101
|
Alipanah L, Winge P, Rohloff J, Najafi J, Brembu T, Bones AM. Molecular adaptations to phosphorus deprivation and comparison with nitrogen deprivation responses in the diatom Phaeodactylum tricornutum. PLoS One 2018; 13:e0193335. [PMID: 29474408 PMCID: PMC5825098 DOI: 10.1371/journal.pone.0193335] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 02/08/2018] [Indexed: 01/12/2023] Open
Abstract
Phosphorus, an essential element for all living organisms, is a limiting nutrient in many regions of the ocean due to its fast recycling. Changes in phosphate (Pi) availability in aquatic systems affect diatom growth and productivity. We investigated the early adaptive mechanisms in the marine diatom Phaeodactylum tricornutum to P deprivation using a combination of transcriptomics, metabolomics, physiological and biochemical experiments. Our analysis revealed strong induction of gene expression for proteins involved in phosphate acquisition and scavenging, and down-regulation of processes such as photosynthesis, nitrogen assimilation and nucleic acid and ribosome biosynthesis. P deprivation resulted in alterations of carbon allocation through the induction of the pentose phosphate pathway and cytosolic gluconeogenesis, along with repression of the Calvin cycle. Reorganization of cellular lipids was indicated by coordinated induced expression of phospholipases, sulfolipid biosynthesis enzymes and a putative betaine lipid biosynthesis enzyme. A comparative analysis of nitrogen- and phosphorus-deprived P. tricornutum revealed both common and distinct regulation patterns in response to phosphate and nitrate stress. Regulation of central carbon metabolism and amino acid metabolism was similar, whereas unique responses were found in nitrogen assimilation and phosphorus scavenging in nitrogen-deprived and phosphorus-deprived cells, respectively.
Collapse
Affiliation(s)
- Leila Alipanah
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Per Winge
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jens Rohloff
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Javad Najafi
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Tore Brembu
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Atle M. Bones
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
- * E-mail:
| |
Collapse
|
102
|
Ji N, Lin L, Li L, Yu L, Zhang Y, Luo H, Li M, Shi X, Wang DZ, Lin S. Metatranscriptome analysis reveals environmental and diel regulation of a Heterosigma akashiwo
(raphidophyceae) bloom. Environ Microbiol 2018; 20:1078-1094. [DOI: 10.1111/1462-2920.14045] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 01/09/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Nanjing Ji
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
- Department of Marine Sciences; University of Connecticut; Groton CT 06340 USA
| | - Lingxiao Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Yaqun Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Hao Luo
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Meizhen Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Xinguo Shi
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
- Department of Marine Sciences; University of Connecticut; Groton CT 06340 USA
| |
Collapse
|
103
|
Burge DRL, Edlund MB, Frisch D. Paleolimnology and resurrection ecology: The future of reconstructing the past. Evol Appl 2018; 11:42-59. [PMID: 29302271 PMCID: PMC5748527 DOI: 10.1111/eva.12556] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 09/08/2017] [Indexed: 12/21/2022] Open
Abstract
Paleolimnologists have utilized lake sediment records to understand historical lake and landscape development, timing and magnitude of environmental change at lake, watershed, regional and global scales, and as historical datasets to target watershed and lake management. Resurrection ecologists have long recognized lake sediments as sources of viable propagules ("seed or egg banks") with which to explore questions of community ecology, ecological response, and evolutionary ecology. Most researchers consider Daphnia as the primary model organism in these efforts, but many other aquatic biota, from viruses to macrophytes, similarly produce viable propagules that are incorporated in the sediment record but have been underutilized in resurrection ecology. The common goals shared by these two disciplines have led to mutualistic and synergistic collaborations-a development that must be encouraged to expand. We give an overview of the achievements of paleolimnology and the reconstruction of environmental history of lakes, review the untapped diversity of aquatic organisms that produce dormant propagules, compare Daphnia as a model of resurrection ecology with other organisms amenable to resurrection studies, especially diatoms, and consider new research directions that represent the nexus of these two fields.
Collapse
Affiliation(s)
- David R. L. Burge
- St. Croix Watershed Research StationScience Museum of MinnesotaMarine on St. CroixMNUSA
- Water Resources Science Graduate ProgramUniversity of MinnesotaSt. PaulMNUSA
| | - Mark B. Edlund
- St. Croix Watershed Research StationScience Museum of MinnesotaMarine on St. CroixMNUSA
| | - Dagmar Frisch
- School of BiosciencesUniversity of BirminghamBirminghamUK
| |
Collapse
|
104
|
Stukenberg D, Zauner S, Dell’Aquila G, Maier UG. Optimizing CRISPR/Cas9 for the Diatom Phaeodactylum tricornutum. FRONTIERS IN PLANT SCIENCE 2018; 9:740. [PMID: 29928285 PMCID: PMC5998643 DOI: 10.3389/fpls.2018.00740] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 05/15/2018] [Indexed: 05/18/2023]
Abstract
CRISPR/Cas9 is a powerful tool for genome editing. We constructed an easy-to-handle expression vector for application in the model organism Phaeodactylum tricornutum and tested its capabilities in order to apply CRISPR/Cas9 technology for our purpose. In our experiments, we targeted two different genes, screened for mutations and analyzed mutated diatoms in a three-step process. In the end, we identified cells, showing either monoallelic or homo-biallelic targeted mutations. Thus, we confirm that application of the CRISPR/Cas9 system for P. tricornutum is very promising, although, as discussed, overlooked pitfalls have to be considered.
Collapse
Affiliation(s)
- Daniel Stukenberg
- Department for Cell Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Stefan Zauner
- Department for Cell Biology, Philipps-Universität Marburg, Marburg, Germany
| | | | - Uwe G. Maier
- Department for Cell Biology, Philipps-Universität Marburg, Marburg, Germany
- LOEWE-Zentrum für Synthetische Mikrobiologie (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
- *Correspondence: Uwe G. Maier,
| |
Collapse
|
105
|
Mühlroth A, Winge P, El Assimi A, Jouhet J, Maréchal E, Hohmann-Marriott MF, Vadstein O, Bones AM. Mechanisms of Phosphorus Acquisition and Lipid Class Remodeling under P Limitation in a Marine Microalga. PLANT PHYSIOLOGY 2017; 175:1543-1559. [PMID: 29051196 PMCID: PMC5717724 DOI: 10.1104/pp.17.00621] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 10/17/2017] [Indexed: 05/03/2023]
Abstract
Molecular mechanisms of phosphorus (P) limitation are of great interest for understanding algal production in aquatic ecosystems. Previous studies point to P limitation-induced changes in lipid composition. As, in microalgae, the molecular mechanisms of this specific P stress adaptation remain unresolved, we reveal a detailed phospholipid-recycling scheme in Nannochloropsis oceanica and describe important P acquisition genes based on highly corresponding transcriptome and lipidome data. Initial responses to P limitation showed increased expression of genes involved in P uptake and an expansion of the P substrate spectrum based on purple acid phosphatases. Increase in P trafficking displayed a rearrangement between compartments by supplying P to the chloroplast and carbon to the cytosol for lipid synthesis. We propose a novel phospholipid-recycling scheme for algae that leads to the rapid reduction of phospholipids and synthesis of the P-free lipid classes. P mobilization through membrane lipid degradation is mediated mainly by two glycerophosphoryldiester phosphodiesterases and three patatin-like phospholipases A on the transcriptome level. To compensate for low phospholipids in exponential growth, N. oceanica synthesized sulfoquinovosyldiacylglycerol and diacylglyceroltrimethylhomoserine. In this study, it was shown that an N. oceanica strain has a unique repertoire of genes that facilitate P acquisition and the degradation of phospholipids compared with other stramenopiles. The novel phospholipid-recycling scheme opens new avenues for metabolic engineering of lipid composition in algae.
Collapse
Affiliation(s)
- Alice Mühlroth
- Department of Biology, NTNU Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Per Winge
- Department of Biology, NTNU Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Aimen El Assimi
- Department of Biology, NTNU 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
| | - Martin F Hohmann-Marriott
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Olav Vadstein
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Atle M Bones
- Department of Biology, NTNU Norwegian University of Science and Technology, 7491 Trondheim, Norway
| |
Collapse
|
106
|
Sherman RE, Chowdhury PR, Baker KD, Weider LJ, Jeyasingh PD. Genotype-specific relationships among phosphorus use, growth and abundance in Daphnia pulicaria. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170770. [PMID: 29308224 PMCID: PMC5749992 DOI: 10.1098/rsos.170770] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 11/06/2017] [Indexed: 06/07/2023]
Abstract
The framework ecological stoichiometry uses elemental composition of species to make predictions about growth and competitive ability in defined elemental supply conditions. Although intraspecific differences in stoichiometry have been observed, we have yet to understand the mechanisms generating and maintaining such variation. We used variation in phosphorus (P) content within a Daphnia species to test the extent to which %P can explain variation in growth and competition. Further, we measured 33P kinetics (acquisition, assimilation, incorporation and retention) to understand the extent to which such variables improved predictions. Genotypes showed significant variation in P content, 33P kinetics and growth rate. P content alone was a poor predictor of growth rate and competitive ability. While most genotypes exhibited the typical growth penalty under P limitation, a few varied little in growth between P diets. These observations indicate that some genotypes can maintain growth under P-limited conditions by altering P use, suggesting that decomposing P content of an individual into physiological components of P kinetics will improve stoichiometric models. More generally, attention to the interplay between nutrient content and nutrient-use is required to make inferences regarding the success of genotypes in defined conditions of nutrient supply.
Collapse
Affiliation(s)
- Ryan E. Sherman
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | | | - Kristina D. Baker
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Lawrence J. Weider
- Department of Biology, Program in Ecology and Evolutionary Biology, University of Oklahoma, Norman, OK, USA
| | - Punidan D. Jeyasingh
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
| |
Collapse
|
107
|
Luo H, Lin X, Li L, Lin L, Zhang C, Lin S. Transcriptomic and physiological analyses of the dinoflagellate Karenia mikimotoi reveal non-alkaline phosphatase-based molecular machinery of ATP utilisation. Environ Microbiol 2017; 19:4506-4518. [PMID: 28856827 DOI: 10.1111/1462-2920.13899] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/11/2017] [Accepted: 08/15/2017] [Indexed: 11/28/2022]
Abstract
The ability to utilize dissolved organic phosphorus (DOP) is important for phytoplankton to survive the scarcity of dissolved inorganic phosphorus (DIP), and alkaline phosphatase (AP) has been the major research focus as a facilitating mechanism. Here, we employed a unique molecular ecological approach and conducted a broader search for underpinning molecular mechanisms of adenosine triphosphate (ATP) utilisation. Cultures of the dinoflagellate Karenia mikimotoi were set up in L1 medium (+P), DIP-depleted L1 medium (-P) and ATP-replacing-DIP medium (ATP). Differential gene expression was profiled for ATP and +P cultures using suppression subtractive hybridisation (SSH) followed by 454 pyrosequencing, and RT-qPCR methods. We found that ATP supported a similar growth rate and cell yield as L1 medium and observed DIP release from ATP into the medium, suggesting that K. mikimotoi cells were expressing extracellular hydrolases to hydrolyse ATP. However, our SSH, qPCR and enzymatic activity assays indicated that 5'-nucleotidase (5NT), rather than AP, was responsible for ATP hydrolysis. Further gene expression analyses uncovered that intercellular purine metabolism was significantly changed following the utilisation of ATP. Our findings reveal a multi-faceted machinery regulating ATP utilisation and P metabolism in K. mikimotoi, and underscore AP activity is not the exclusive indicator of DOP utilisation.
