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Wang C, Li J, Li S, Lin S. Effects and mechanisms of glyphosate as phosphorus nutrient on element stoichiometry and metabolism in the diatom Phaeodactylum tricornutum. Appl Environ Microbiol 2024; 90:e0213123. [PMID: 38265214 PMCID: PMC10880665 DOI: 10.1128/aem.02131-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 12/24/2023] [Indexed: 01/25/2024] Open
Abstract
The ability to utilize dissolved organic phosphorus (DOP) gives phytoplankton competitive advantages in P-limited environments. Our previous research indicates that the diatom Phaeodactylum tricornutum could grow on glyphosate, a DOP with carbon-phosphorus (C-P) bond and an herbicide, as sole P source. However, direct evidence and mechanism of glyphosate utilization are still lacking. In this study, using physiological and isotopic analysis, combined with transcriptomic profiling, we demonstrated the uptake of glyphosate by P. tricornutum and revealed the candidate responsible genes. Our data showed a low efficiency of glyphosate utilization by P. tricornutum, suggesting that glyphosate utilization costs energy and that the alga possessed an herbicide-resistant type of 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase. Compared to the P-limited cultures, the glyphosate-grown P. tricornutum cells up-regulated genes involved in DNA replication, cell growth, transcription, translation, carbon metabolism, and many genes encoding antioxidants. Additionally, cellular C and silicon (Si) increased remarkably while cellular nitrogen (N) declined in the glyphosate-grown P. tricornutum, leading to higher Si:C and Si:N ratios, which corresponded to the up-regulation of genes involved in the C metabolism and Si uptake and the down-regulation of those encoding N uptake. This has the potential to enhance C and Si export to the deep sea when P is limited but phosphonate is available. In sum, our study documented how P. tricornutum could utilize the herbicide glyphosate as P nutrient and how glyphosate utilization may affect the element content and stoichiometry in this diatom, which have important ecological implications in the future ocean.IMPORTANCEGlyphosate is the most widely used herbicide in the world and could be utilized as phosphorus (P) source by some bacteria. Our study first revealed that glyphosate could be transported into Phaeodactylum tricornutum cells for utilization and identified putative genes responsible for glyphosate uptake. This uncovers an alternative strategy of phytoplankton to cope with P deficiency considering phosphonate accounts for about 25% of the total dissolved organic phosphorus (DOP) in the ocean. Additionally, accumulation of carbon (C) and silicon (Si), as well as elevation of Si:C ratio in P. tricornutum cells when grown on glyphosate indicates glyphosate as the source of P nutrient has the potential to result in more C and Si export into the deep ocean. This, along with the differential ability to utilize glyphosate among different species, glyphosate supply in dissolved inorganic phosphorus (DIP)-depleted ecosystems may cause changes in phytoplankton community structure. These insights have implications in evaluating the effects of human activities (use of Roundup) and climate change (potentially reducing DIP supply in sunlit layer) on phytoplankton in the future ocean.
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Affiliation(s)
- Cong Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Jiashun Li
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Sihan Li
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, USA
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Yu G, Nakajima K, Gruber A, Rio Bartulos C, Schober AF, Lepetit B, Yohannes E, Matsuda Y, Kroth PG. Mitochondrial phosphoenolpyruvate carboxylase contributes to carbon fixation in the diatom Phaeodactylum tricornutum at low inorganic carbon concentrations. THE NEW PHYTOLOGIST 2022; 235:1379-1393. [PMID: 35596716 DOI: 10.1111/nph.18268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
Photosynthetic carbon fixation is often limited by CO2 availability, which led to the evolution of CO2 concentrating mechanisms (CCMs). Some diatoms possess CCMs that employ biochemical fixation of bicarbonate, similar to C4 plants, but whether biochemical CCMs are commonly found in diatoms is a subject of debate. In the diatom Phaeodactylum tricornutum, phosphoenolpyruvate carboxylase (PEPC) is present in two isoforms, PEPC1 in the plastids and PEPC2 in the mitochondria. We used real-time quantitative polymerase chain reaction, Western blots, and enzymatic assays to examine PEPC expression and PEPC activity, under low and high concentrations of dissolved inorganic carbon (DIC). We generated and analyzed individual knockout cell lines of PEPC1 and PEPC2, as well as a PEPC1/2 double-knockout strain. While we could not detect an altered phenotype in the PEPC1 knockout strains at ambient, low or high DIC concentrations, PEPC2 and the double-knockout strains grown under ambient air or lower DIC availability conditions showed reduced growth and photosynthetic affinity for DIC while behaving similarly to wild-type (WT) cells at high DIC concentrations. These mutants furthermore exhibited significantly lower 13 C/12 C ratios compared to the WT. Our data imply that in P. tricornutum at least parts of the CCM rely on biochemical bicarbonate fixation catalyzed by the mitochondrial PEPC2.
