1
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Torcello-Requena A, Murphy ARJ, Lidbury IDEA, Pitt FD, Stark R, Millard AD, Puxty RJ, Chen Y, Scanlan DJ. A distinct, high-affinity, alkaline phosphatase facilitates occupation of P-depleted environments by marine picocyanobacteria. Proc Natl Acad Sci U S A 2024; 121:e2312892121. [PMID: 38713622 PMCID: PMC11098088 DOI: 10.1073/pnas.2312892121] [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: 07/27/2023] [Accepted: 04/06/2024] [Indexed: 05/09/2024] Open
Abstract
Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus, the two most abundant phototrophs on Earth, thrive in oligotrophic oceanic regions. While it is well known that specific lineages are exquisitely adapted to prevailing in situ light and temperature regimes, much less is known of the molecular machinery required to facilitate occupancy of these low-nutrient environments. Here, we describe a hitherto unknown alkaline phosphatase, Psip1, that has a substantially higher affinity for phosphomonoesters than other well-known phosphatases like PhoA, PhoX, or PhoD and is restricted to clade III Synechococcus and a subset of high light I-adapted Prochlorococcus strains, suggesting niche specificity. We demonstrate that Psip1 has undergone convergent evolution with PhoX, requiring both iron and calcium for activity and likely possessing identical key residues around the active site, despite generally very low sequence homology. Interrogation of metagenomes and transcriptomes from TARA oceans and an Atlantic Meridional transect shows that psip1 is abundant and highly expressed in picocyanobacterial populations from the Mediterranean Sea and north Atlantic gyre, regions well recognized to be phosphorus (P)-deplete. Together, this identifies psip1 as an important oligotrophy-specific gene for P recycling in these organisms. Furthermore, psip1 is not restricted to picocyanobacteria and is abundant and highly transcribed in some α-proteobacteria and eukaryotic algae, suggesting that such a high-affinity phosphatase is important across the microbial taxonomic world to occupy low-P environments.
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Affiliation(s)
| | - Andrew R. J. Murphy
- School of Life Sciences, University of Warwick, CoventryCV4 7AL, United Kingdom
| | - Ian D. E. A. Lidbury
- Molecular Microbiology: Biochemistry to Disease, School of Biosciences, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Frances D. Pitt
- School of Life Sciences, University of Warwick, CoventryCV4 7AL, United Kingdom
| | - Richard Stark
- School of Life Sciences, University of Warwick, CoventryCV4 7AL, United Kingdom
| | - Andrew D. Millard
- Centre for Phage Research, Department of Genetics and Genome Biology, University of Leicester, LeicesterLE1 7RH, United Kingdom
| | - Richard J. Puxty
- School of Life Sciences, University of Warwick, CoventryCV4 7AL, United Kingdom
| | - Yin Chen
- School of Biosciences, University of Birmingham, BirminghamB15 2TT, United Kingdom
| | - David J. Scanlan
- School of Life Sciences, University of Warwick, CoventryCV4 7AL, United Kingdom
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2
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Liang Z, McCabe K, Fawcett SE, Forrer HJ, Hashihama F, Jeandel C, Marconi D, Planquette H, Saito MA, Sohm JA, Thomas RK, Letscher RT, Knapp AN. A global ocean dissolved organic phosphorus concentration database (DOPv2021). Sci Data 2022; 9:772. [PMID: 36526638 PMCID: PMC9758185 DOI: 10.1038/s41597-022-01873-7] [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: 07/18/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
Dissolved organic phosphorus (DOP) concentration distributions in the global surface ocean inform our understanding of marine biogeochemical processes such as nitrogen fixation and primary production. The spatial distribution of DOP concentrations in the surface ocean reflect production by primary producers and consumption as an organic nutrient by phytoplankton including diazotrophs and other microbes, as well as other loss processes such as photolysis. Compared to dissolved organic carbon and nitrogen, however, relatively few marine DOP concentration measurements have been made, largely due to the lack of automated analysis techniques. Here we present a database of marine DOP concentration measurements (DOPv2021) that includes new (n = 730) and previously published (n = 3140) observations made over the last ~30 years (1990-2021), including 1751 observations in the upper 50 m. This dataset encompasses observations from all major ocean basins including the poorly represented Indian, South Pacific, and Southern Oceans and provides insight into spatial distributions of DOP in the ocean. It is also valuable for researchers who work on marine primary production and nitrogen fixation.
