants, and cannot be digested by non-ruminant animals. Hence, it is potentially a significant component of the DOP pool in the coastal waters. Despite the potential importance, there is little information about its bioavailability to phytoplankton as a source of P nutrient and if so what molecular mechanisms are involved. In this study, we found that part of PA could be utilized by the diatom P. tricornutum to support growth, and another portion of PA can act as a substrate directly participating in various metabolism pathways and cellular processes. However, our physiological and transcriptomic data show that PA-grown cells still exhibited signs of P stress and potential Fe stress. These results have significant implications in phytoplankton P nutrient ecology and provide a novel insight into multi-faceted impacts of DOP utilization on phytoplankton nutrition and metabolism.
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18
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Zhang K, Zhou Z, Li J, Wang J, Yu L, Lin S. SPX-related genes regulate phosphorus homeostasis in the marine phytoplankton, Phaeodactylum tricornutum. Commun Biol 2021; 4:797. [PMID: 34172821 PMCID: PMC8233357 DOI: 10.1038/s42003-021-02284-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 06/01/2021] [Indexed: 11/18/2022] Open
Abstract
Phosphorus (P) is an essential nutrient for marine phytoplankton. Maintaining intracellular P homeostasis against environmental P variability is critical for phytoplankton, but how they achieve this is poorly understood. Here we identify a SPX gene and investigate its role in Phaeodactylum tricornutum. SPX knockout led to significant increases in the expression of phosphate transporters, alkaline phosphatases (the P acquisition machinery) and phospholipid hydrolases (a mechanism to reduce P demand). These demonstrate that SPX is a negative regulator of both P uptake and P-stress responses. Furthermore, we show that SPX regulation of P uptake and metabolism involves a phosphate starvation response regulator (PHR) as an intermediate. Additionally, we find the SPX related genes exist and operate across the phytoplankton phylogenetic spectrum and in the global oceans, indicating its universal importance in marine phytoplankton. This study lays a foundation for better understanding phytoplankton adaptation to P variability in the future changing oceans.
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Affiliation(s)
- Kaidian Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Zhi Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, China
| | - Jiashun Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Jingtian Wang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China.
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA.
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao, China.
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19
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Moog D, Zarzycki J, Rexer KH, Erb TJ, Maier UG. Engineering microalgae as a whole cell catalyst for PET degradation. Methods Enzymol 2021; 648:435-455. [PMID: 33579415 DOI: 10.1016/bs.mie.2020.12.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Plastic pollution has become a serious issue on Earth. Although efficient industrial recycling processes exist, a significant fraction of plastic waste still ends up in nature, where it can endure for centuries. Slow mechanical and chemical decay lead to the formation of micro- and nanoplastics, which are washed from land into rivers and finally end up in the oceans. As such particles cannot be efficiently removed from the environment, biological degradation mechanisms are highly desirable. Several enzymes have been described that are capable of degrading certain plastic materials such as polyethylene terephthalate (PET). Such enzymes have a huge potential for future biotechnology applications. However, they require model systems that can be efficiently adapted to very specific conditions. Here, we present detailed instructions, how to convert the model diatom Phaeodactylum into a solar-fueled microbial cell factory for PETase expression, resulting in a whole cell catalyst for PET degradation at moderate temperatures under saltwater conditions.
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Affiliation(s)
- Daniel Moog
- Laboratory for Cell Biology, University of Marburg, Marburg, Germany; SYNMIKRO Research Center, Marburg, Germany.
| | - Jan Zarzycki
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Karl-Heinz Rexer
- Department for Evolutionary Ecology of Plants, University of Marburg, Marburg, Germany
| | - Tobias J Erb
- SYNMIKRO Research Center, Marburg, Germany; Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Uwe G Maier
- Laboratory for Cell Biology, University of Marburg, Marburg, Germany; SYNMIKRO Research Center, Marburg, Germany
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20
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Dell'Aquila G, Maier UG. Specific acclimations to phosphorus limitation in the marine diatom Phaeodactylum tricornutum. Biol Chem 2020; 401:1495-1501. [PMID: 32845857 DOI: 10.1515/hsz-2020-0197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/19/2020] [Indexed: 11/15/2022]
Abstract
Phosphorus (P) is a crucial element and diatoms, unicellular phototrophic organisms, evolved efficient strategies to handle limiting phosphorus concentrations in the oceans. In the last decade, several groups investigated the model diatom Phaeodactylum tricornutum concerning phosphate homeostasis mechanisms. Here, we summarize the actual status of knowledge by linking the available data sets, thereby indicating experimental limits but also future research directions.
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Affiliation(s)
- Gianluca Dell'Aquila
- Cell Biology Laboratory, Philipps Universität Marburg, Karl-von-Frisch Strasse 8, D-35043Marburg, Germany
| | - Uwe G Maier
- SYNMIKRO Research Center, Hans-Meerwein-Str. 6, D-35032Marburg, Germany
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