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Affiliation(s)
- Guilan Yu
- Fachbereich Biologie, Universität Konstanz, 78457, Konstanz, Germany
| | - Kensuke Nakajima
- Department of Bioscience, School of Biological and Environmental Sciences, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1330, Japan
| | - Ansgar Gruber
- Fachbereich Biologie, Universität Konstanz, 78457, Konstanz, Germany
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic
| | | | | | - Bernard Lepetit
- Fachbereich Biologie, Universität Konstanz, 78457, Konstanz, Germany
| | | | - Yusuke Matsuda
- Department of Bioscience, School of Biological and Environmental Sciences, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1330, Japan
| | - Peter G Kroth
- Fachbereich Biologie, Universität Konstanz, 78457, Konstanz, Germany
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Wu S, Gu W, Jia S, Wang L, Wang L, Liu X, Zhou L, Huang A, Wang G. Proteomic and biochemical responses to different concentrations of CO 2 suggest the existence of multiple carbon metabolism strategies in Phaeodactylum tricornutum. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:235. [PMID: 34906223 PMCID: PMC8670125 DOI: 10.1186/s13068-021-02088-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Diatoms are well known for high photosynthetic efficiency and rapid growth rate, which are not only important oceanic primary producer, but also ideal feedstock for microalgae industrialization. Their high success is mainly due to the rapid response of photosynthesis to inorganic carbon fluctuations. Thus, an in-depth understanding of the photosynthetic carbon fixation mechanism of diatoms will be of great help to microalgae-based applications. This work directed toward the analysis of whether C4 photosynthetic pathway functions in the model marine diatom Phaeodactylum tricornutum, which possesses biophysical CO2-concentrating mechanism (CCM) as well as metabolic enzymes potentially involved in C4 photosynthetic pathway. RESULTS For P. tricornutum, differential proteome, enzyme activities and transcript abundance of carbon metabolism-related genes especially biophysical and biochemical CCM-related genes in response to different concentrations of CO2 were tracked in this study. The upregulated protein abundance of a carbonic anhydrases and a bicarbonate transporter suggested biophysical CCM activated under low CO2 (LC). The upregulation of a number of key C4-related enzymes in enzymatic activity, transcript and protein abundance under LC indicated the induction of a mitochondria-mediated CCM in P. tricornutum. Moreover, protein abundance of a number of glycolysis, tricarboxylic acid cycle, photorespiration and ornithine-urea cycle related proteins upregulated under LC, while numbers of proteins involved in the Calvin cycle and pentose phosphate pathway were downregulated. Under high CO2 (HC), protein abundance of most central carbon metabolism and photosynthesis-related proteins were upregulated. CONCLUSIONS The proteomic and biochemical responses to different concentrations of CO2 suggested multiple carbon metabolism strategies exist in P. tricornutum. Namely, LC might induce a mitochondrial-mediated C4-like CCM and the improvement of glycolysis, tricarboxylic acid cycle, photorespiration and ornithine-urea cycle activity contribute to the energy supply and carbon and nitrogen recapture in P. tricornutum to cope with the CO2 limitation, while P. tricornutum responds to the HC environment by improving photosynthesis and central carbon metabolism activity. These findings can not only provide evidences for revealing the global picture of biophysical and biochemical CCM in P. tricornutum, but also provide target genes for further microalgal strain modification to improve carbon fixation and biomass yield in algal-based industry.
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Affiliation(s)
- Songcui Wu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Wenhui Gu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Shuao Jia
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lepu Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lijun Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Xuehua Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lu Zhou
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Aiyou Huang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
- College of Marine Sciences, Hainan University, Haikou, 570228, China.
| | - Guangce Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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Zhang H, Zhou Y, Liu TQ, Yin XJ, Lin L, Lin Q, Wang DZ. Initiation of efficient C 4 pathway in response to low ambient CO 2 during the bloom period of a marine dinoflagellate. Environ Microbiol 2021; 23:3196-3211. [PMID: 33938118 DOI: 10.1111/1462-2920.15545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 04/26/2021] [Indexed: 11/29/2022]
Abstract
Dinoflagellates are important primary producers and major causative agents of harmful algal blooms in the global ocean. Despite the great ecological significance, the photosynthetic carbon acquisition by dinoflagellates is still poorly understood. The pathways of photosynthetic carbon assimilation in a marine dinoflagellate Prorocentrum donghaiense under both in situ and laboratory-simulated bloom conditions were investigated using a combination of metaproteomics, qPCR, stable carbon isotope and targeted metabolomics approaches. A rapid consumption of dissolved CO2 to generate high biomass was observed as the bloom proceeded. The carbon assimilation genes and proteins including intracellular carbonic anhydrase 2, phosphoenolpyruvate carboxylase, phosphoenolpyruvate carboxykinase and RubisCO as well as their enzyme activities were all highly expressed at the low CO2 level, indicating that C4 photosynthetic pathway functioned in the blooming P. donghaiense cells. Furthermore, δ13 C values and content of C4 compound (malate) significantly increased with the decreasing CO2 concentration. The transition from C3 to C4 pathway minimizes the internal CO2 leakage and guarantees efficient carbon fixation at the low CO2 level. This study demonstrates the existence of C4 photosynthetic pathway in a marine dinoflagellate and reveals its important complementary role to assist carbon assimilation for cell proliferation during the bloom period.
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Affiliation(s)
- Hao Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China.,CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Youping Zhou
- Isotopomics in Chemical Biology & Shaanxi Key Laboratory of Chemical Additives for Industry, School of Chemistry & Chemical Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Tian-Qi Liu
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Xi-Jie Yin
- Laboratory of Marine & Coastal Geology, MNR Third Institute of Oceanology, Xiamen, 361005, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
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Zhang M, Zhen Y, Mi T, Lin S. Integrated RNA-seq and Proteomic Studies Reveal Resource Reallocation towards Energy Metabolism and Defense in Skeletonema marinoi in Response to CO 2 Increase. Appl Environ Microbiol 2021; 87:AEM.02614-20. [PMID: 33355106 PMCID: PMC8090871 DOI: 10.1128/aem.02614-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/05/2020] [Indexed: 11/20/2022] Open
Abstract
Rising atmospheric CO2 concentrations are causing ocean acidification (OA) with significant consequences for marine organisms. Because CO2 is essential for photosynthesis, the effect of elevated CO2 on phytoplankton is more complex and the mechanism is poorly understood. Here we applied RNA-seq and iTRAQ proteomics to investigate the impacts of CO2 increase (from ∼400 to 1000 ppm) on the temperate coastal marine diatom Skeletonema marinoi We identified 32,389 differentially expressed genes (DEGs) and 1,826 differentially expressed proteins (DEPs) from elevated CO2 conditions, accounting for 48.5% of total genes and 25.9% of total proteins we detected, respectively. Elevated pCO2 significantly inhibited the growth of S marinoi, and the 'omic' data suggested that this might be due to compromised photosynthesis in the chloroplast and raised mitochondrial energy metabolism. Furthermore, many genes/proteins associated with nitrogen metabolism, transcriptional regulation, and translational regulation were markedly up-regulated, suggesting enhanced protein synthesis. In addition, S marinoi exhibited higher capacity of ROS production and resistance to oxidative stress. Overall, elevated pCO2 seems to repress photosynthesis and growth of S marinoi, and through massive gene expression reconfiguration induce cells to increase investment in protein synthesis, energy metabolism and antioxidative stress defense, likely to maintain pH homeostasis and population survival. This survival strategy may deprive this usually dominant diatom in temperate coastal waters of its competitive advantages in acidified environments.Importance Rising atmospheric CO2 concentrations are causing ocean acidification with significant consequences for marine organisms. Chain-forming centric diatoms of Skeletonema is one of the most successful groups of eukaryotic primary producers with widespread geographic distribution. Among the recognized 28 species, S. marinoi can be a useful model for investigating the ecological, genetic, physiological, and biochemical characteristics of diatoms in temperate coastal regions. In this study, we found that the elevated pCO2 seems to repress photosynthesis and growth of S. marinoi, and through massive gene expression reconfiguration induce cells to increase investment in protein synthesis, energy metabolism and antioxidative stress defense, likely to maintain pH homeostasis and population survival. This survival strategy may deprive this usually dominant diatom in temperate coastal waters of its competitive advantages in acidified environments.