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Affiliation(s)
- Zhou Liang
- grid.255986.50000 0004 0472 0419Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL USA
| | - Kelly McCabe
- grid.214458.e0000000086837370Copperative Institute for Great Lakes Research (CIGLR), School for Environment and Sustainability, University of Michigan, Ann Arbor, MI USA
| | - Sarah E. Fawcett
- grid.7836.a0000 0004 1937 1151Department of Oceanography, Faculty of Science, University of Cape Town, Cape Town, South Africa ,grid.7836.a0000 0004 1937 1151Marine and Antarctic Research centre for Innovation and Sustainability (MARIS), University of Cape Town, Cape Town, South Africa
| | - Heather J. Forrer
- grid.255986.50000 0004 0472 0419Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL USA
| | - Fuminori Hashihama
- grid.412785.d0000 0001 0695 6482Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Catherine Jeandel
- grid.503277.40000 0004 0384 4620LEGOS, Université de Toulouse, CNRS, IRD, CNES, UPS, Toulouse, France
| | - Dario Marconi
- grid.16750.350000 0001 2097 5006Department of Geosciences, Princeton University, Princeton, NJ USA
| | - Hélène Planquette
- grid.463763.30000 0004 0638 0577Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280 Plouzane, France
| | - Mak A. Saito
- grid.56466.370000 0004 0504 7510Woods Hole Oceanographic Institution, Falmouth, MA USA
| | - Jill A. Sohm
- grid.42505.360000 0001 2156 6853Department of Biological Sciences, University of Southern California, Los Angeles, CA USA
| | - Rachel K. Thomas
- grid.255986.50000 0004 0472 0419Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL USA
| | - Robert T. Letscher
- grid.167436.10000 0001 2192 7145Earth Sciences & Ocean Process Analysis Laboratory, University of New Hampshire, Durham, NH USA
| | - Angela N. Knapp
- grid.255986.50000 0004 0472 0419Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL USA
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3
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Environmental nitrogen and phosphorus nutrient variability triggers intracellular resource reallocation in Gracilariopsis lemaneiformis (Rhodophyta). ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102778] [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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4
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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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5
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Cytoklepty in the plankton: A host strategy to optimize the bioenergetic machinery of endosymbiotic algae. Proc Natl Acad Sci U S A 2021; 118:2025252118. [PMID: 34215695 DOI: 10.1073/pnas.2025252118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Endosymbioses have shaped the evolutionary trajectory of life and remain ecologically important. Investigating oceanic photosymbioses can illuminate how algal endosymbionts are energetically exploited by their heterotrophic hosts and inform on putative initial steps of plastid acquisition in eukaryotes. By combining three-dimensional subcellular imaging with photophysiology, carbon flux imaging, and transcriptomics, we show that cell division of endosymbionts (Phaeocystis) is blocked within hosts (Acantharia) and that their cellular architecture and bioenergetic machinery are radically altered. Transcriptional evidence indicates that a nutrient-independent mechanism prevents symbiont cell division and decouples nuclear and plastid division. As endosymbiont plastids proliferate, the volume of the photosynthetic machinery volume increases 100-fold in correlation with the expansion of a reticular mitochondrial network in close proximity to plastids. Photosynthetic efficiency tends to increase with cell size, and photon propagation modeling indicates that the networked mitochondrial architecture enhances light capture. This is accompanied by 150-fold higher carbon uptake and up-regulation of genes involved in photosynthesis and carbon fixation, which, in conjunction with a ca.15-fold size increase of pyrenoids demonstrates enhanced primary production in symbiosis. Mass spectrometry imaging revealed major carbon allocation to plastids and transfer to the host cell. As in most photosymbioses, microalgae are contained within a host phagosome (symbiosome), but here, the phagosome invaginates into enlarged microalgal cells, perhaps to optimize metabolic exchange. This observation adds evidence that the algal metamorphosis is irreversible. Hosts, therefore, trigger and benefit from major bioenergetic remodeling of symbiotic microalgae with potential consequences for the oceanic carbon cycle. Unlike other photosymbioses, this interaction represents a so-called cytoklepty, which is a putative initial step toward plastid acquisition.