Collapse
Affiliation(s)
- Hao Luo
- State Key Laboratory of Marine Environmental Science, Department of Marine Biological Sciences and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science, Department of Marine Biological Sciences and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, Department of Marine Biological Sciences and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Lingxiao Lin
- State Key Laboratory of Marine Environmental Science, Department of Marine Biological Sciences and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Chao Zhang
- Department of Biochemistry, Province Key Laboratory of Biochip, School of Basic Medical Science and Institute of Genetic Engineering, Southern Medical University, Guangzhou, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, Department of Marine Biological Sciences and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China.,Department of Marine Sciences, University of Connecticut, Groton, CT 06405, USA
| |
Collapse
|
108
|
Lin Q, Liang JR, Huang QQ, Luo CS, Anderson DM, Bowler C, Chen CP, Li XS, Gao YH. Differential cellular responses associated with oxidative stress and cell fate decision under nitrate and phosphate limitations in Thalassiosira pseudonana: Comparative proteomics. PLoS One 2017; 12:e0184849. [PMID: 28910417 PMCID: PMC5599023 DOI: 10.1371/journal.pone.0184849] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/31/2017] [Indexed: 01/09/2023] Open
Abstract
Diatoms are important components of marine ecosystems and contribute greatly to the world's primary production. Despite their important roles in ecosystems, the molecular basis of how diatoms cope with oxidative stress caused by nutrient fluctuations remains largely unknown. Here, an isobaric tags for relative and absolute quantitation (iTRAQ) proteomic method was coupled with a series of physiological and biochemical techniques to explore oxidative stress- and cell fate decision-related cellular and metabolic responses of the diatom Thalassiosira pseudonana to nitrate (N) and inorganic phosphate (P) stresses. A total of 1151 proteins were detected; 122 and 56 were significantly differentially expressed from control under N- and P-limited conditions, respectively. In N-limited cells, responsive proteins were related to reactive oxygen species (ROS) accumulation, oxidative stress responses and cell death, corresponding to a significant decrease in photosynthetic efficiency, marked intracellular ROS accumulation, and caspase-mediated programmed cell death activation. None of these responses were identified in P-limited cells; however, a significant up-regulation of alkaline phosphatase proteins was observed, which could be the major contributor for P-limited cells to cope with ambient P deficiency. These findings demonstrate that fundamentally different metabolic responses and cellular regulations are employed by the diatom in response to different nutrient stresses and to keep the cells viable.
Collapse
Affiliation(s)
- Qun Lin
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Jun-Rong Liang
- School of Life Sciences, Xiamen University, Xiamen, China
- Key Laboratory of the Coastal and Wetland Ecosystems (Xiamen University), Ministry of Education, Xiamen, China
- * E-mail:
| | | | - Chun-Shan Luo
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Donald M. Anderson
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
| | - Chris Bowler
- Ecology and Evolutionary Biology Section, CNRS UMR8197 INSERM U1024, Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, 46 rue d’Ulm, Paris, France
| | - Chang-Ping Chen
- School of Life Sciences, Xiamen University, Xiamen, China
- Key Laboratory of the Coastal and Wetland Ecosystems (Xiamen University), Ministry of Education, Xiamen, China
| | - Xue-Song Li
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Ya-Hui Gao
- School of Life Sciences, Xiamen University, Xiamen, China
- Key Laboratory of the Coastal and Wetland Ecosystems (Xiamen University), Ministry of Education, Xiamen, China
| |
Collapse
|
109
|
Haley ST, Alexander H, Juhl AR, Dyhrman ST. Transcriptional response of the harmful raphidophyte Heterosigma akashiwo to nitrate and phosphate stress. HARMFUL ALGAE 2017; 68:258-270. [PMID: 28962986 DOI: 10.1016/j.hal.2017.07.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 06/30/2017] [Accepted: 07/01/2017] [Indexed: 06/07/2023]
Abstract
The marine eukaryotic alga Heterosigma akashiwo (Raphidophyceae) is known for forming ichthyotoxic harmful algal blooms (HABs). In the past 50 years, H. akashiwo blooms have increased, occurring globally in highly eutrophic coastal and estuarine systems. These systems often incur dramatic physicochemical changes, including macronutrient (nitrogen and phosphorus) enrichment and depletion, on short timescales. Here, H. akashiwo cultures grown under nutrient replete, low N and low P growth conditions were examined for changes in biochemical and physiological characteristics in concert with transcriptome sequencing to provide a mechanistic perspective on the metabolic processes involved in responding to N and P stress. There was a marked difference in the overall transcriptional pattern between low N and low P transcriptomes. Both nutrient stresses led to significant changes in the abundance of thousands of contigs related to a wide diversity of metabolic pathways, with limited overlap between the transcriptomic responses to low N and low P. Enriched contigs under low N included many related to nitrogen metabolism, acquisition, and transport. In addition, metabolic modules like photosynthesis and carbohydrate metabolism changed significantly under low N, coincident with treatment-specific changes in photosynthetic efficiency and particulate carbohydrate content. P-specific contigs responsible for P transport and organic P use were more enriched in the low P treatment than in the replete control and low N treatment. These results provide new insight into the genetic mechanisms that distinguish how this HAB species responds to these two common nutrient stresses, and the results can inform future field studies, linking transcriptional patterns to the physiological ecology of H. akashiwo in situ.
Collapse
Affiliation(s)
- Sheean T Haley
- Columbia University, Lamont-Doherty Earth Observatory, Palisades, NY, USA
| | - Harriet Alexander
- Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Andrew R Juhl
- Columbia University, Lamont-Doherty Earth Observatory, Palisades, NY, USA; Columbia University, Department of Earth and Environmental Sciences, Palisades, NY, USA
| | - Sonya T Dyhrman
- Columbia University, Lamont-Doherty Earth Observatory, Palisades, NY, USA; Columbia University, Department of Earth and Environmental Sciences, Palisades, NY, USA.
| |
Collapse
|
110
|
Jian J, Zeng D, Wei W, Lin H, Li P, Liu W. The Combination of RNA and Protein Profiling Reveals the Response to Nitrogen Depletion in Thalassiosira pseudonana. Sci Rep 2017; 7:8989. [PMID: 28827639 PMCID: PMC5566445 DOI: 10.1038/s41598-017-09546-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 07/24/2017] [Indexed: 12/21/2022] Open
Abstract
Nitrogen (N) is essential for the growth of algae, and its concentration varies greatly in the ocean, which has been regarded as a limitation for phytoplankton growth. Despite its great importance, most of the existing studies on the mechanisms underlying the effects of N on diatoms have focused on physiology, biochemistry and a few target genes and have rarely involved whole genomic analyses. Therefore, in this study, we integrated physiological data with RNA and protein profiling data to reveal the response strategy of Thalassiosira pseudonana under N-depleted conditions. Physiological measurements indicated that the cell growth capacity and chlorophyll content of the cells decreased, as did the expression of photosynthesis- and chlorophyll biosynthesis-related genes or proteins. The RNA-Seq profile results showed that T. pseudonana responded to N deprivation through increases in glycolysis, the TCA cycle and N metabolism as well as down-regulation in the Calvin cycle, gluconeogenesis, pentose phosphate, oxidative phosphorylation and lipid synthesis. These results provide a basic understanding for further research addressing how N affects phytoplankton in terms of genomics.
Collapse
Affiliation(s)
- Jianbo Jian
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Dezhi Zeng
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Wei Wei
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Hongmin Lin
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Ping Li
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. China.
| | - Wenhua Liu
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. China.
| |
Collapse
|
111
|
Harke MJ, Juhl AR, Haley ST, Alexander H, Dyhrman ST. Conserved Transcriptional Responses to Nutrient Stress in Bloom-Forming Algae. Front Microbiol 2017; 8:1279. [PMID: 28769884 PMCID: PMC5513979 DOI: 10.3389/fmicb.2017.01279] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/26/2017] [Indexed: 11/13/2022] Open
Abstract
The concentration and composition of bioavailable nitrogen (N) and phosphorus (P) in the upper ocean shape eukaryotic phytoplankton communities and influence their physiological responses. Phytoplankton are known to exhibit similar physiological responses to limiting N and P conditions such as decreased growth rates, chlorosis, and increased assimilation of N and P. Are these responses similar at the molecular level across multiple species? To interrogate this question, five species from biogeochemically important, bloom-forming taxa (Bacillariophyta, Dinophyta, and Haptophyta) were grown under similar low N, low P, and replete nutrient conditions to identify transcriptional patterns and associated changes in biochemical pools related to N and P stress. Metabolic profiles, revealed through the transcriptomes of these taxa, clustered together based on species rather than nutrient stressor, suggesting that the global metabolic response to nutrient stresses was largely, but not exclusively, species-specific. Nutrient stress led to few transcriptional changes in the two dinoflagellates, consistent with other research. An orthologous group analysis examined functionally conserved (i.e., similarly changed) responses to nutrient stress and therefore focused on the diatom and haptophytes. Most conserved ortholog changes were specific to a single nutrient treatment, but a small number of orthologs were similarly changed under both N and P stress in 2 or more species. Many of these orthologs were related to photosynthesis and may represent generalized stress responses. A greater number of orthologs were conserved across more than one species under low P compared to low N. Screening the conserved orthologs for functions related to N and P metabolism revealed increased relative abundance of orthologs for nitrate, nitrite, ammonium, and amino acid transporters under N stress, and increased relative abundance of orthologs related to acquisition of inorganic and organic P substrates under P stress. Although the global transcriptional responses were dominated by species-specific changes, the analysis of conserved responses revealed functional similarities in resource acquisition pathways among different phytoplankton taxa. This overlap in nutrient stress responses observed among species may be useful for tracking the physiological ecology of phytoplankton field populations.
Collapse
Affiliation(s)
- Matthew J Harke
- Lamont-Doherty Earth Observatory, Columbia UniversityPalisades, NY, United States
| | - Andrew R Juhl
- Lamont-Doherty Earth Observatory, Columbia UniversityPalisades, NY, United States.,Department of Earth and Environmental Sciences, Columbia UniversityPalisades, NY, United States
| | - Sheean T Haley
- Lamont-Doherty Earth Observatory, Columbia UniversityPalisades, NY, United States
| | - Harriet Alexander
- Department of Population Health and Reproduction, University of California, DavisDavis, CA, United States
| | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Columbia UniversityPalisades, NY, United States.,Department of Earth and Environmental Sciences, Columbia UniversityPalisades, NY, United States
| |
Collapse
|
112
|
Moore ER, Bullington BS, Weisberg AJ, Jiang Y, Chang J, Halsey KH. Morphological and transcriptomic evidence for ammonium induction of sexual reproduction in Thalassiosira pseudonana and other centric diatoms. PLoS One 2017; 12:e0181098. [PMID: 28686696 PMCID: PMC5501676 DOI: 10.1371/journal.pone.0181098] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/26/2017] [Indexed: 11/19/2022] Open
Abstract
The reproductive strategy of diatoms includes asexual and sexual phases, but in many species, including the model centric diatom Thalassiosira pseudonana, sexual reproduction has never been observed. Furthermore, the environmental factors that trigger sexual reproduction in diatoms are not understood. Although genome sequences of a few diatoms are available, little is known about the molecular basis for sexual reproduction. Here we show that ammonium reliably induces the key sexual morphologies, including oogonia, auxospores, and spermatogonia, in two strains of T. pseudonana, T. weissflogii, and Cyclotella cryptica. RNA sequencing revealed 1,274 genes whose expression patterns changed when T. pseudonana was induced into sexual reproduction by ammonium. Some of the induced genes are linked to meiosis or encode flagellar structures of heterokont and cryptophyte algae. The identification of ammonium as an environmental trigger suggests an unexpected link between diatom bloom dynamics and strategies for enhancing population genetic diversity.
Collapse
Affiliation(s)
- Eric R. Moore
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
| | - Briana S. Bullington
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
| | - Alexandra J. Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Yuan Jiang
- Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America
| | - Jeff Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Kimberly H. Halsey
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
| |
Collapse
|
113
|
Yang SY, Huang TK, Kuo HF, Chiou TJ. Role of vacuoles in phosphorus storage and remobilization. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3045-3055. [PMID: 28077447 DOI: 10.1093/jxb/erw481] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Vacuoles play a fundamental role in storage and remobilization of various nutrients, including phosphorus (P), an essential element for cell growth and development. Cells acquire P primarily in the form of inorganic orthophosphate (Pi). However, the form of P stored in vacuoles varies by organism and tissue. Algae and yeast store polyphosphates (polyPs), whereas plants store Pi and inositol phosphates (InsPs) in vegetative tissues and seeds, respectively. In this review, we summarize how vacuolar P molecules are stored and reallocated and how these processes are regulated and co-ordinated. The roles of SYG1/PHO81/XPR1 (SPX)-domain-containing membrane proteins in allocating vacuolar P are outlined. We also highlight the importance of vacuolar P in buffering the cytoplasmic Pi concentration to maintain cellular homeostasis when the external P supply fluctuates, and present additional roles for vacuolar polyP and InsP besides being a P reserve. Furthermore, we discuss the possibility of alternative pathways to recycle Pi from other P metabolites in vacuoles. Finally, future perspectives for researching this topic and its potential application in agriculture are proposed.