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Affiliation(s)
- Mei Zhang
- Key Laboratory of Marine Environment and Ecology, Ocean University of China, Ministry of Education, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
- Department of marine science, University of Connecticut, Groton, CT 06340, USA
| | - Yu Zhen
- Key Laboratory of Marine Environment and Ecology, Ocean University of China, Ministry of Education, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Tiezhu Mi
- Key Laboratory of Marine Environment and Ecology, Ocean University of China, Ministry of Education, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Senjie Lin
- Department of marine science, University of Connecticut, Groton, CT 06340, USA
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Pierella Karlusich JJ, Bowler C, Biswas H. Carbon Dioxide Concentration Mechanisms in Natural Populations of Marine Diatoms: Insights From Tara Oceans. FRONTIERS IN PLANT SCIENCE 2021; 12:657821. [PMID: 33995455 PMCID: PMC8119650 DOI: 10.3389/fpls.2021.657821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/23/2021] [Indexed: 05/08/2023]
Abstract
Marine diatoms, the most successful photoautotrophs in the ocean, efficiently sequester a significant part of atmospheric CO2 to the ocean interior through their participation in the biological carbon pump. However, it is poorly understood how marine diatoms fix such a considerable amount of CO2, which is vital information toward modeling their response to future CO2 levels. The Tara Oceans expeditions generated molecular data coupled with in situ biogeochemical measurements across the main ocean regions, and thus provides a framework to compare diatom genetic and transcriptional flexibility under natural CO2 variability. The current study investigates the interlink between the environmental variability of CO2 and other physicochemical parameters with the gene and transcript copy numbers of five key enzymes of diatom CO2 concentration mechanisms (CCMs): Rubisco activase and carbonic anhydrase (CA) as part of the physical pathway, together with phosphoenolpyruvate carboxylase, phosphoenolpyruvate carboxykinase, and malic enzyme as part of the potential C4 biochemical pathway. Toward this aim, we mined >200 metagenomes and >220 metatranscriptomes generated from samples of the surface layer of 66 globally distributed sampling sites and corresponding to the four main size fractions in which diatoms can be found: 0.8-5 μm, 5-20 μm, 20-180 μm, and 180-2,000 μm. Our analyses revealed that the transcripts for the enzymes of the putative C4 biochemical CCM did not in general display co-occurring profiles. The transcripts for CAs were the most abundant, with an order of magnitude higher values than the other enzymes, thus implying the importance of physical CCMs in diatom natural communities. Among the different classes of this enzyme, the most prevalent was the recently characterized iota class. Consequently, very little information is available from natural diatom assemblages about the distribution of this class. Biogeographic distributions for all the enzymes show different abundance hotspots according to the size fraction, pointing to the influence of cell size and aggregation in CCMs. Environmental correlations showed a complex pattern of responses to CO2 levels, total phytoplankton biomass, temperature, and nutrient concentrations. In conclusion, we propose that biophysical CCMs are prevalent in natural diatom communities.
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Affiliation(s)
- Juan José Pierella Karlusich
- Institut de Biologie de l’ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Chris Bowler
- Institut de Biologie de l’ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Haimanti Biswas
- CSIR National Institute of Oceanography, Biological Oceanography Division, Dona Paula, India
- *Correspondence: Haimanti Biswas,
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Zeng X, Jin P, Zou D, Liu Y, Xia J. Responses of carbonic anhydrases and Rubisco to abrupt CO 2 changes of seawater in two marine diatoms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:16388-16395. [PMID: 30982194 DOI: 10.1007/s11356-019-05101-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/04/2019] [Indexed: 06/09/2023]
Abstract
Diatoms are experiencing striking fluctuations in seawater carbonate chemistry in the natural marine environment, especially in coastal seawaters. Here, we show that the diatoms Thalassiosira weissflogii and Phaeodactylum tricornutum, which utilize different carbon acquisition mechanisms, respond differently to short-term changes in seawater carbonate chemistry. Our results showed that T. weissflogii showed significantly higher photosynthetic oxygen evolution rates than that of P. tricornutum at low levels of CO2 or HCO3-. This suggests that T. weissflogii had higher affinities for CO2 or HCO3- when their concentrations were not sufficient to support saturated growth and photosynthesis. While the activity of Rubisco in P. tricornutum positively correlated with carbonic anhydrases (CA), we observed negative relationship between Rubisco and CA activity in the diatom T. weissflogii. These contrasting physiological responses of diatoms with varied carbon acquisition mechanisms indicate different abilities to cope up with abrupt changes in seawater carbonate chemistry. We propose that the ability to respond to varying carbonate chemistry may act as one determinant of the diatom distributions and phytoplankton community structures.