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6
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Zhang K, Li J, Zhou Z, Huang R, Lin S. Roles of Alkaline Phosphatase PhoA in Algal Metabolic Regulation under Phosphorus-replete Conditions. JOURNAL OF PHYCOLOGY 2021; 57:703-707. [PMID: 33608874 DOI: 10.1111/jpy.13151] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/24/2021] [Accepted: 02/10/2021] [Indexed: 06/12/2023]
Abstract
Alkaline phosphatase (AP) in plants and algae is known to hydrolyze dissolved organophosphate (DOP) in order to obtain phosphorus when the preferred dissolved inorganic phosphorus (DIP) is present in limited supply. By conducting comparative analyses of physiologies and transcriptomes on a mutant of PhoA type AP (mPhoA) and wild type (WT) of the marine diatom Phaeodactylum tricornutum CCAP 1055/1 under P-replete and P-depleted conditions, we document other roles of this gene than DOP scavenging. PhoA mutation created by CRISPR/Cas9 diminished its DOP hydrolase activity but led to significant increases in cellular contents of pigment, carbon, and lipids, photosynthetic rate, growth rate, and the transcriptional levels of their corresponding metabolic pathways. All the results in concert indicate that besides P-nutrient scavenging under DIP deficiency, AP also functions, under the P-replete condition, to constrain pigment biosynthesis, photosynthesis, fatty acid biosynthesis, and cell division. These functions have important implications in maintaining metabolic homeostasis and preventing premature cell division.
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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, Connecticut, USA
| | - Jiashun Li
- 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
| | - Ruiping Huang
- 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, Connecticut, USA
- Laboratory of Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
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7
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Li H, Li L, Yu L, Yang X, Shi X, Wang J, Li J, Lin S. Transcriptome profiling reveals versatile dissolved organic nitrogen utilization, mixotrophy, and N conservation in the dinoflagellate Prorocentrum shikokuense under N deficiency. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 763:143013. [PMID: 33203560 DOI: 10.1016/j.scitotenv.2020.143013] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
Harmful algal blooms formed by certain dinoflagellate species often occur when environmental nitrogen nutrients (N) are limited. However, the molecular mechanism by which dinoflagellates adapt to low N environments is poorly understood. In this study, we characterized the transcriptomic responses of Prorocentrum shikokuense to N deficiency, along with its physiological impact. Under N deficiency, P. shikokuense cultures exhibited growth inhibition, a reduction in cell size, and decreases in cellular chlorophyll a and nitrogen contents but an increase in carbon content. Accordingly, gene expression profiles indicated that carbon fixation and catabolism and fatty acid metabolism were enhanced. Transporter genes of nitrate/nitrite, ammonium, urea, and amino acids were significantly upregulated, indicating that P. shikokuense cells invest to enhance the uptake of available dissolved N. Notably, upregulated genes included those involved in endocytosis and phagosomes, evidence that P. shikokuense is a mixotrophic organism that activates phagotrophy to overcome N deficiency. Additionally, vacuolar amino acid transporters, the urea cycle, and urea hydrolysis genes were upregulated, indicating N recycling within the cells under N deficiency. Our study indicates that P. shikokuense copes with N deficiency by economizing nitrogen use and adopting multiple strategies to maximize N acquisition and reuse while maintaining carbon fixation. The remarkable low N adaptability may confer competitive advantages to P. shikokuense for forming harmful blooms in DIN-limited environments.
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Affiliation(s)
- Hongfei Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; Department of Marine Sciences, University of Connecticut, Groton CT06405, USA
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xiaohong Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xinguo Shi
- College of Biological Science and Engineering, Fuzhou University, Fujian 350116, China
| | - Jierui Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Jiashun Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; Department of Marine Sciences, University of Connecticut, Groton CT06405, USA..