Collapse
Affiliation(s)
- Shu-Yi Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Teng-Kuei Huang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Hui-Fen Kuo
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Tzyy-Jen Chiou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
| |
Collapse
|
114
|
Transcriptomic and microRNAomic profiling reveals multi-faceted mechanisms to cope with phosphate stress in a dinoflagellate. ISME JOURNAL 2017; 11:2209-2218. [PMID: 28548660 DOI: 10.1038/ismej.2017.81] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 04/18/2017] [Accepted: 04/25/2017] [Indexed: 12/21/2022]
Abstract
Although gene regulation can occur at both transcriptional and epigenetic (microRNA) levels, combined transcriptomic and microRNAomic responses to environmental stress are still largely unexplored for marine plankton. Here, we conducted transcriptome and microRNAome sequencing for Prorocentrum donghaiense to understand the molecular mechanisms by which this dinoflagellate copes with phosphorus (P) deficiency. Under P-depleted conditions, G1/S specific cyclin gene was markedly downregulated, consistent with growth inhibition, and genes related to dissolved organic phosphorus (DOP) hydrolysis, carbon fixation, nitrate assimilation, glycolysis, and cellular motility were upregulated. The elevated expression of ATP-generating genes (for example, rhodopsin) and ATP-consuming genes suggests some metabolic reconfiguration towards accelerated ATP recycling under P deficiency. MicroRNAome sequencing revealed 17 microRNAs, potentially regulating 3268 protein-coding genes. Functional enrichment analysis of these microRNA-targeted genes predicted decreases in sulfatide (sulfolipid) catabolism under P deficiency. Strikingly, we detected a significant increase in sulfolipid sulfatide content (but not in sulphoquinovosyldiacylglycerol content) and its biosynthesis gene expression, indicating a different sulfolipid-substituting-phospholipid mechanism in this dinoflagellate than other phytoplankters studied previously. Taken together, our integrative transcriptomic and microRNAomic analyses show that enhanced DOP utilization, accelerated ATP cycling and repressed sulfolipid degradation constitute a comprehensive strategy to cope with P deficiency in a model dinoflagellate.
Collapse
|
115
|
Cañavate JP, Armada I, Hachero-Cruzado I. Polar Lipids Analysis of Cultured Phytoplankton Reveals Significant Inter-taxa Changes, Low Influence of Growth Stage, and Usefulness in Chemotaxonomy. MICROBIAL ECOLOGY 2017; 73:755-774. [PMID: 27837252 DOI: 10.1007/s00248-016-0893-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/31/2016] [Indexed: 06/06/2023]
Abstract
The high lipid diversity of microalgae has been used to taxonomically differentiate phytoplankton taxa at the class level. However, important lipids such as phospholipids (PL) and betaine lipids (BL) with potential chemotaxonomy application in phytoplankton ecology have been scarcely studied. The chemotaxonomy value of PL and BL depends on their intraspecific extent of variation as microalgae respond to external changing factors. To determine such effects, lipid class changes occurring at different growth stages in 15 microalgae from ten different classes were analyzed. BL occurred in 14 species and were the less affected lipids by growth stage with diacylglyceryl-hydroxymethyl-N,N,N-trimethyl-b-alanine (DGTA) showing the highest stability. PL were more influenced by growth stage with phosphatidylcholine (PC), phosphatidylglycerol (PG), and phosphatidyletanolamine (PE) declining towards older culture stages in some species. Glycolipids were the more common lipids, and no evident age-related variability pattern could be associated to taxonomic diversity. Selecting BL and PL as descriptor variables optimally distinguished microalgae taxonomic variability at all growth stages. Principal coordinate analysis arranged species through a main tendency from diacylglyceryl-hydroxymethyl-N,N,N-trimethyl-b-alanine (DGCC) containing species (mainly dinoflagellates and haptophytes) to DGTA or PC containing species (mainly cryptophytes). Two diatom classes with similar fatty acid profiles could be distinguished from their respective content in DGTA (Bacillariophyceae) or DGCC (Mediophyceae). In green lineage classes (Trebouxiophyceae, Porphyridophyceae, and Chlorodendrophyceae), PC was a better descriptor than BL. BL and PL explained a higher proportion of microalgae taxonomic variation than did fatty acids and played a complementary role as lipid markers.
Collapse
Affiliation(s)
- José Pedro Cañavate
- IFAPA Centro El Toruño, Andalusia Research and Training Institute for Fisheries and Agriculture, 11500-El Puerto de Santa Maria, Cádiz, Spain.
| | - Isabel Armada
- IFAPA Centro El Toruño, Andalusia Research and Training Institute for Fisheries and Agriculture, 11500-El Puerto de Santa Maria, Cádiz, Spain
| | - Ismael Hachero-Cruzado
- IFAPA Centro El Toruño, Andalusia Research and Training Institute for Fisheries and Agriculture, 11500-El Puerto de Santa Maria, Cádiz, Spain
| |
Collapse
|
116
|
Matthijs M, Fabris M, Obata T, Foubert I, Franco-Zorrilla JM, Solano R, Fernie AR, Vyverman W, Goossens A. The transcription factor bZIP14 regulates the TCA cycle in the diatom Phaeodactylum tricornutum. EMBO J 2017; 36:1559-1576. [PMID: 28420744 DOI: 10.15252/embj.201696392] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/14/2017] [Accepted: 03/15/2017] [Indexed: 11/09/2022] Open
Abstract
Diatoms are amongst the most important marine microalgae in terms of biomass, but little is known concerning the molecular mechanisms that regulate their versatile metabolism. Here, the pennate diatom Phaeodactylum tricornutum was studied at the metabolite and transcriptome level during nitrogen starvation and following imposition of three other stresses that impede growth. The coordinated upregulation of the tricarboxylic acid (TCA) cycle during the nitrogen stress response was the most striking observation. Through co-expression analysis and DNA binding assays, the transcription factor bZIP14 was identified as a regulator of the TCA cycle, also beyond the nitrogen starvation response, namely in diurnal regulation. Accordingly, metabolic and transcriptional shifts were observed upon overexpression of bZIP14 in transformed P. tricornutum cells. Our data indicate that the TCA cycle is a tightly regulated and important hub for carbon reallocation in the diatom cell during nutrient starvation and that bZIP14 is a conserved regulator of this cycle.
Collapse
Affiliation(s)
- Michiel Matthijs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium.,Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Michele Fabris
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium.,Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Toshihiro Obata
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Imogen Foubert
- Research Unit Food & Lipids, Department of Molecular and Microbial Systems Kulak, Leuven Food Science and Nutrition Research Centre (LFoRCe), Kortrijk, Belgium
| | | | - Roberto Solano
- Genomics Unit, Centro Nacional de Biotecnología-CSIC, Madrid, Spain.,Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Madrid, Spain
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium .,Center for Plant Systems Biology, VIB, Ghent, Belgium
| |
Collapse
|
117
|
Thornton DCO, Chen J. Exopolymer production as a function of cell permeability and death in a diatom (Thalassiosira weissflogii) and a cyanobacterium (Synechococcus elongatus). JOURNAL OF PHYCOLOGY 2017; 53:245-260. [PMID: 27690180 DOI: 10.1111/jpy.12470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/26/2016] [Indexed: 05/23/2023]
Abstract
Exopolymer particles are found throughout the ocean and play a significant biogeochemical role in carbon cycling. Transparent exopolymer particles (TEP) are composed of acid polysaccharides, and Coomassie staining particles (CSP) are proteins. TEPs have been extensively studied in the ocean, while CSP have been largely overlooked. The objective of this research was to determine the role of stress and cell permeability in the formation of TEP and CSP. The diatom Thalassiosira weissflogii and cyanobacterium Synechococcus elongatus were grown in batch cultures and exposed to hydrogen peroxide (0, 10, and 100 μM) as an environmental stressor. There was no correlation between TEP and CSP concentrations, indicating that they are different populations of particles rather than different chemical components of the same particles. CSP concentrations were not affected by hydrogen peroxide concentration and did not correlate with indicators of stress and cell death. In contrast, TEP concentrations in both taxa were correlated with a decrease in the effective quantum yield of photosystem II, increased activity of caspase-like enzymes, and an increase in the proportion of the population with permeable cell membranes, indicating that TEP production was associated with the process of cell death. These data show that different environmental factors and physiological processes affected the production of TEP and CSP by phytoplankton. TEP and CSP are separate populations of exopolymer particles with potentially different biogeochemical roles in the ocean.
Collapse
Affiliation(s)
- Daniel C O Thornton
- Department of Oceanography, Texas A & M University, College Station, Texas, 77843, USA
| | - Jie Chen
- Department of Oceanography, Texas A & M University, College Station, Texas, 77843, USA
| |
Collapse
|
118
|
Degraeve-Guilbault C, Bréhélin C, Haslam R, Sayanova O, Marie-Luce G, Jouhet J, Corellou F. Glycerolipid Characterization and Nutrient Deprivation-Associated Changes in the Green Picoalga Ostreococcus tauri. PLANT PHYSIOLOGY 2017; 173:2060-2080. [PMID: 28235892 PMCID: PMC5373045 DOI: 10.1104/pp.16.01467] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 02/23/2017] [Indexed: 05/23/2023]
Abstract
The picoalga Ostreococcus tauri is a minimal photosynthetic eukaryote that has been used as a model system. O. tauri is known to efficiently produce docosahexaenoic acid (DHA). We provide a comprehensive study of the glycerolipidome of O. tauri and validate this species as model for related picoeukaryotes. O. tauri lipids displayed unique features that combined traits from the green and the chromalveolate lineages. The betaine lipid diacylglyceryl-hydroxymethyl-trimethyl-β-alanine and phosphatidyldimethylpropanethiol, both hallmarks of chromalveolates, were identified as presumed extraplastidial lipids. DHA was confined to these lipids, while plastidial lipids of prokaryotic type were characterized by the overwhelming presence of ω-3 C18 polyunsaturated fatty acids (FAs), 18:5 being restricted to galactolipids. C16:4, an FA typical of green microalgae galactolipids, also was a major component of O. tauri extraplastidial lipids, while the 16:4-coenzyme A (CoA) species was not detected. Triacylglycerols (TAGs) displayed the complete panel of FAs, and many species exhibited combinations of FAs diagnostic for plastidial and extraplastidial lipids. Importantly, under nutrient deprivation, 16:4 and ω-3 C18 polyunsaturated FAs accumulated into de novo synthesized TAGs while DHA-TAG species remained rather stable, indicating an increased contribution of FAs of plastidial origin to TAG synthesis. Nutrient deprivation further severely down-regulated the conversion of 18:3 to 18:4, resulting in obvious inversion of the 18:3/18:4 ratio in plastidial lipids, TAGs, as well as acyl-CoAs. The fine-tuned and dynamic regulation of the 18:3/18:4 ratio suggested an important physiological role of these FAs in photosynthetic membranes. Acyl position in structural and storage lipids together with acyl-CoA analysis further help to determine mechanisms possibly involved in glycerolipid synthesis.
Collapse
Affiliation(s)
- Charlotte Degraeve-Guilbault
- Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200, Centre National de la Recherche Scientifique, Université de Bordeaux BP81, F-33882 Villenave D'Ornon, France (C.D.-G., C.B., G.M.-L., F.C.)