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Affiliation(s)
- Xiaopeng Zeng
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Peng Jin
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, People's Republic of China
| | - Dinghui Zou
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Yuxian Liu
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, People's Republic of China
- Linköping University - Guangzhou University Research Centre on Urban Sustainable Development, Guangzhou, 510006, China
| | - Jianrong Xia
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, People's Republic of China.
- Guangzhou Higher Education Mega Center, Wai Huan Xi Road, Guangzhou, 510006, People's Republic of China.
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Wei L, El Hajjami M, Shen C, You W, Lu Y, Li J, Jing X, Hu Q, Zhou W, Poetsch A, Xu J. Transcriptomic and proteomic responses to very low CO 2 suggest multiple carbon concentrating mechanisms in Nannochloropsis oceanica. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:168. [PMID: 31297156 PMCID: PMC6599299 DOI: 10.1186/s13068-019-1506-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/18/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND In industrial oleaginous microalgae such as Nannochloropsis spp., the key components of the carbon concentration mechanism (CCM) machineries are poorly defined, and how they are mobilized to facilitate cellular utilization of inorganic carbon remains elusive. RESULTS For Nannochloropsis oceanica, to unravel genes specifically induced by CO2 depletion which are thus potentially underpinning its CCMs, transcriptome, proteome and metabolome profiles were tracked over 0 h, 3 h, 6 h, 12 h and 24 h during cellular response from high CO2 level (HC; 50,000 ppm) to very low CO2 (VLC; 100 ppm). The activity of a biophysical CCM is evidenced based on induction of transcripts encoding a bicarbonate transporter and two carbonic anhydrases under VLC. Moreover, the presence of a potential biochemical CCM is supported by the upregulation of a number of key C4-like pathway enzymes in both protein abundance and enzymatic activity under VLC, consistent with a mitochondria-implicated C4-based CCM. Furthermore, a basal CCM underpinned by VLC-induced upregulation of photorespiration and downregulation of ornithine-citrulline shuttle and the ornithine urea cycles is likely present, which may be responsible for efficient recycling of mitochondrial CO2 for chloroplastic carbon fixation. CONCLUSIONS Nannochloropsis oceanica appears to mobilize a comprehensive set of CCMs in response to very low CO2. Its genes induced by the stress are quite distinct from those of Chlamydomonas reinhardtii and Phaeodactylum tricornutum, suggesting tightly regulated yet rather unique CCMs. These findings can serve the first step toward rational engineering of the CCMs for enhanced carbon fixation and biomass productivity in industrial microalgae.
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Affiliation(s)
- Li Wei
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong China
- University of Chinese Academy of Science, Beijing, China
| | - Mohamed El Hajjami
- Department of Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Chen Shen
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong China
- University of Chinese Academy of Science, Beijing, China
| | - Wuxin You
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong China
- Department of Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Yandu Lu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong China
- University of Chinese Academy of Science, Beijing, China
| | - Jing Li
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong China
- University of Chinese Academy of Science, Beijing, China
| | - Xiaoyan Jing
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong China
- University of Chinese Academy of Science, Beijing, China
| | - Qiang Hu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei China
- University of Chinese Academy of Science, Beijing, China
| | - Wenxu Zhou
- Department of Chemistry and Biochemistry, Center for Chemical Biology, Texas Tech University, Lubbock, TX USA
| | - Ansgar Poetsch
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong China
- Department of Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
- School of Biomedical and Healthcare Sciences, University of Plymouth, Plymouth, UK
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong China
- University of Chinese Academy of Science, Beijing, China
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Hennon GMM, Hernández Limón MD, Haley ST, Juhl AR, Dyhrman ST. Diverse CO 2-Induced Responses in Physiology and Gene Expression among Eukaryotic Phytoplankton. Front Microbiol 2017; 8:2547. [PMID: 29312232 PMCID: PMC5742204 DOI: 10.3389/fmicb.2017.02547] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/08/2017] [Indexed: 01/15/2023] Open
Abstract
With rising atmospheric CO2, phytoplankton face shifts in ocean chemistry including increased dissolved CO2 and acidification that will likely influence the relative competitive fitness of different phytoplankton taxa. Here we compared the physiological and gene expression responses of six species of phytoplankton including a diatom, a raphidophyte, two haptophytes, and two dinoflagellates to ambient (~400 ppm) and elevated (~800 ppm) CO2. Dinoflagellates had significantly slower growth rates and higher, yet variable, chlorophyll a per cell under elevated CO2. The other phytoplankton tended to have increased growth rates and/or decreased chlorophyll a per cell. Carbon and nitrogen partitioning of cells shifted under elevated CO2 in some species, indicating potential changes in energy fluxes due to changes in carbon concentrating mechanisms (CCM) or photorespiration. Consistent with these phenotypic changes, gene set enrichment analyses revealed shifts in energy, carbon and nitrogen metabolic pathways, though with limited overlap between species in the genes and pathways involved. Similarly, gene expression responses across species revealed few conserved CO2-responsive genes within CCM and photorespiration categories, and a survey of available transcriptomes found high diversity in biophysical CCM and photorespiration expressed gene complements between and within the four phyla represented by these species. The few genes that displayed similar responses to CO2 across phyla were from understudied gene families, making them targets for further research to uncover the mechanisms of phytoplankton acclimation to elevated CO2. These results underscore that eukaryotic phytoplankton have diverse gene complements and gene expression responses to CO2 perturbations and highlight the value of cross-phyla comparisons for identifying gene families that respond to environmental change.