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Kumar Sharma A, Mühlroth A, Jouhet J, Maréchal E, Alipanah L, Kissen R, Brembu T, Bones AM, Winge P. The Myb-like transcription factor phosphorus starvation response (PtPSR) controls conditional P acquisition and remodelling in marine microalgae. THE NEW PHYTOLOGIST 2020; 225:2380-2395. [PMID: 31598973 DOI: 10.1111/nph.16248] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 09/29/2019] [Indexed: 05/10/2023]
Abstract
Phosphorus (P) is one of the limiting macronutrients for algal growth in marine environments. Microalgae have developed adaptation mechanisms to P limitation that involve remodelling of internal phosphate resources and accumulation of lipids. Here, we used in silico analyses to identify the P-stress regulator PtPSR (Phaeodactylum tricornutum phosphorus starvation response) in the diatom P. tricornutum. ptpsr mutant lines were generated using gene editing and characterised by various molecular, genetics and biochemical tools. PtPSR belongs to a clade of Myb transcription factors that are conserved in stramenopiles and distantly related to plant P-stress regulators. PtPSR bound specifically to a conserved cis-regulatory element found in the regulatory region of P-stress-induced genes. ptpsr knockout mutants showed reduction in cell growth under P limitation. P-stress responses were impaired in ptpsr mutants compared with wild-type, including reduced induction of P-stress response genes, near to complete loss of alkaline phosphatase activity and reduced phospholipid degradation. We conclude that PtPSR is a key transcription factor influencing P scavenging, phospholipid remodelling and cell growth in adaptation to P stress in diatoms.
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Affiliation(s)
- Amit Kumar Sharma
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Alice Mühlroth
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire Végétale, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, Institut National de la Recherche Agronomique, Université Grenoble Alpes, 38000, Grenoble, France
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire Végétale, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, Institut National de la Recherche Agronomique, Université Grenoble Alpes, 38000, Grenoble, France
| | - Leila Alipanah
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Ralph Kissen
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Tore Brembu
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Atle M Bones
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Per Winge
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
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9
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Ou L, Qin X, Shi X, Feng Q, Zhang S, Lu S, Qi Y. Alkaline phosphatase activities and regulation in three harmful Prorocentrum species from the coastal waters of the East China Sea. MICROBIAL ECOLOGY 2020; 79:459-471. [PMID: 31267157 DOI: 10.1007/s00248-019-01399-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 06/07/2019] [Indexed: 06/09/2023]
Abstract
Harmful blooms of Prorocentrum donghaiense occur annually in the phosphorus-scarce coastal waters of the East China Sea (ECS). The enzymatic activities of alkaline phosphatase (AP) and its regulation by external phosphorus were studied during a P. donghaiense bloom in this area. The AP characteristics of P. donghaiense was further compared with Prorocentrum minimum and Prorocentrum micans in monocultures with both bulk and single-cell enzyme-labeled fluorescence AP assays. Concentrations of dissolved inorganic phosphorus (DIP) varied between 0.04 and 0.73 μmol l-1, with more than half recording stations registering concentrations below 0.10 μmol l-1. Concentrations of dissolved organic phosphorus (DOP) were comparable or even higher than those of DIP. P. donghaiense suffered phosphorus stress and expressed abundant AP, especially when DIP was lower than 0.10 μmol l-1. The AP activities showed a negative correlation with DIP but a positive correlation with DOP. The AP activities were also regulated by internal phosphorus pool. The sharp increase in AP activities was observed until cellular phosphorus was exhausted. Most AP of P. donghaiense was located on the cell surface and some were released into the water with time. Compared with P. minimum and P. micans, P. donghaiense showed a higher AP affinity for organic phosphorus substrates, a more efficient and energy-saving AP expression quantity as a response to phosphorus deficiency. The unique AP characteristic of P. donghaiense suggests that it benefits from the efficient utilization of DOP, and outcompete other species in the phosphorus-scarce ECS.
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Affiliation(s)
- Linjian Ou
- Research Center of Harmful Algae and Marine Biology, and Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Jinan University, Guangzhou, 510632, People's Republic of China.
| | - Xianling Qin
- Research Center of Harmful Algae and Marine Biology, and Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Jinan University, Guangzhou, 510632, People's Republic of China
- Guangxi Key Laboratory of Marine Environmental Science, and Guangxi Academy of Sciences, Nanning, 530007, People's Republic of China
| | - Xiaoyong Shi
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, 266100, People's Republic of China
- National Marine Hazard Mitigation Service, Beijing, 100194, People's Republic of China
| | - Qingliang Feng
- Research Center of Harmful Algae and Marine Biology, and Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Shuwen Zhang
- Research Center of Harmful Algae and Marine Biology, and Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Songhui Lu
- Research Center of Harmful Algae and Marine Biology, and Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Jinan University, Guangzhou, 510632, People's Republic of China.