- Rothamsted Research, Biological, Chemistry, Harpenden AL5 2JQ, United Kingdom (R.H., O.S.); and
- Laboratoire de Biologie Cellulaire et Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, Institut National de la Recherche Agronomique, Université Grenoble Alpes, BIG, Commissariat à l'Energie Atomique-Grenoble, 38054 Grenoble cedex 9, France (J.J.)
| | - Claire Bréhélin
- Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200, Centre National de la Recherche Scientifique, Université de Bordeaux BP81, F-33882 Villenave D'Ornon, France (C.D.-G., C.B., G.M.-L., F.C.)
- Rothamsted Research, Biological, Chemistry, Harpenden AL5 2JQ, United Kingdom (R.H., O.S.); and
- Laboratoire de Biologie Cellulaire et Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, Institut National de la Recherche Agronomique, Université Grenoble Alpes, BIG, Commissariat à l'Energie Atomique-Grenoble, 38054 Grenoble cedex 9, France (J.J.)
| | - Richard Haslam
- Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200, Centre National de la Recherche Scientifique, Université de Bordeaux BP81, F-33882 Villenave D'Ornon, France (C.D.-G., C.B., G.M.-L., F.C.)
- Rothamsted Research, Biological, Chemistry, Harpenden AL5 2JQ, United Kingdom (R.H., O.S.); and
- Laboratoire de Biologie Cellulaire et Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, Institut National de la Recherche Agronomique, Université Grenoble Alpes, BIG, Commissariat à l'Energie Atomique-Grenoble, 38054 Grenoble cedex 9, France (J.J.)
| | - Olga Sayanova
- Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200, Centre National de la Recherche Scientifique, Université de Bordeaux BP81, F-33882 Villenave D'Ornon, France (C.D.-G., C.B., G.M.-L., F.C.)
- Rothamsted Research, Biological, Chemistry, Harpenden AL5 2JQ, United Kingdom (R.H., O.S.); and
- Laboratoire de Biologie Cellulaire et Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, Institut National de la Recherche Agronomique, Université Grenoble Alpes, BIG, Commissariat à l'Energie Atomique-Grenoble, 38054 Grenoble cedex 9, France (J.J.)
| | - Glawdys Marie-Luce
- Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200, Centre National de la Recherche Scientifique, Université de Bordeaux BP81, F-33882 Villenave D'Ornon, France (C.D.-G., C.B., G.M.-L., F.C.)
- Rothamsted Research, Biological, Chemistry, Harpenden AL5 2JQ, United Kingdom (R.H., O.S.); and
- Laboratoire de Biologie Cellulaire et Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, Institut National de la Recherche Agronomique, Université Grenoble Alpes, BIG, Commissariat à l'Energie Atomique-Grenoble, 38054 Grenoble cedex 9, France (J.J.)
| | - Juliette Jouhet
- Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200, Centre National de la Recherche Scientifique, Université de Bordeaux BP81, F-33882 Villenave D'Ornon, France (C.D.-G., C.B., G.M.-L., F.C.)
- Rothamsted Research, Biological, Chemistry, Harpenden AL5 2JQ, United Kingdom (R.H., O.S.); and
- Laboratoire de Biologie Cellulaire et Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, Institut National de la Recherche Agronomique, Université Grenoble Alpes, BIG, Commissariat à l'Energie Atomique-Grenoble, 38054 Grenoble cedex 9, France (J.J.)
| | - Florence Corellou
- Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200, Centre National de la Recherche Scientifique, Université de Bordeaux BP81, F-33882 Villenave D'Ornon, France (C.D.-G., C.B., G.M.-L., F.C.);
- Rothamsted Research, Biological, Chemistry, Harpenden AL5 2JQ, United Kingdom (R.H., O.S.); and
- Laboratoire de Biologie Cellulaire et Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, Institut National de la Recherche Agronomique, Université Grenoble Alpes, BIG, Commissariat à l'Energie Atomique-Grenoble, 38054 Grenoble cedex 9, France (J.J.)
| |
Collapse
|
119
|
Ghaffar S, Stevenson RJ, Khan Z. Effect of phosphorus stress on Microcystis aeruginosa growth and phosphorus uptake. PLoS One 2017; 12:e0174349. [PMID: 28328927 PMCID: PMC5362216 DOI: 10.1371/journal.pone.0174349] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 03/07/2017] [Indexed: 12/03/2022] Open
Abstract
This study was designed to advance understanding of phosphorus regulation of Microcystis aeruginosa growth, phosphorus uptake and storage in changing phosphorus (P) conditions as would occur in lakes. We hypothesized that Microcystis growth and nutrient uptake would fit classic models by Monod, Droop, and Michaelis-Menten in these changing conditions. Microcystis grown in luxury nutrient concentrations was transferred to treatments with phosphorus concentrations ranging from 0–256 μg P∙L-1 and luxury nitrogen. Dissolved phosphorus concentration, cell phosphorus quota, P uptake rate and cell densities were measured at day 3 and 6. Results showed little relationship to predicted models. Microcystis growth was asymptotically related to P treatment from day 0–3, fitting Monod model well, but negatively related to P treatment and cell quota from day 3–6. From day 0–3, cell quota was negatively related to P treatments at <2 μg∙L-1, but increased slightly at higher P. Cell quota decreased greatly in low P treatments from day 3–6, which may have enabled high growths in low P treatments. P uptake was positively and linearly related to P treatment during both periods. Negative uptake rates and increases in measured culture phosphorus concentrations to 5 μg∙L-1 in the lowest P treatments indicated P leaked from cells into culture medium. This leakage during early stages of the experiment may have been sufficient to stimulate metabolism and use of intracellular P stores in low P treatments for rapid growth. Our study shows P regulation of Microcystis growth can be complex as a result of changing P concentrations, and this complexity may be important for modeling Microcystis for nutrient and ecosystem management.
Collapse
Affiliation(s)
- Sajeela Ghaffar
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering (IESE-SCEE), National University of Sciences and Technology (NUST), Sector H-12 Campus, Islamabad, Pakistan
- * E-mail:
| | - R. Jan Stevenson
- Center for Water Sciences & Department of Integrative Biology, Michigan State University, East Lansing, Michigan United States of America
| | - Zahiruddin Khan
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering (IESE-SCEE), National University of Sciences and Technology (NUST), Sector H-12 Campus, Islamabad, Pakistan
| |
Collapse
|
120
|
Cui Y, Zhang H, Lin S. Enhancement of Non-photochemical Quenching as an Adaptive Strategy under Phosphorus Deprivation in the Dinoflagellate Karlodinium veneficum. Front Microbiol 2017; 8:404. [PMID: 28360892 PMCID: PMC5350143 DOI: 10.3389/fmicb.2017.00404] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/27/2017] [Indexed: 11/18/2022] Open
Abstract
Intensified water column stratification due to global warming has the potential to decrease nutrient availability while increasing excess light for the photosynthesis of phytoplankton in the euphotic zone, which together will increase the need for photoprotective strategies such as non-photochemical quenching (NPQ). We investigated whether NPQ is enhanced and how it is regulated molecularly under phosphorus (P) deprivation in the dinoflagellate Karlodinium veneficum. We grew K. veneficum under P-replete and P-depleted conditions, monitored their growth rates and chlorophyll fluorescence, and conducted gene expression and comparative proteomic analyses. The results were used to characterize NPQ modulation and associated gene expression dynamics under P deprivation. We found that NPQ in K. veneficum was elevated significantly under P deprivation. Accordingly, the abundances of three light-harvesting complex stress-related proteins increased under P-depleted condition. Besides, many proteins related to genetic information flow were down-regulated while many proteins related to energy production and conversion were up-regulated under P deprivation. Taken together, our results indicate that K. veneficum cells respond to P deprivation by reconfiguring the metabolic landscape and up-tuning NPQ to increase the capacity to dissipate excess light energy and maintain the fluency of energy flow, which provides a new perspective about what adaptive strategy dinoflagellates have evolved to cope with P deprivation.
Collapse
Affiliation(s)
- Yudong Cui
- State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Xiamen City Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University Xiamen, China
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, Groton CT, USA
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Xiamen City Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen UniversityXiamen, China; Department of Marine Sciences, University of Connecticut, GrotonCT, USA
| |
Collapse
|
121
|
Responses of the marine diatom Thalassiosira pseudonana to changes in CO 2 concentration: a proteomic approach. Sci Rep 2017; 7:42333. [PMID: 28181560 PMCID: PMC5299434 DOI: 10.1038/srep42333] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 01/10/2017] [Indexed: 12/18/2022] Open
Abstract
The concentration of CO2 in many aquatic systems is variable, often lower than the KM of the primary carboxylating enzyme Rubisco, and in order to photosynthesize efficiently, many algae operate a facultative CO2 concentrating mechanism (CCM). Here we measured the responses of a marine diatom, Thalassiosira pseudonana, to high and low concentrations of CO2 at the level of transcripts, proteins and enzyme activity. Low CO2 caused many metabolic pathways to be remodeled. Carbon acquisition enzymes, primarily carbonic anhydrase, stress, degradation and signaling proteins were more abundant while proteins associated with nitrogen metabolism, energy production and chaperones were less abundant. A protein with similarities to the Ca2+/ calmodulin dependent protein kinase II_association domain, having a chloroplast targeting sequence, was only present at low CO2. This protein might be a specific response to CO2 limitation since a previous study showed that other stresses caused its reduction. The protein sequence was found in other marine diatoms and may play an important role in their response to low CO2 concentration.
Collapse
|
122
|
Garnier M, Bougaran G, Pavlovic M, Berard JB, Carrier G, Charrier A, Le Grand F, Lukomska E, Rouxel C, Schreiber N, Cadoret JP, Rogniaux H, Saint-Jean B. Use of a lipid rich strain reveals mechanisms of nitrogen limitation and carbon partitioning in the haptophyte Tisochrysis lutea. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.10.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
123
|
Caron DA, Alexander H, Allen AE, Archibald JM, Armbrust EV, Bachy C, Bell CJ, Bharti A, Dyhrman ST, Guida SM, Heidelberg KB, Kaye JZ, Metzner J, Smith SR, Worden AZ. Probing the evolution, ecology and physiology of marine protists using transcriptomics. Nat Rev Microbiol 2016; 15:6-20. [DOI: 10.1038/nrmicro.2016.160] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
124
|
Enzymes of yeast polyphosphate metabolism: structure, enzymology and biological roles. Biochem Soc Trans 2016; 44:234-9. [PMID: 26862210 DOI: 10.1042/bst20150213] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Inorganic polyphosphate (polyP) is found in all living organisms. The known polyP functions in eukaryotes range from osmoregulation and virulence in parasitic protozoa to modulating blood coagulation, inflammation, bone mineralization and cellular signalling in mammals. However mechanisms of regulation and even the identity of involved proteins in many cases remain obscure. Most of the insights obtained so far stem from studies in the yeast Saccharomyces cerevisiae. Here, we provide a short overview of the properties and functions of known yeast polyP metabolism enzymes and discuss future directions for polyP research.
Collapse
|
125
|
Graff van Creveld S, Rosenwasser S, Levin Y, Vardi A. Chronic Iron Limitation Confers Transient Resistance to Oxidative Stress in Marine Diatoms. PLANT PHYSIOLOGY 2016; 172:968-979. [PMID: 27503604 PMCID: PMC5047098 DOI: 10.1104/pp.16.00840] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 08/02/2016] [Indexed: 05/04/2023]
Abstract
Diatoms are single-celled, photosynthetic, bloom-forming algae that are responsible for at least 20% of global primary production. Nevertheless, more than 30% of the oceans are considered "ocean deserts" due to iron limitation. We used the diatom Phaeodactylum tricornutum as a model system to explore diatom's response to iron limitation and its interplay with susceptibility to oxidative stress. By analyzing physiological parameters and proteome profiling, we defined two distinct phases: short-term (<3 d, phase I) and chronic (>5 d, phase II) iron limitation. While at phase I no significant changes in physiological parameters were observed, molecular markers for iron starvation, such as Iron Starvation Induced Protein and flavodoxin, were highly up-regulated. At phase II, down-regulation of numerous iron-containing proteins was detected in parallel to reduction in growth rate, chlorophyll content, photosynthetic activity, respiration rate, and antioxidant capacity. Intriguingly, while application of oxidative stress to phase I and II iron-limited cells similarly oxidized the reduced glutathione (GSH) pool, phase II iron limitation exhibited transient resistance to oxidative stress, despite the down regulation of many antioxidant proteins. By comparing proteomic profiles of P. tricornutum under iron limitation and metatranscriptomic data of an iron enrichment experiment conducted in the Pacific Ocean, we propose that iron-limited cells in the natural environment resemble the phase II metabolic state. These results provide insights into the trade-off between optimal growth rate and susceptibility to oxidative stress in the response of diatoms to iron quota in the marine environment.