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Affiliation(s)
- Gwenn M M Hennon
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Palisades, NY, United States
| | - María D Hernández Limón
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Palisades, NY, United States
| | - Sheean T Haley
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Palisades, NY, United States
| | - Andrew R Juhl
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Palisades, NY, United States.,Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States
| | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Palisades, NY, United States.,Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States
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10
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Clement R, Jensen E, Prioretti L, Maberly SC, Gontero B. Diversity of CO2-concentrating mechanisms and responses to CO2 concentration in marine and freshwater diatoms. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3925-3935. [PMID: 28369472 DOI: 10.1093/jxb/erx035] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The presence of CO2-concentrating mechanisms (CCMs) is believed to be one of the characteristics that allows diatoms to thrive in many environments and to be major contributors to global productivity. Here, the type of CCM and the responses to variable CO2 concentration were studied in marine and freshwater diatoms. At 400 ppm, there was a large diversity in physiological and biochemical mechanisms among the species. While Phaeodactylum tricornutum mainly used HCO3-, Thalassiosira pseudonana mainly used CO2. Carbonic anhydrase was an important component of the CCM in all species and C4 metabolism was absent, even with T. weissflogii. For all species, at 20 000 ppm, the affinity for dissolved inorganic carbon was lower than at 400 ppm CO2 and the reliance on CO2 was higher. Despite the difference in availability of inorganic carbon in marine and fresh waters, there were only small differences in CCMs between species from the two environments, and Navicula pelliculosa behaved similarly when grown in the two environments. The results suggest that species-specific differences are great, and more important than environmental differences in determining the nature and effectiveness of the CCM in diatoms.
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Affiliation(s)
- Romain Clement
- Aix Marseille Univ, CNRS, BIP, UMR 7281, IMM, 31 Chemin J. Aiguier, 13 402 Marseille Cedex 20, France
| | - Erik Jensen
- Aix Marseille Univ, CNRS, BIP, UMR 7281, IMM, 31 Chemin J. Aiguier, 13 402 Marseille Cedex 20, France
| | - Laura Prioretti
- Aix Marseille Univ, CNRS, BIP, UMR 7281, IMM, 31 Chemin J. Aiguier, 13 402 Marseille Cedex 20, France
| | - Stephen C Maberly
- Lake Ecosystems Group, Centre for Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster LA1 4APUK
| | - Brigitte Gontero
- Aix Marseille Univ, CNRS, BIP, UMR 7281, IMM, 31 Chemin J. Aiguier, 13 402 Marseille Cedex 20, France
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11
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Goldman JAL, Bender ML, Morel FMM. The effects of pH and pCO 2 on photosynthesis and respiration in the diatom Thalassiosira weissflogii. PHOTOSYNTHESIS RESEARCH 2017; 132:83-93. [PMID: 28062941 DOI: 10.1007/s11120-016-0330-2] [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: 09/20/2016] [Accepted: 12/20/2016] [Indexed: 06/06/2023]
Abstract
The response of marine phytoplankton to the ongoing increase in atmospheric pCO2 reflects the consequences of both increased CO2 concentration and decreased pH in surface seawater. In the model diatom Thalassiosira weissflogii, we explored the effects of varying pCO2 and pH, independently and in concert, on photosynthesis and respiration by incubating samples in water enriched in H218O. In long-term experiments (~6-h) at saturating light intensity, we observed no effects of pH or pCO2 on growth rate, photosynthesis or respiration. This absence of a measurable response reflects the very small change in energy used by the carbon concentrating mechanism (CCM) compared to the energy used in carbon fixation. In short-term experiments (~3 min), we also observed no effects of pCO2 or pH, even under limiting light intensity. We surmise that in T. weissflogii, it is the photosynthetic production of NADPH and ATP, rather than the CO2-saturation of Rubisco that controls the rate of photosynthesis at low irradiance. In short-term experiments, we observed a slightly higher respiration rate at low pH at the onset of the dark period, possibly reflecting the energy used for exporting H+ and maintaining pH homeostasis. Based on what is known of the biochemistry of marine phytoplankton, our results are likely generalizable to other diatoms and a number of other eukaryotic species. The direct effects of ocean acidification on growth, photosynthesis and respiration in these organisms should be small over the range of atmospheric pCO2 predicted for the twenty-first century.
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Affiliation(s)
- Johanna A L Goldman
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA.
- Center for Environmental Genomics, School of Oceanography, University of Washington, Seattle, WA, 98105, USA.
| | - Michael L Bender
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
| | - François M M Morel
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
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12
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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.
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13
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Ryan DE, Campbell L. Identification and phylogeny of putative PEPC genes in three toxin-producing Karenia (Dinophyta) species. JOURNAL OF PHYCOLOGY 2016; 52:618-625. [PMID: 27136041 DOI: 10.1111/jpy.12423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 02/17/2016] [Indexed: 06/05/2023]
Abstract
Dense blooms of toxin-producing Karenia brevis increase local surface ocean pH through CO2 uptake. To identify genes that may contribute to bloom-related environmental pH and pCO2 changes, transcriptomes with RNA from K. brevis Wilson cultures that had been acclimated to low CO2 (250 ppm) or recent CO2 (350 ppm) pCO2 levels were assembled. Among the annotated transcripts were PEPC, PPDK, and PEPCK enzymes found in the model C4 carbon fixation pathway. Previous studies have demonstrated that the enzymatic activity of PEPC, PPDK, and/or PEPCK in some algae species, including marine diatoms, is influenced by variations in dissolved inorganic carbon. We found significantly similar PEPC, PPDK, and PEPCK enzymes in the transcriptomes of K. brevis and two sister species Karenia papilionacea, and Karenia mikimotoi. One or more isoforms of PEPC were also identified in the transcriptomes of thirty additional photosynthetic phytoplankton species from nine phyla. Phylogenetic trees were constructed with neighbor joining and maximum likelihood techniques to characterize the evolutionary relationship among phytoplankton, terrestrial plant C4, and terrestrial plant C3 PEPC sequences. Based on the nucleotide trees constructed during this study, the Karenia PEPC transcripts were more closely related to the terrestrial C4 genes than the terrestrial C3 genes. Furthermore, PEPC phylogeny among phytoplankton closely resembles phylogenetic trees constructed with ribosomal RNA. This study confirmed that the toxin-producing dinoflagellates K. brevis, K. mikimotoi, and K. papilionacea express putative PEPC, PEPCK, and PPDK transcripts.