| | - Yuzao Qi
- Research Center of Harmful Algae and Marine Biology, and Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Jinan University, Guangzhou, 510632, People's Republic of China
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10
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Li T, Yu L, Song B, Song Y, Li L, Lin X, Lin S. Genome Improvement and Core Gene Set Refinement of Fugacium kawagutii. Microorganisms 2020; 8:microorganisms8010102. [PMID: 31940756 PMCID: PMC7023079 DOI: 10.3390/microorganisms8010102] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/01/2020] [Accepted: 01/08/2020] [Indexed: 01/15/2023] Open
Abstract
Cataloging an accurate functional gene set for the Symbiodiniaceae species is crucial for addressing biological questions of dinoflagellate symbiosis with corals and other invertebrates. To improve the gene models of Fugacium kawagutii, we conducted high-throughput chromosome conformation capture (Hi-C) for the genome and Illumina combined with PacBio sequencing for the transcriptome to achieve a new genome assembly and gene prediction. A 0.937-Gbp assembly of F. kawagutii were obtained, with a N50 > 13 Mbp and the longest scaffold of 121 Mbp capped with telomere motif at both ends. Gene annotation produced 45,192 protein-coding genes, among which, 11,984 are new compared to previous versions of the genome. The newly identified genes are mainly enriched in 38 KEGG pathways including N-Glycan biosynthesis, mRNA surveillance pathway, cell cycle, autophagy, mitophagy, and fatty acid synthesis, which are important for symbiosis, nutrition, and reproduction. The newly identified genes also included those encoding O-methyltransferase (O-MT), 3-dehydroquinate synthase, homologous-pairing protein 2-like (HOP2) and meiosis protein 2 (MEI2), which function in mycosporine-like amino acids (MAAs) biosynthesis and sexual reproduction, respectively. The improved version of the gene set (Fugka_Geneset _V3) raised transcriptomic read mapping rate from 33% to 54% and BUSCO match from 29% to 55%. Further differential gene expression analysis yielded a set of stably expressed genes under variable trace metal conditions, of which 115 with annotated functions have recently been found to be stably expressed under three other conditions, thus further developing the "core gene set" of F. kawagutii. This improved genome will prove useful for future Symbiodiniaceae transcriptomic, gene structure, and gene expression studies, and the refined "core gene set" will be a valuable resource from which to develop reference genes for gene expression studies.
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Affiliation(s)
- Tangcheng Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (T.L.); (L.Y.); (L.L.)
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (T.L.); (L.Y.); (L.L.)
| | - Bo Song
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China;
| | - Yue Song
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China;
| | - Ling Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (T.L.); (L.Y.); (L.L.)
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (T.L.); (L.Y.); (L.L.)
- Correspondence: (X.L.); (S.L.)
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (T.L.); (L.Y.); (L.L.)
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao 266237, China
- Correspondence: (X.L.); (S.L.)
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Non-Conventional Metal Ion Cofactor Requirement of Dinoflagellate Alkaline Phosphatase and Translational Regulation by Phosphorus Limitation. Microorganisms 2019; 7:microorganisms7080232. [PMID: 31374942 PMCID: PMC6723241 DOI: 10.3390/microorganisms7080232] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/15/2019] [Accepted: 07/30/2019] [Indexed: 12/30/2022] Open
Abstract
Alkaline phosphatase (AP) enables marine phytoplankton to utilize dissolved organic phosphorus (DOP) when dissolved inorganic phosphate (DIP) is depleted in the ocean. Dinoflagellate AP (Dino-AP) represents a newly classified atypical type of AP, PhoAaty. Despite While being a conventional AP, PhoAEC is known to recruit Zn2+ and Mg2+ in the active center, and the cofactors required by PhoAaty have been contended and remain unclear. In this study, we investigated the metal ion requirement of AP in five dinoflagellate species. After AP activity was eliminated by using EDTA to chelate metal ions, the enzymatic activity could be recovered by the supplementation of Ca2+, Mg2+ and Mn2+ in all cases but not by that of Zn2+. Furthermore, the same analysis conducted on the purified recombinant ACAAP (AP of Amphidinium carterae) verified that the enzyme could be activated by Ca2+, Mg2+, and Mn2+ but not Zn2+. We further developed an antiserum against ACAAP, and a western blot analysis using this antibody showed a remarkable up-regulation of ACAAP under a phosphate limitation, consistent with elevated AP activity. The unconventional metal cofactor requirement of Dino-AP may be an adaptation to trace metal limitations in the ocean, which warrants further research to understand the niche differentiation between dinoflagellates and other phytoplankton that use Zn–Mg AP in utilizing DOP.
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