Collapse
Affiliation(s)
- Shiri Graff van Creveld
- Department of Plant and Environmental Sciences (S.G.v.C., S.R., A.V.),and Israel National Center for Personalized Medicine (Y.L.), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shilo Rosenwasser
- Department of Plant and Environmental Sciences (S.G.v.C., S.R., A.V.),and Israel National Center for Personalized Medicine (Y.L.), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yishai Levin
- Department of Plant and Environmental Sciences (S.G.v.C., S.R., A.V.),and Israel National Center for Personalized Medicine (Y.L.), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences (S.G.v.C., S.R., A.V.),and Israel National Center for Personalized Medicine (Y.L.), Weizmann Institute of Science, Rehovot 7610001, Israel
| |
Collapse
|
126
|
Zhang SF, Yuan CJ, Chen Y, Chen XH, Li DX, Liu JL, Lin L, Wang DZ. Comparative Transcriptomic Analysis Reveals Novel Insights into the Adaptive Response of Skeletonema costatum to Changing Ambient Phosphorus. Front Microbiol 2016; 7:1476. [PMID: 27703451 PMCID: PMC5028394 DOI: 10.3389/fmicb.2016.01476] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/05/2016] [Indexed: 12/11/2022] Open
Abstract
Phosphorus (P) is a limiting macronutrient for diatom growth and productivity in the ocean. Much effort has been devoted to the physiological response of marine diatoms to ambient P change, however, the whole-genome molecular mechanisms are poorly understood. Here, we utilized RNA-Seq to compare the global gene expression patterns of a marine diatom Skeletonema costatum grown in inorganic P-replete, P-deficient, and inorganic- and organic-P resupplied conditions. In total 34,942 unique genes were assembled and 20.8% of them altered significantly in abundance under different P conditions. Genes encoding key enzymes/proteins involved in P utilization, nucleotide metabolism, photosynthesis, glycolysis, and cell cycle regulation were significantly up-regulated in P-deficient cells. Genes participating in circadian rhythm regulation, such as circadian clock associated 1, were also up-regulated in P-deficient cells. The response of S. costatum to ambient P deficiency shows several similarities to the well-described responses of other marine diatom species, but also has its unique features. S. costatum has evolved the ability to re-program its circadian clock and intracellular biological processes in response to ambient P deficiency. This study provides new insights into the adaptive mechanisms to ambient P deficiency in marine diatoms.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science, Department of Environmental Science and Engineering, College of the Environment and Ecology, Xiamen UniversityXiamen, China
| |
Collapse
|
127
|
Longworth J, Wu D, Huete-Ortega M, Wright PC, Vaidyanathan S. Proteome response of Phaeodactylum tricornutum, during lipid accumulation induced by nitrogen depletion. ALGAL RES 2016; 18:213-224. [PMID: 27812494 PMCID: PMC5070409 DOI: 10.1016/j.algal.2016.06.015] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 05/08/2016] [Accepted: 06/14/2016] [Indexed: 11/26/2022]
Abstract
Nitrogen stress is a common strategy employed to stimulate lipid accumulation in microalgae, a biofuel feedstock of topical interest. Although widely investigated, the underlying mechanism of this strategy is still poorly understood. We examined the proteome response of lipid accumulation in the model diatom, Phaeodactylum tricornutum (CCAP 1055/1), at an earlier stage of exposure to selective nitrogen exclusion than previously investigated, and at a time point when changes would reflect lipid accumulation more than carbohydrate accumulation. In total 1043 proteins were confidently identified (≥ 2 unique peptides) with 645 significant (p < 0.05) changes observed, in the LC-MS/MS based iTRAQ investigation. Analysis of significant changes in KEGG pathways and individual proteins showed that under nitrogen starvation P. tricornutum reorganizes its proteome in favour of nitrogen scavenging and reduced lipid degradation whilst rearranging the central energy metabolism that deprioritizes photosynthetic pathways. By doing this, this species appears to increase nitrogen availability inside the cell and limit its use to the pathways where it is needed most. Compared to previously published proteomic analysis of nitrogen starvation in Chlamydomonas reinhardtii, central energy metabolism and photosynthesis appear to be affected more in the diatom, whilst the green algae appears to invest its energy in reorganizing respiration and the cellular organization pathways.
Collapse
|
128
|
Brandsma J. Phytoplankton phenotype plasticity induced by phosphorus starvation may play a significant role in marine microbial ecology and biogeochemistry. THE NEW PHYTOLOGIST 2016; 211:765-766. [PMID: 27397523 DOI: 10.1111/nph.14085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Joost Brandsma
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, SO16 6YD, UK
| |
Collapse
|
129
|
Shemi A, Schatz D, Fredricks HF, Van Mooy BAS, Porat Z, Vardi A. Phosphorus starvation induces membrane remodeling and recycling in Emiliania huxleyi. THE NEW PHYTOLOGIST 2016; 211:886-898. [PMID: 27111716 DOI: 10.1111/nph.13940] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 02/20/2016] [Indexed: 06/05/2023]
Abstract
Nutrient availability is an important factor controlling phytoplankton productivity. Phytoplankton contribute c. 50% of the global photosynthesis and possess efficient acclimation mechanisms to cope with nutrient stress. We investigate the cellular response of the bloom-forming coccolithophore Emiliania huxleyi to phosphorus (P) scarcity, which is often a limiting factor in marine ecosystems. We combined mass spectrometry, fluorescence microscopy, transmission electron microscopy (TEM) and gene expression analyses in order to assess diverse cellular features in cells exposed to P limitation and recovery. Early starvation-induced substitution of phospholipids in the cells' membranes with galacto- and betaine lipids. Lipid remodeling was rapid and reversible upon P resupply. The PI3K inhibitor wortmannin reduced phospholipid substitution, suggesting a possible involvement of PI3K- signaling in this process. In addition, P limitation enhanced the formation and acidification of membrane vesicles in the cytoplasm. Intracellular vesicles may facilitate the recycling of cytoplasmic content, which is engulfed in the vesicles and delivered to the main vacuole. Long-term starvation was characterized by a profound increase in cell size and morphological alterations in cellular ultrastructure. This study provides cellular and molecular basis for future ecophysiological assessment of natural E. huxleyi populations in oligotrophic regions.
Collapse
Affiliation(s)
- Adva Shemi
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Helen F Fredricks
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Benjamin A S Van Mooy
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Ziv Porat
- Biological Services Department, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| |
Collapse
|
130
|
Rai V, Karthikaichamy A, Das D, Noronha S, Wangikar PP, Srivastava S. Multi-omics Frontiers in Algal Research: Techniques and Progress to Explore Biofuels in the Postgenomics World. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 20:387-99. [DOI: 10.1089/omi.2016.0065] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Vineeta Rai
- Department of Biosciences and Bioengineering, Proteomics Laboratory, Indian Institute of Technology Bombay, Mumbai, India
| | | | - Debasish Das
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, India
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
| | - Santosh Noronha
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
- Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Pramod P. Wangikar
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
- Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Proteomics Laboratory, Indian Institute of Technology Bombay, Mumbai, India
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
- Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| |
Collapse
|
131
|
Taddei L, Stella GR, Rogato A, Bailleul B, Fortunato AE, Annunziata R, Sanges R, Thaler M, Lepetit B, Lavaud J, Jaubert M, Finazzi G, Bouly JP, Falciatore A. Multisignal control of expression of the LHCX protein family in the marine diatom Phaeodactylum tricornutum. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3939-51. [PMID: 27225826 PMCID: PMC4915529 DOI: 10.1093/jxb/erw198] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Diatoms are phytoplanktonic organisms that grow successfully in the ocean where light conditions are highly variable. Studies of the molecular mechanisms of light acclimation in the marine diatom Phaeodactylum tricornutum show that carotenoid de-epoxidation enzymes and LHCX1, a member of the light-harvesting protein family, both contribute to dissipate excess light energy through non-photochemical quenching (NPQ). In this study, we investigate the role of the other members of the LHCX family in diatom stress responses. Our analysis of available genomic data shows that the presence of multiple LHCX genes is a conserved feature of diatom species living in different ecological niches. Moreover, an analysis of the levels of four P. tricornutum LHCX transcripts in relation to protein expression and photosynthetic activity indicates that LHCXs are differentially regulated under different light intensities and nutrient starvation, mostly modulating NPQ capacity. We conclude that multiple abiotic stress signals converge to regulate the LHCX content of cells, providing a way to fine-tune light harvesting and photoprotection. Moreover, our data indicate that the expansion of the LHCX gene family reflects functional diversification of its members which could benefit cells responding to highly variable ocean environments.
Collapse
Affiliation(s)
- Lucilla Taddei
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 15 rue de l'Ecole de Médecine, 75006 Paris, France
| | - Giulio Rocco Stella
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 15 rue de l'Ecole de Médecine, 75006 Paris, France Department of Biotechnology, University of Verona, Strada Le Grazie, I-37134 Verona, Italy
| | - Alessandra Rogato
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 15 rue de l'Ecole de Médecine, 75006 Paris, France Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, 80131 Naples, Italy Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Benjamin Bailleul
- Institut de Biologie Physico-Chimique, UMR 7141 CNRS-UPMC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Antonio Emidio Fortunato
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 15 rue de l'Ecole de Médecine, 75006 Paris, France
| | - Rossella Annunziata
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 15 rue de l'Ecole de Médecine, 75006 Paris, France
| | - Remo Sanges
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Michael Thaler
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 15 rue de l'Ecole de Médecine, 75006 Paris, France
| | - Bernard Lepetit
- Zukunftskolleg, Department of Plant Ecophysiology, University of Konstanz, D-78457 Konstanz, Germany
| | - Johann Lavaud
- UMI 3376 TAKUVIK, CNRS/Université Laval, Département de Biologie, Pavillon Alexandre-Vachon, 1045 avenue de la Médecine, Québec (Québec) G1V 0A6, Canada
| | - Marianne Jaubert
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 15 rue de l'Ecole de Médecine, 75006 Paris, France
| | - Giovanni Finazzi
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, Centre National de la Recherche Scientifique (CNRS), Institut National Recherche Agronomique (INRA), Université Grenoble Alpes, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Biosciences et Biotechnologies de Grenoble, (BIG), CEA Grenoble, F-38054 Grenoble cedex 9, France
| | - Jean-Pierre Bouly
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 15 rue de l'Ecole de Médecine, 75006 Paris, France
| | - Angela Falciatore
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 15 rue de l'Ecole de Médecine, 75006 Paris, France
| |
Collapse
|
132
|
Whitney LP, Lomas MW. Growth on ATP Elicits a P-Stress Response in the Picoeukaryote Micromonas pusilla. PLoS One 2016; 11:e0155158. [PMID: 27167623 PMCID: PMC4864187 DOI: 10.1371/journal.pone.0155158] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 04/25/2016] [Indexed: 11/18/2022] Open
Abstract
The surface waters of oligotrophic oceans have chronically low phosphate (Pi) concentrations, which renders dissolved organic phosphorus (DOP) an important nutrient source. In the subtropical North Atlantic, cyanobacteria are often numerically dominant, but picoeukaryotes can dominate autotrophic biomass and productivity making them important contributors to the ocean carbon cycle. Despite their importance, little is known regarding the metabolic response of picoeukaryotes to changes in phosphorus (P) source and availability. To understand the molecular mechanisms that regulate P utilization in oligotrophic environments, we evaluated transcriptomes of the picoeukaryote Micromonas pusilla grown under Pi-replete and -deficient conditions, with an additional investigation of growth on DOP in replete conditions. Genes that function in sulfolipid substitution and Pi uptake increased in expression with Pi-deficiency, suggesting cells were reallocating cellular P and increasing P acquisition capabilities. Pi-deficient M. pusilla cells also increased alkaline phosphatase activity and reduced their cellular P content. Cells grown with DOP were able to maintain relatively high growth rates, however the transcriptomic response was more similar to the Pi-deficient response than that seen in cells grown under Pi-replete conditions. The results demonstrate that not all P sources are the same for growth; while M. pusilla, a model picoeukaryote, may grow well on DOP, the metabolic demand is greater than growth on Pi. These findings provide insight into the cellular strategies which may be used to support growth in a stratified future ocean predicted to favor picoeukaryotes.