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Affiliation(s)
- Darcie E Ryan
- Department of Oceanography, Texas A & M University, College Station, Texas, 77843, USA
| | - Lisa Campbell
- Department of Oceanography, Texas A & M University, College Station, Texas, 77843, USA
- Department of Oceanography and Department of Biology, Texas A & M University, College Station, Texas, 77843, USA
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14
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Curien G, Flori S, Villanova V, Magneschi L, Giustini C, Forti G, Matringe M, Petroutsos D, Kuntz M, Finazzi G. The Water to Water Cycles in Microalgae. PLANT & CELL PHYSIOLOGY 2016; 57:1354-1363. [PMID: 26955846 DOI: 10.1093/pcp/pcw048] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 02/23/2016] [Indexed: 05/28/2023]
Abstract
In oxygenic photosynthesis, light produces ATP plus NADPH via linear electron transfer, i.e. the in-series activity of the two photosystems: PSI and PSII. This process, however, is thought not to be sufficient to provide enough ATP per NADPH for carbon assimilation in the Calvin-Benson-Bassham cycle. Thus, it is assumed that additional ATP can be generated by alternative electron pathways. These circuits produce an electrochemical proton gradient without NADPH synthesis, and, although they often represent a small proportion of the linear electron flow, they could have a huge importance in optimizing CO2 assimilation. In Viridiplantae, there is a consensus that alternative electron flow comprises cyclic electron flow around PSI and the water to water cycles. The latter processes include photosynthetic O2 reduction via the Mehler reaction at PSI, the plastoquinone terminal oxidase downstream of PSII, photorespiration (the oxygenase activity of Rubisco) and the export of reducing equivalents towards the mitochondrial oxidases, through the malate shuttle. In this review, we summarize current knowledge about the role of the water to water cycles in photosynthesis, with a special focus on their occurrence and physiological roles in microalgae.
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Affiliation(s)
- Gilles Curien
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'Energie Atomique-Université Grenoble Alpes, UMR 1414 Institut National de la Recherche Agronomique (INRA) Biosciences and Biotechnology Institute of Grenoble (BIG), Commissariat à l'Energie Atomique (CEA) Grenoble, 38054 Grenoble cedex 9, France
| | - Serena Flori
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'Energie Atomique-Université Grenoble Alpes, UMR 1414 Institut National de la Recherche Agronomique (INRA) Biosciences and Biotechnology Institute of Grenoble (BIG), Commissariat à l'Energie Atomique (CEA) Grenoble, 38054 Grenoble cedex 9, France
| | | | - Leonardo Magneschi
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'Energie Atomique-Université Grenoble Alpes, UMR 1414 Institut National de la Recherche Agronomique (INRA) Biosciences and Biotechnology Institute of Grenoble (BIG), Commissariat à l'Energie Atomique (CEA) Grenoble, 38054 Grenoble cedex 9, France
| | - Cécile Giustini
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'Energie Atomique-Université Grenoble Alpes, UMR 1414 Institut National de la Recherche Agronomique (INRA) Biosciences and Biotechnology Institute of Grenoble (BIG), Commissariat à l'Energie Atomique (CEA) Grenoble, 38054 Grenoble cedex 9, France
| | - Giorgio Forti
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Michel Matringe
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'Energie Atomique-Université Grenoble Alpes, UMR 1414 Institut National de la Recherche Agronomique (INRA) Biosciences and Biotechnology Institute of Grenoble (BIG), Commissariat à l'Energie Atomique (CEA) Grenoble, 38054 Grenoble cedex 9, France
| | - Dimitris Petroutsos
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'Energie Atomique-Université Grenoble Alpes, UMR 1414 Institut National de la Recherche Agronomique (INRA) Biosciences and Biotechnology Institute of Grenoble (BIG), Commissariat à l'Energie Atomique (CEA) Grenoble, 38054 Grenoble cedex 9, France
| | - Marcel Kuntz
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'Energie Atomique-Université Grenoble Alpes, UMR 1414 Institut National de la Recherche Agronomique (INRA) Biosciences and Biotechnology Institute of Grenoble (BIG), Commissariat à l'Energie Atomique (CEA) Grenoble, 38054 Grenoble cedex 9, France
| | - Giovanni Finazzi
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'Energie Atomique-Université Grenoble Alpes, UMR 1414 Institut National de la Recherche Agronomique (INRA) Biosciences and Biotechnology Institute of Grenoble (BIG), Commissariat à l'Energie Atomique (CEA) Grenoble, 38054 Grenoble cedex 9, France
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15
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Yang J, Pan Y, Bowler C, Zhang L, Hu H. Knockdown of phosphoenolpyruvate carboxykinase increases carbon flux to lipid synthesis in Phaeodactylum tricornutum. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.02.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Clement R, Dimnet L, Maberly SC, Gontero B. The nature of the CO2 -concentrating mechanisms in a marine diatom, Thalassiosira pseudonana. THE NEW PHYTOLOGIST 2016; 209:1417-27. [PMID: 26529678 DOI: 10.1111/nph.13728] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 09/25/2015] [Indexed: 05/19/2023]
Abstract
Diatoms are widespread in aquatic ecosystems where they may be limited by the supply of inorganic carbon. Their carbon dioxide-concentrating mechanisms (CCMs) involving transporters and carbonic anhydrases (CAs) are well known, but the contribution of a biochemical CCM involving C4 metabolism is contentious. The CCM(s) present in the marine-centric diatom, Thalassiosira pseudonana, were studied in cells exposed to high or low concentrations of CO2 , using a range of approaches. At low CO2 , cells possessed a CCM based on active uptake of CO2 (70% contribution) and bicarbonate, while at high CO2 , cells were restricted to CO2 . CA was highly and rapidly activated on transfer to low CO2 and played a key role because inhibition of external CA produced uptake kinetics similar to cells grown at high CO2 . The activities of phosphoenolpyruvate (PEP) carboxylase (PEPC) and the PEP-regenerating enzyme, pyruvate phosphate dikinase (PPDK), were lower in cells grown at low than at high CO2 . The ratios of PEPC and PPDK to ribulose bisphosphate carboxylase were substantially lower than 1, even at low CO2 . Our data suggest that the kinetic properties of this species results from a biophysical CCM and not from C4 type metabolism.