Collapse
Affiliation(s)
- LeAnn P. Whitney
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America
- * E-mail:
| | - Michael W. Lomas
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America
| |
Collapse
|
133
|
Smith SR, Glé C, Abbriano RM, Traller JC, Davis A, Trentacoste E, Vernet M, Allen AE, Hildebrand M. Transcript level coordination of carbon pathways during silicon starvation-induced lipid accumulation in the diatom Thalassiosira pseudonana. THE NEW PHYTOLOGIST 2016; 210:890-904. [PMID: 26844818 PMCID: PMC5067629 DOI: 10.1111/nph.13843] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 12/03/2015] [Indexed: 05/06/2023]
Abstract
Diatoms are one of the most productive and successful photosynthetic taxa on Earth and possess attributes such as rapid growth rates and production of lipids, making them candidate sources of renewable fuels. Despite their significance, few details of the mechanisms used to regulate growth and carbon metabolism are currently known, hindering metabolic engineering approaches to enhance productivity. To characterize the transcript level component of metabolic regulation, genome-wide changes in transcript abundance were documented in the model diatom Thalassiosira pseudonana on a time-course of silicon starvation. Growth, cell cycle progression, chloroplast replication, fatty acid composition, pigmentation, and photosynthetic parameters were characterized alongside lipid accumulation. Extensive coordination of large suites of genes was observed, highlighting the existence of clusters of coregulated genes as a key feature of global gene regulation in T. pseudonana. The identity of key enzymes for carbon metabolic pathway inputs (photosynthesis) and outputs (growth and storage) reveals these clusters are organized to synchronize these processes. Coordinated transcript level responses to silicon starvation are probably driven by signals linked to cell cycle progression and shifts in photophysiology. A mechanistic understanding of how this is accomplished will aid efforts to engineer metabolism for development of algal-derived biofuels.
Collapse
Affiliation(s)
- Sarah R. Smith
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
- J. Craig Venter Institute4120 Capricorn LaneLa JollaCA92037USA
| | - Corine Glé
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
| | - Raffaela M. Abbriano
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
| | - Jesse C. Traller
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
| | - Aubrey Davis
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
| | - Emily Trentacoste
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
| | - Maria Vernet
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
| | - Andrew E. Allen
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
- J. Craig Venter Institute4120 Capricorn LaneLa JollaCA92037USA
| | - Mark Hildebrand
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
| |
Collapse
|
134
|
Milici M, Tomasch J, Wos-Oxley ML, Decelle J, Jáuregui R, Wang H, Deng ZL, Plumeier I, Giebel HA, Badewien TH, Wurst M, Pieper DH, Simon M, Wagner-Döbler I. Bacterioplankton Biogeography of the Atlantic Ocean: A Case Study of the Distance-Decay Relationship. Front Microbiol 2016; 7:590. [PMID: 27199923 PMCID: PMC4845060 DOI: 10.3389/fmicb.2016.00590] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/11/2016] [Indexed: 11/13/2022] Open
Abstract
In order to determine the influence of geographical distance, depth, and Longhurstian province on bacterial community composition and compare it with the composition of photosynthetic micro-eukaryote communities, 382 samples from a depth-resolved latitudinal transect (51°S–47°N) from the epipelagic zone of the Atlantic ocean were analyzed by Illumina amplicon sequencing. In the upper 100 m of the ocean, community similarity decreased toward the equator for 6000 km, but subsequently increased again, reaching similarity values of 40–60% for samples that were separated by ~12,000 km, resulting in a U-shaped distance-decay curve. We conclude that adaptation to local conditions can override the linear distance-decay relationship in the upper epipelagial of the Atlantic Ocean which is apparently not restrained by barriers to dispersal, since the same taxa were shared between the most distant communities. The six Longhurstian provinces covered by the transect were comprised of distinct microbial communities; ~30% of variation in community composition could be explained by province. Bacterial communities belonging to the deeper layer of the epipelagic zone (140–200 m) lacked a distance-decay relationship altogether and showed little provincialism. Interestingly, those biogeographical patterns were consistently found for bacteria from three different size fractions of the plankton with different taxonomic composition, indicating conserved underlying mechanisms. Analysis of the chloroplast 16S rRNA gene sequences revealed that phytoplankton composition was strongly correlated with both free-living and particle associated bacterial community composition (R between 0.51 and 0.62, p < 0.002). The data show that biogeographical patterns commonly found in macroecology do not hold for marine bacterioplankton, most likely because dispersal and evolution occur at drastically different rates in bacteria.
Collapse
Affiliation(s)
- Mathias Milici
- Group Microbial Communication, Helmholtz-Center for Infection Research Braunschweig, Germany
| | - Jürgen Tomasch
- Group Microbial Communication, Helmholtz-Center for Infection Research Braunschweig, Germany
| | - Melissa L Wos-Oxley
- Group Microbial Interactions and Processes, Helmholtz-Center for Infection Research Braunschweig, Germany
| | - Johan Decelle
- UMR 7144 - Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de RoscoffRoscoff, France; Centre National de la Recherche Scientifique, UMR 7144, Station Biologique de RoscoffRoscoff, France
| | - Ruy Jáuregui
- Group Microbial Interactions and Processes, Helmholtz-Center for Infection Research Braunschweig, Germany
| | - Hui Wang
- Group Microbial Communication, Helmholtz-Center for Infection Research Braunschweig, Germany
| | - Zhi-Luo Deng
- Group Microbial Communication, Helmholtz-Center for Infection Research Braunschweig, Germany
| | - Iris Plumeier
- Group Microbial Interactions and Processes, Helmholtz-Center for Infection Research Braunschweig, Germany
| | - Helge-Ansgar Giebel
- Department of Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg Oldenburg, Germany
| | - Thomas H Badewien
- Department of Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg Oldenburg, Germany
| | - Mascha Wurst
- Department of Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg Oldenburg, Germany
| | - Dietmar H Pieper
- Department of Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg Oldenburg, Germany
| | - Meinhard Simon
- Department of Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg Oldenburg, Germany
| | - Irene Wagner-Döbler
- Group Microbial Communication, Helmholtz-Center for Infection Research Braunschweig, Germany
| |
Collapse
|
135
|
Cruz de Carvalho MH, Sun HX, Bowler C, Chua NH. Noncoding and coding transcriptome responses of a marine diatom to phosphate fluctuations. THE NEW PHYTOLOGIST 2016; 210:497-510. [PMID: 26680538 DOI: 10.1111/nph.13787] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 10/27/2015] [Indexed: 05/20/2023]
Abstract
Phosphorus (P) is an essential element to all living cells, yet fluctuations in P concentrations are recurrent in the marine environment. Diatoms are amongst the most successful phytoplankton groups, adapting to and surviving periods of suboptimal conditions and resuming growth as soon as nutrient concentrations permit. A knowledge of the molecular underpinnings of diatom ecological success is, however, still very incomplete. By strand-specific RNA sequencing, we analyzed the global transcriptome changes of the diatom Phaeodactylum tricornutum in response to P fluctuations over a course of 8 d, defining five distinct physiological states. This study reports previously unidentified genes highly responsive to P stress in P. tricornutum. Our data also uncover the complexity of the P. tricornutum P-responsive sensory and signaling system that combines bacterial two-component systems with more complex pathways reminiscent of metazoans. Finally, we identify a multitude of novel long intergenic nonprotein coding RNAs (lincRNAs) specifically responsive to P depletion, suggesting putative regulatory roles in the regulation of P homeostasis. Our work provides additional molecular insights into the resilience of diatoms and their ecological success, and opens up novel routes to address and explore the function and regulatory roles of P. tricornutum lincRNAs in the context of nutrient stress.
Collapse
Affiliation(s)
- Maria Helena Cruz de Carvalho
- Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY, 10065, USA
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 INSERM U1024, 46 Rue d'Ulm, 75005, Paris, France
| | - Hai-Xi Sun
- Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY, 10065, USA
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 INSERM U1024, 46 Rue d'Ulm, 75005, Paris, France
| | - Nam-Hai Chua
- Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY, 10065, USA
| |
Collapse
|
136
|
Shemi A, Ben-Dor S, Vardi A. Elucidating the composition and conservation of the autophagy pathway in photosynthetic eukaryotes. Autophagy 2016; 11:701-15. [PMID: 25915714 DOI: 10.1080/15548627.2015.1034407] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Aquatic photosynthetic eukaryotes represent highly diverse groups (green, red, and chromalveolate algae) derived from multiple endosymbiosis events, covering a wide spectrum of the tree of life. They are responsible for about 50% of the global photosynthesis and serve as the foundation for oceanic and fresh water food webs. Although the ecophysiology and molecular ecology of some algal species are extensively studied, some basic aspects of algal cell biology are still underexplored. The recent wealth of genomic resources from algae has opened new frontiers to decipher the role of cell signaling pathways and their function in an ecological and biotechnological context. Here, we took a bioinformatic approach to explore the distribution and conservation of TOR and autophagy-related (ATG) proteins (Atg in yeast) in diverse algal groups. Our genomic analysis demonstrates conservation of TOR and ATG proteins in green algae. In contrast, in all 5 available red algal genomes, we could not detect the sequences that encode for any of the 17 core ATG proteins examined, albeit TOR and its interacting proteins are conserved. This intriguing data suggests that the autophagy pathway is not conserved in red algae as it is in the entire eukaryote domain. In contrast, chromalveolates, despite being derived from the red-plastid lineage, retain and express ATG genes, which raises a fundamental question regarding the acquisition of ATG genes during algal evolution. Among chromalveolates, Emiliania huxleyi (Haptophyta), a bloom-forming coccolithophore, possesses the most complete set of ATG genes, and may serve as a model organism to study autophagy in marine protists with great ecological significance.
Collapse
Key Words
- ATG, autophagy related
- ATG8
- ATG9
- DUF, domain of unknown function
- EST, expressed sequence tag
- EhV, Emiliania huxleyi virus
- GABARAP, GABA(A) receptor-associated protein
- PtdIns3K, phosphatidylinositol 3-kinase
- RPTOR, regulatory associated protein of MTOR, complex 1
- TOR, target of rapamycin
- TORC, target of rapamycin complex
- Ubl, ubiquitin-like
- Vps, vacuolar protein sorting
- algae
- autophagy
- blooms
- chromalveolata
- phylogenetics
- phytoplankton
- rhodophyta
- stress
Collapse
Affiliation(s)
- Adva Shemi
- a Department of Plant Sciences ; Weizmann Institute of Science ; Rehovot , Israel
| | | | | |
Collapse
|
137
|
Piccinetti CC, Ricci R, Pennesi C, Radaelli G, Totti C, Norici A, Giordano M, Olivotto I. Herbivory in the soft coral Sinularia flexibilis (Alcyoniidae). Sci Rep 2016; 6:22679. [PMID: 26951778 PMCID: PMC4782107 DOI: 10.1038/srep22679] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/17/2016] [Indexed: 11/09/2022] Open
Abstract
Our work provides strong support for the hypothesis that Sinularia flexibilis ingests diatoms such as Thalassiosira pseudonana. We assessed algal ingestion by S. flexibilis through estimates of algal removal, histological analyses, scanning electron microscopy observations, and gene expression determination (18S and silicon transporter 1) by real time PCR. Cell counts are strongly suggestive of algal removal by the coral; light and scanning microscopy provide qualitative evidence for the ingestion of T. pseudonana by S. flexibilis, while molecular markers did not prove to be sufficiently selective/specific to give clear results. We thus propose that previous instances of inability of corals to ingest algae are reconsidered using different technical approach, before concluding that coral herbivory is not a general feature.
Collapse
Affiliation(s)
- Chiara C Piccinetti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Roberta Ricci
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Chiara Pennesi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Giuseppe Radaelli
- Dipartimento di Biomedicina Comparata e Alimentazione, Università degli Studi di Padova, Agripolis, Viale dell'Università, 16, 35020 Legnaro, Italy
| | - Cecilia Totti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Alessandra Norici
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Mario Giordano
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.,Institute of Microbiology ASCR, Centrum Algatech, Laboratory of photosynthesis, Opatovický mlýn, 379 81 Třeboň, Czech Republic.,National Research Council, Institute of Marine Science, Venezia, Italy
| | - Ike Olivotto
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| |
Collapse
|
138
|
Abstract
Dissolved organic matter (DOM) in the oceans is one of the largest pools of reduced carbon on Earth, comparable in size to the atmospheric CO2 reservoir. A vast number of compounds are present in DOM, and they play important roles in all major element cycles, contribute to the storage of atmospheric CO2 in the ocean, support marine ecosystems, and facilitate interactions between organisms. At the heart of the DOM cycle lie molecular-level relationships between the individual compounds in DOM and the members of the ocean microbiome that produce and consume them. In the past, these connections have eluded clear definition because of the sheer numerical complexity of both DOM molecules and microorganisms. Emerging tools in analytical chemistry, microbiology, and informatics are breaking down the barriers to a fuller appreciation of these connections. Here we highlight questions being addressed using recent methodological and technological developments in those fields and consider how these advances are transforming our understanding of some of the most important reactions of the marine carbon cycle.
Collapse
|
139
|
Bajhaiya AK, Dean AP, Zeef LAH, Webster RE, Pittman JK. PSR1 Is a Global Transcriptional Regulator of Phosphorus Deficiency Responses and Carbon Storage Metabolism in Chlamydomonas reinhardtii. PLANT PHYSIOLOGY 2016; 170:1216-34. [PMID: 26704642 PMCID: PMC4775146 DOI: 10.1104/pp.15.01907] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 12/23/2015] [Indexed: 05/18/2023]
Abstract
Many eukaryotic microalgae modify their metabolism in response to nutrient stresses such as phosphorus (P) starvation, which substantially induces storage metabolite biosynthesis, but the genetic mechanisms regulating this response are poorly understood. Here, we show that P starvation-induced lipid and starch accumulation is inhibited in a Chlamydomonas reinhardtii mutant lacking the transcription factor Pi Starvation Response1 (PSR1). Transcriptomic analysis identified specific metabolism transcripts that are induced by P starvation but misregulated in the psr1 mutant. These include transcripts for starch and triacylglycerol synthesis but also transcripts for photosynthesis-, redox-, and stress signaling-related proteins. To further examine the role of PSR1 in regulating lipid and starch metabolism, PSR1 complementation lines in the psr1 strain and PSR1 overexpression lines in a cell wall-deficient strain were generated. PSR1 expression in the psr1 lines was shown to be functional due to rescue of the psr1 phenotype. PSR1 overexpression lines exhibited increased starch content and number of starch granules per cell, which correlated with a higher expression of specific starch metabolism genes but reduced neutral lipid content. Furthermore, this phenotype was consistent in the presence and absence of acetate. Together, these results identify a key transcriptional regulator in global metabolism and demonstrate transcriptional engineering in microalgae to modulate starch biosynthesis.
Collapse
Affiliation(s)
- Amit K Bajhaiya
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Andrew P Dean
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Leo A H Zeef
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Rachel E Webster
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Jon K Pittman
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| |
Collapse
|
140
|
Lin S, Litaker RW, Sunda WG. Phosphorus physiological ecology and molecular mechanisms in marine phytoplankton. JOURNAL OF PHYCOLOGY 2016; 52:10-36. [PMID: 26987085 DOI: 10.1111/jpy.12365] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 09/26/2015] [Indexed: 05/24/2023]
Abstract
Phosphorus (P) is an essential nutrient for marine phytoplankton and indeed all life forms. Current data show that P availability is growth-limiting in certain marine systems and can impact algal species composition. Available P occurs in marine waters as dissolved inorganic phosphate (primarily orthophosphate [Pi]) or as a myriad of dissolved organic phosphorus (DOP) compounds. Despite numerous studies on P physiology and ecology and increasing research on genomics in marine phytoplankton, there have been few attempts to synthesize information from these different disciplines. This paper is aimed to integrate the physiological and molecular information on the acquisition, utilization, and storage of P in marine phytoplankton and the strategies used by these organisms to acclimate and adapt to variations in P availability. Where applicable, we attempt to identify gaps in our current knowledge that warrant further research and examine possible metabolic pathways that might occur in phytoplankton from well-studied bacterial models. Physical and chemical limitations governing cellular P uptake are explored along with physiological and molecular mechanisms to adapt and acclimate to temporally and spatially varying P nutrient regimes. Topics covered include cellular Pi uptake and feedback regulation of uptake systems, enzymatic utilization of DOP, P acquisition by phagotrophy, P-limitation of phytoplankton growth in oceanic and coastal waters, and the role of P-limitation in regulating cell size and toxin levels in phytoplankton. Finally, we examine the role of P and other nutrients in the transition of phytoplankton communities from early succession species (diatoms) to late succession ones (e.g., dinoflagellates and haptophytes).
Collapse
Affiliation(s)
- Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
| | - Richard Wayne Litaker
- National Oceanic and Atmospheric Administration, National Ocean Service, Center for Coastal Fisheries and Habitat Research, Beaufort, North Carolina, 28516, USA
| | - William G Sunda
- National Oceanic and Atmospheric Administration, National Ocean Service, Center for Coastal Fisheries and Habitat Research, Beaufort, North Carolina, 28516, USA
| |
Collapse
|
141
|
Harke MJ, Davis TW, Watson SB, Gobler CJ. Nutrient-Controlled Niche Differentiation of Western Lake Erie Cyanobacterial Populations Revealed via Metatranscriptomic Surveys. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:604-615. [PMID: 26654276 DOI: 10.1021/acs.est.5b03931] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Although toxic cyanobacterial blooms in western Lake Erie threaten drinking water supplies and are promoted by nutrient loading, the precise nutrient regime that selects specific cyanobacteria populations is poorly understood. Here, we assess shifts in cyanobacterial abundances and global gene-expression patterns in response to natural and manipulated gradients in nitrogen and phosphorus to identify gene pathways that facilitate dominance by different cyanobacteria. Gradients in soluble reactive phosphorus shaped cyanobacterial communities and elicited the largest transcriptomic responses. Under high-P conditions (closest to the mouth of the Maumee River), Anabaena and Planktothrix were the dominant cyanobacterial populations, and experimental P and ammonium enrichment promoted nitrogen fixation gene (nifH) expression in Anabaena. For Microcystis, experimental additions of P up-regulated genes involved in phage defense, genomic rearrangement, and nitrogen acquisition but led to lower abundances. Within offshore, low-P regions of the western basin of Lake Erie, Microcystis up-regulated genes associated with P scavenging (pstSCAB, phoX) and dominated cyanobacterial communities. Experimental additions of ammonium and urea did not alter Microcystis abundances but did up-regulate protease inhibitors (aer and mcn gene sets) and microcystin synthetase genes (mcy), with urea enrichment yielding significant increases in microcystin concentrations. Our findings suggest that management plans that reduce P loads alone may not significantly reduce the risk of cyanobacterial blooms in western Lake Erie but rather may promote a shift among cyanobacterial populations (Microcystis, Anabaena, and Planktothrix) toward a greater dominance by toxic strains of Microcystis.
Collapse
Affiliation(s)
- Matthew J Harke
- School of Marine and Atmospheric Sciences, Stony Brook University , Stony Brook, New York 11794, United States
| | - Timothy W Davis
- NOAA Great Lakes Environmental Research Laboratory , 4840 S. State Road, Ann Arbor, Michigan 48108, United States
| | - Susan B Watson
- Canadian Centre for Inland Waters, Environment Canada , Burlington, Ontario L7R 4A6, Canada
| | - Christopher J Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University , Stony Brook, New York 11794, United States
| |
Collapse
|
142
|
Gu H, Jinkerson RE, Davies FK, Sisson LA, Schneider PE, Posewitz MC. Modulation of Medium-Chain Fatty Acid Synthesis in Synechococcus sp. PCC 7002 by Replacing FabH with a Chaetoceros Ketoacyl-ACP Synthase. FRONTIERS IN PLANT SCIENCE 2016; 7:690. [PMID: 27303412 PMCID: PMC4880568 DOI: 10.3389/fpls.2016.00690] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/05/2016] [Indexed: 05/12/2023]
Abstract
The isolation or engineering of algal cells synthesizing high levels of medium-chain fatty acids (MCFAs) is attractive to mitigate the high clouding point of longer chain fatty acids in algal based biodiesel. To develop a more informed understanding of MCFA synthesis in photosynthetic microorganisms, we isolated several algae from Great Salt Lake and screened this collection for MCFA accumulation to identify strains naturally accumulating high levels of MCFA. A diatom, Chaetoceros sp. GSL56, accumulated particularly high levels of C14 (up to 40%), with the majority of C14 fatty acids allocated in triacylglycerols. Using whole cell transcriptome sequencing and de novo assembly, putative genes encoding fatty acid synthesis enzymes were identified. Enzymes from this Chaetoceros sp. were expressed in the cyanobacterium Synechococcus sp. PCC 7002 to validate gene function and to determine whether eukaryotic enzymes putatively lacking bacterial evolutionary control mechanisms could be used to improve MCFA production in this promising production strain. Replacement of the Synechococcus 7002 native FabH with a Chaetoceros ketoacyl-ACP synthase III increased MCFA synthesis up to fivefold. The level of increase is dependent on promoter strength and culturing conditions.
Collapse
Affiliation(s)
- Huiya Gu
- Department of Chemistry and Geochemistry, Colorado School of Mines, GoldenCO, USA
| | - Robert E. Jinkerson
- Department of Plant Biology, Carnegie Institution for Science, StanfordCA, USA
| | - Fiona K. Davies
- Department of Chemistry and Geochemistry, Colorado School of Mines, GoldenCO, USA
| | - Lyle A. Sisson
- Department of Chemistry and Geochemistry, Colorado School of Mines, GoldenCO, USA
| | - Philip E. Schneider
- Department of Chemistry and Geochemistry, Colorado School of Mines, GoldenCO, USA
| | - Matthew C. Posewitz
- Department of Chemistry and Geochemistry, Colorado School of Mines, GoldenCO, USA
- *Correspondence: Matthew C. Posewitz,
| |
Collapse
|
143
|
Functional group-specific traits drive phytoplankton dynamics in the oligotrophic ocean. Proc Natl Acad Sci U S A 2015; 112:E5972-9. [PMID: 26460011 DOI: 10.1073/pnas.1518165112] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A diverse microbial assemblage in the ocean is responsible for nearly half of global primary production. It has been hypothesized and experimentally demonstrated that nutrient loading can stimulate blooms of large eukaryotic phytoplankton in oligotrophic systems. Although central to balancing biogeochemical models, knowledge of the metabolic traits that govern the dynamics of these bloom-forming phytoplankton is limited. We used eukaryotic metatranscriptomic techniques to identify the metabolic basis of functional group-specific traits that may drive the shift between net heterotrophy and autotrophy in the oligotrophic ocean. Replicated blooms were simulated by deep seawater (DSW) addition to mimic nutrient loading in the North Pacific Subtropical Gyre, and the transcriptional responses of phytoplankton functional groups were assayed. Responses of the diatom, haptophyte, and dinoflagellate functional groups in simulated blooms were unique, with diatoms and haptophytes significantly (95% confidence) shifting their quantitative metabolic fingerprint from the in situ condition, whereas dinoflagellates showed little response. Significantly differentially abundant genes identified the importance of colimitation by nutrients, metals, and vitamins in eukaryotic phytoplankton metabolism and bloom formation in this system. The variable transcript allocation ratio, used to quantify transcript reallocation following DSW amendment, differed for diatoms and haptophytes, reflecting the long-standing paradigm of phytoplankton r- and K-type growth strategies. Although the underlying metabolic potential of the large eukaryotic phytoplankton was consistently present, the lack of a bloom during the study period suggests a crucial dependence on physical and biogeochemical forcing, which are susceptible to alteration with changing climate.