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Affiliation(s)
- Romain Clement
- Aix-Marseille Université CNRS, BIP UMR 7281, 31 Chemin Joseph Aiguier, Marseille Cedex 20, 13402, France
| | - Laura Dimnet
- Aix-Marseille Université CNRS, BIP UMR 7281, 31 Chemin Joseph Aiguier, Marseille Cedex 20, 13402, France
| | - Stephen C Maberly
- Centre for Ecology & Hydrology, Lake Ecosystems Group, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP, UK
| | - Brigitte Gontero
- Aix-Marseille Université CNRS, BIP UMR 7281, 31 Chemin Joseph Aiguier, Marseille Cedex 20, 13402, France
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17
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Huang A, Liu L, Zhao P, Yang C, Wang GC. Metabolic flux ratio analysis and cell staining suggest the existence of C4 photosynthesis in Phaeodactylum tricornutum. J Appl Microbiol 2015; 120:705-13. [PMID: 26661799 DOI: 10.1111/jam.13020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 08/15/2015] [Accepted: 09/21/2015] [Indexed: 12/20/2022]
Abstract
AIMS Mechanisms for carbon fixation via photosynthesis in the diatom Phaeodactylum tricornutum Bohlin were studied recently but there remains a long-standing debate concerning the occurrence of C4 photosynthesis in this species. A thorough investigation of carbon metabolism and the evidence for C4 photosynthesis based on organelle partitioning was needed. METHODS AND RESULTS In this study, we identified the flux ratios between C3 and C4 compounds in P. tricornutum using (13)C-labelling metabolic flux ratio analysis, and stained cells with various cell-permeant fluorescent probes to investigate the likely organelle partitioning required for single-cell C4 photosynthesis. Metabolic flux ratio analysis indicated the C3/C4 exchange ratios were high. Cell staining indicated organelle partitioning required for single-cell C4 photosynthesis might exist in P. tricornutum. CONCLUSION The results of (13)C-labelling metabolic flux ratio analysis and cell staining suggest single-cell C4 photosynthesis exists in P. tricornutum. SIGNIFICANCE AND IMPACT OF THE STUDY This study provides insights into photosynthesis patterns of P. tricornutum and the evidence for C4 photosynthesis based on (13)C-labelling metabolic flux ratio analysis and organelle partitioning.
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Affiliation(s)
- A Huang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Science, Qingdao, Shandong, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - L Liu
- Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - P Zhao
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Science, Qingdao, Shandong, China
| | - C Yang
- Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - G C Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Science, Qingdao, Shandong, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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18
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Kustka AB, Milligan AJ, Zheng H, New AM, Gates C, Bidle KD, Reinfelder JR. Low CO2 results in a rearrangement of carbon metabolism to support C4 photosynthetic carbon assimilation in Thalassiosira pseudonana. THE NEW PHYTOLOGIST 2014; 204:507-520. [PMID: 25046577 DOI: 10.1111/nph.12926] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 05/28/2014] [Indexed: 05/20/2023]
Abstract
The mechanisms of carbon concentration in marine diatoms are controversial. At low CO2 , decreases in O2 evolution after inhibition of phosphoenolpyruvate carboxylases (PEPCs), and increases in PEPC transcript abundances, have been interpreted as evidence for a C4 mechanism in Thalassiosira pseudonana, but the ascertainment of which proteins are responsible for the subsequent decarboxylation and PEP regeneration steps has been elusive. We evaluated the responses of T. pseudonana to steady-state differences in CO2 availability, as well as to transient shifts to low CO2 , by integrated measurements of photosynthetic parameters, transcript abundances and quantitative proteomics. On shifts to low CO2 , two PEPC transcript abundances increased and then declined on timescales consistent with recoveries of Fv /Fm , non-photochemical quenching (NPQ) and maximum chlorophyll a-specific carbon fixation (Pmax ), but transcripts for archetypical decarboxylation enzymes phosphoenolpyruvate carboxykinase (PEPCK) and malic enzyme (ME) did not change. Of 3688 protein abundances measured, 39 were up-regulated under low CO2 , including both PEPCs and pyruvate carboxylase (PYC), whereas ME abundance did not change and PEPCK abundance declined. We propose a closed-loop biochemical model, whereby T. pseudonana produces and subsequently decarboxylates a C4 acid via PEPC2 and PYC, respectively, regenerates phosphoenolpyruvate (PEP) from pyruvate in a pyruvate phosphate dikinase-independent (but glycine decarboxylase (GDC)-dependent) manner, and recuperates photorespiratory CO2 as oxaloacetate (OAA).