Collapse
|
144
|
Muhseen ZT, Xiong Q, Chen Z, Ge F. Proteomics studies on stress responses in diatoms. Proteomics 2015; 15:3943-53. [PMID: 26364674 DOI: 10.1002/pmic.201500165] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 08/09/2015] [Accepted: 09/09/2015] [Indexed: 01/09/2023]
Abstract
Diatoms are a highly diverse group of eukaryotic phytoplankton that are distributed throughout marine and freshwater environments and are believed to be responsible for approximately 40% of the total marine primary productivity. The ecological success of diatoms suggests that they have developed a range of strategies to cope with various biotic and abiotic stress factors. It is of great interest to understand the adaptive responses of diatoms to different stresses in the marine environment. Proteomic technologies have been applied to the adaptive responses of marine diatoms under different growth conditions in recent years such as nitrogen starvation, iron limitation and phosphorus deficiency. These studies have provided clues to elucidate the sophisticated sensing mechanisms that control their adaptive responses. Although only a very limited number of proteomic studies were conducted in diatoms, the obtained data have led to a better understanding of the biochemical processes that contribute to their ecological success. This review presents the current status of proteomic studies of diatom stress responses and discusses the novel developments and applications for the analysis of protein post-translational modification in diatoms. The potential future application of proteomics could contribute to a better understanding of the physiological mechanisms underlying diatom acclimation to a given stress and the acquisition of an enhanced diatom stress tolerance. Future challenges and research opportunities in the proteomics studies of diatoms are also discussed.
Collapse
Affiliation(s)
- Ziyad Tariq Muhseen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Qian Xiong
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Zhuo Chen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| |
Collapse
|
145
|
McKew BA, Metodieva G, Raines CA, Metodiev MV, Geider RJ. Acclimation of Emiliania huxleyi (1516) to nutrient limitation involves precise modification of the proteome to scavenge alternative sources of N and P. Environ Microbiol 2015; 17:4050-62. [PMID: 26119724 PMCID: PMC4989451 DOI: 10.1111/1462-2920.12957] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 06/15/2015] [Accepted: 06/15/2015] [Indexed: 11/26/2022]
Abstract
Limitation of marine primary production by the availability of nitrogen or phosphorus is common. Emiliania huxleyi, a ubiquitous phytoplankter that plays key roles in primary production, calcium carbonate precipitation and production of dimethyl sulfide, often blooms in mid-latitude at the beginning of summer when inorganic nutrient concentrations are low. To understand physiological mechanisms that allow such blooms, we examined how the proteome of E. huxleyi (strain 1516) responds to N and P limitation. We observed modest changes in much of the proteome despite large physiological changes (e.g. cellular biomass, C, N and P) associated with nutrient limitation of growth rate. Acclimation to nutrient limitation did however involve significant increases in the abundance of transporters for ammonium and nitrate under N limitation and for phosphate under P limitation. More notable were large increases in proteins involved in the acquisition of organic forms of N and P, including urea and amino acid/polyamine transporters and numerous C-N hydrolases under N limitation and a large upregulation of alkaline phosphatase under P limitation. This highly targeted reorganization of the proteome towards scavenging organic forms of macronutrients gives unique insight into the molecular mechanisms that underpin how E. huxleyi has found its niche to bloom in surface waters depleted of inorganic nutrients.
Collapse
Affiliation(s)
- Boyd A McKew
- School of Biological Sciences, University of Essex, Wivenhoe Park, Wivenhoe, Colchester, CO4 3SQ, UK
| | - Gergana Metodieva
- School of Biological Sciences, University of Essex, Wivenhoe Park, Wivenhoe, Colchester, CO4 3SQ, UK
| | - Christine A Raines
- School of Biological Sciences, University of Essex, Wivenhoe Park, Wivenhoe, Colchester, CO4 3SQ, UK
| | - Metodi V Metodiev
- School of Biological Sciences, University of Essex, Wivenhoe Park, Wivenhoe, Colchester, CO4 3SQ, UK
| | - Richard J Geider
- School of Biological Sciences, University of Essex, Wivenhoe Park, Wivenhoe, Colchester, CO4 3SQ, UK
| |
Collapse
|
146
|
Kulakovskaya TV, Lichko LP, Ryazanova LP. Diversity of phosphorus reserves in microorganisms. BIOCHEMISTRY (MOSCOW) 2015; 79:1602-14. [PMID: 25749167 DOI: 10.1134/s0006297914130100] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Phosphorus compounds are indispensable components of the Earth's biomass metabolized by all living organisms. Under excess of phosphorus compounds in the environment, microorganisms accumulate reserve phosphorus compounds that are used under phosphorus limitation. These compounds vary in their structure and also perform structural and regulatory functions in microbial cells. The most common phosphorus reserve in microorganism is inorganic polyphosphates, but in some archae and bacteria insoluble magnesium phosphate plays this role. Some yeasts produce phosphomannan as a phosphorus reserve. This review covers also other topics, i.e. accumulation of phosphorus reserves under nutrient limitation, phosphorus reserves in activated sludge, mycorrhiza, and the role of mineral phosphorus compounds in mammals.
Collapse
Affiliation(s)
- T V Kulakovskaya
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | | | | |
Collapse
|
147
|
Irreversibly increased nitrogen fixation in Trichodesmium experimentally adapted to elevated carbon dioxide. Nat Commun 2015; 6:8155. [PMID: 26327191 PMCID: PMC4569722 DOI: 10.1038/ncomms9155] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 07/23/2015] [Indexed: 11/09/2022] Open
Abstract
Nitrogen fixation rates of the globally distributed, biogeochemically important marine cyanobacterium Trichodesmium increase under high carbon dioxide (CO2) levels in short-term studies due to physiological plasticity. However, its long-term adaptive responses to ongoing anthropogenic CO2 increases are unknown. Here we show that experimental evolution under extended selection at projected future elevated CO2 levels results in irreversible, large increases in nitrogen fixation and growth rates, even after being moved back to lower present day CO2 levels for hundreds of generations. This represents an unprecedented microbial evolutionary response, as reproductive fitness increases acquired in the selection environment are maintained after returning to the ancestral environment. Constitutive rate increases are accompanied by irreversible shifts in diel nitrogen fixation patterns, and increased activity of a potentially regulatory DNA methyltransferase enzyme. High CO2-selected cell lines also exhibit increased phosphorus-limited growth rates, suggesting a potential advantage for this keystone organism in a more nutrient-limited, acidified future ocean. The long-term response of marine cyanobacteria to increased anthropogenic CO2 are not known. Here, Hutchins et al. show that Trichodesmium exposed to long-term selection at elevated CO2 display irreversible increases in nitrogen fixation and growth rates, even after returning to present day conditions.
Collapse
|
148
|
Richardson B, Corcoran AA. Use of dissolved inorganic and organic phosphorus by axenic and nonaxenic clones of Karenia brevis and Karenia mikimotoi. HARMFUL ALGAE 2015; 48:30-36. [PMID: 29724473 DOI: 10.1016/j.hal.2015.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Revised: 05/19/2015] [Accepted: 06/11/2015] [Indexed: 06/08/2023]
Abstract
Nearly annual blooms of the marine dinoflagellate Karenia brevis, which initiate offshore on the West Florida Shelf in oligotrophic waters, cause widespread environmental and economic damage. The success of K. brevis as a bloom-former is partially attributed to its ability to use a diverse suite of nutrients from natural and anthropogenic sources, although relatively little is known about the ability of K. brevis and the closely related Karenia mikimotoi to use a variety of organic sources of phosphorus, including phosphomonoesters, phosphodiesters, and phosphonates. Through a series of bioassays, this study characterized the ability of axenic and nonaxenic K. brevis and K. mikimotoi clones isolated from Florida waters to use a variety of organic phosphorus compounds as the sole source of phosphorus for growth, comparing this utilization to that of inorganic sources of phosphate. Differing abilities of axenic and nonaxenic K. brevis and K. mikimotoi cultures to use phosphorus from the compounds evaluated were documented. Specifically, growth of axenic cultures was greatest on inorganic phosphorus and was not supported on the phosphomonoester phytate, or generally on phosphodiesters or phosphonates. The nonaxenic cultures were able to use organic compounds that the axenic cultures were not able to use, often after lags in growth, highlighting a potential role of co-associated bacterial communities to transform nutrients to bioavailable forms. Given the ability of K. brevis and K. mikimotoi to use a diverse suite of inorganic and organic phosphorus, bloom mitigation strategies should consider all nutrient forms.
Collapse
Affiliation(s)
- Bill Richardson
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, 100 8th Avenue SE, St. Petersburg, FL 33701, USA
| | - Alina A Corcoran
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, 100 8th Avenue SE, St. Petersburg, FL 33701, USA.
| |
Collapse
|
149
|
Lin X, Wang L, Shi X, Lin S. Rapidly diverging evolution of an atypical alkaline phosphatase (PhoA(aty)) in marine phytoplankton: insights from dinoflagellate alkaline phosphatases. Front Microbiol 2015; 6:868. [PMID: 26379645 PMCID: PMC4548154 DOI: 10.3389/fmicb.2015.00868] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 08/10/2015] [Indexed: 11/13/2022] Open
Abstract
Alkaline phosphatase (AP) is a key enzyme that enables marine phytoplankton to scavenge phosphorus (P) from dissolved organic phosphorus (DOP) when inorganic phosphate is scarce in the ocean. Yet how the AP gene has evolved in phytoplankton, particularly dinoflagellates, is poorly understood. We sequenced full-length AP genes and corresponding complementary DNA (cDNA) from 15 strains (10 species), representing four classes of the core dinoflagellate lineage, Gymnodiniales, Prorocentrales, Suessiales, and Gonyaulacales. Dinoflagellate AP gene sequences exhibited high variability, containing variable introns, pseudogenes, single nucleotide polymorphisms and consequent variations in amino acid sequence, indicative of gene duplication events and consistent with the “birth-and-death” model of gene evolution. Further sequence comparison showed that dinoflagellate APs likely belong to an atypical type AP (PhoAaty), which shares conserved motifs with counterparts in marine bacteria, cyanobacteria, green algae, haptophytes, and stramenopiles. Phylogenetic analysis suggested that PhoAaty probably originated from an ancestral gene in bacteria and evolved divergently in marine phytoplankton. Because variations in AP amino acid sequences may lead to differential subcellular localization and potentially different metal ion requirements, the multiple types of APs in algae may have resulted from selection for diversifying strategies to utilize DOP in the P variable marine environment.
Collapse
Affiliation(s)
- Xin Lin
- State Key Laboratory of Marine Environmental Science, Xiamen University Xiamen, China
| | - Lu Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University Xiamen, China
| | - Xinguo Shi
- State Key Laboratory of Marine Environmental Science, Xiamen University Xiamen, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, Xiamen University Xiamen, China ; Department of Marine Sciences, University of Connecticut Groton, CT, USA
| |
Collapse
|
150
|
Zhang H, Wang DZ, Xie ZX, Zhang SF, Wang MH, Lin L. Comparative proteomics reveals highly and differentially expressed proteins in field-collected and laboratory-cultured blooming cells of the diatom S
keletonema costatum. Environ Microbiol 2015; 17:3976-91. [DOI: 10.1111/1462-2920.12914] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Accepted: 05/19/2015] [Indexed: 01/09/2023]
Affiliation(s)
- Hao Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology; Xiamen University; Xiamen 361005 China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology; Xiamen University; Xiamen 361005 China
| | - Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology; Xiamen University; Xiamen 361005 China
| | - Shu-Fei Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology; Xiamen University; Xiamen 361005 China
| | - Ming-Hua Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology; Xiamen University; Xiamen 361005 China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology; Xiamen University; Xiamen 361005 China
| |
Collapse
|