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Affiliation(s)
- Adam B Kustka
- Earth and Environmental Sciences, Rutgers University, 101 Warren Street, Newark, NJ, 07102, USA
| | - Allen J Milligan
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR, 97331, USA
| | - Haiyan Zheng
- Biological Mass Spectrometry Facility, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Ashley M New
- Earth and Environmental Sciences, Rutgers University, 101 Warren Street, Newark, NJ, 07102, USA
| | - Colin Gates
- Earth and Environmental Sciences, Rutgers University, 101 Warren Street, Newark, NJ, 07102, USA
| | - Kay D Bidle
- Institute of Marine and Coastal Sciences, Rutgers University, 71 Dudley Road, New Brunswick, NJ, 08901, USA
| | - John R Reinfelder
- Department of Environmental Sciences, Rutgers University, 14 College Farm Road, New Brunswick, NJ, 08901, USA
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19
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Hopkinson BM. A chloroplast pump model for the CO2 concentrating mechanism in the diatom Phaeodactylum tricornutum. PHOTOSYNTHESIS RESEARCH 2014; 121:223-33. [PMID: 24292858 DOI: 10.1007/s11120-013-9954-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 11/18/2013] [Indexed: 05/19/2023]
Abstract
Prior analysis of inorganic carbon (Ci) fluxes in the diatom Phaeodactylum tricornutum has indicated that transport of Ci into the chloroplast from the cytoplasm is the major Ci flux in the cell and the primary driving force for the CO2 concentrating mechanism (CCM). This flux drives the accumulation of Ci in the chloroplast stroma and generates a CO2 deficit in the cytoplasm, inducing CO2 influx into the cell. Here, the "chloroplast pump" model of the CCM in P. tricornutum is formalized and its consistency with data on CO2 and HCO3 (-) uptake rates, carbonic anhydrase (CA) activity, intracellular Ci concentration, intracellular pH, and RubisCO characteristics is assessed. The chloroplast pump model can account for the major features of the data. Analysis of photosynthetic and Ci uptake rates as a function of external Ci concentration shows that the model has the most difficulty obtaining sufficiently low cytoplasmic CO2 concentrations to support observed CO2 uptake rates at low external Ci concentrations and achieving high rates of photosynthesis. There are multiple ways in which model parameters can be varied, within a plausible range, to match measured rates of photosynthesis and CO2 uptake. To increase CO2 uptake rates, CA activity can be increased, kinetic characteristics of the putative chloroplast pump can be enhanced to increase HCO3 (-) export, or the cytoplasmic pH can be raised. To increase the photosynthetic rate, the permeability of the pyrenoid to CO2 can be reduced or RubisCO content can be increased.
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Affiliation(s)
- Brian M Hopkinson
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA,
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20
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Samukawa M, Shen C, Hopkinson BM, Matsuda Y. Localization of putative carbonic anhydrases in the marine diatom, Thalassiosira pseudonana. PHOTOSYNTHESIS RESEARCH 2014; 121:235-49. [PMID: 24414291 DOI: 10.1007/s11120-014-9967-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Accepted: 12/31/2013] [Indexed: 05/19/2023]
Abstract
Thirteen putative carbonic anhydrase (CA) genes have been identified in the marine multipolar centric diatom, Thalassiosira pseudonana, and two of these CAs have been localized previously. The first, an alpha CA (TpαCA1), was localized in the chloroplast stroma; the second, a zeta-type CA (TpζCA1), was localized to the periplasmic space. In the present study, cloning and localization of the remaining CAs were carried out. TpγCA2, TpγCA3, TpγCA4, TpγCA5, TpδCA1, TpδCA2, TpδCA3, and TpζCA1 were responsive to CO2 availability at the transcriptional level, being significantly reduced in cells grown at 0.4 % CO2, whereas TpαCA1, TpαCA2, TpαCA3, TpγCA1, and TpδCA4 transcript levels were constitutive with respect to CO2 concentration. Full-length cDNAs for TpγCA1, TpγCA2, TpγCA3, TpγCA4, TpδCA1, and TpδCA2 were isolated and fused with the enhanced-green fluorescent gene at their 3' termini. These GFP-fusion constructs were transformed into T. pseudonana, and the resulting GFP fusion products were localized using fluorescence microscopy. The δ-type TpδCA1 was localized on the periphery of the cell, strongly suggesting localization to the periplasmic space or the frustule. The δ-type TpδCA3 and the γ-type TpγCA2 were, respectively, localized in a periplastidal compartment and the cytosol. The δ-type TpδCA2, and the γ-types TpγCA1, 3, and 4 were localized in the mitochondria. The distribution of CAs in T. pseudonana contrasts notably with that of the raphid pennate diatom P. tricornutum, with likely consequences for CCM function including modes of CO2 acquisition, regions in which DIC is accumulated, and needs for minimizing CO2 leakage from the chloroplast.
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Affiliation(s)
- Mio Samukawa
- Department of Bioscience, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo, 669-1337, Japan
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Tanaka R, Kikutani S, Mahardika A, Matsuda Y. Localization of enzymes relating to C4 organic acid metabolisms in the marine diatom, Thalassiosira pseudonana. PHOTOSYNTHESIS RESEARCH 2014; 121:251-63. [PMID: 24414292 DOI: 10.1007/s11120-014-9968-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Accepted: 12/31/2013] [Indexed: 05/23/2023]
Abstract
In the genome of the marine diatom-Thalassiosira pseudonana, there are several putative genes encoding enzymes potentially constitute a classical C4 type biochemical CO2-concentrating mechanism. Two genes encode a carboxylation enzyme phosphoenolpyruvate carboxylase (PEPC)1 and PEPC2; and another two encode decarboxylation enzymes, NAD(+)-dependent malic enzyme (NAD-ME) and phosphoenolpyruvate carboxykinase (PEPCK). These genes were tagged by the enhanced-green fluorescence protein, egfp, ligated in the transformation vector, and transformed into the cells of T. pseudonana for localization of GFP fusion products. The PEPC1:GFP fusion was localized at the matrix of the periplastidal compartment, while the PEPC2:GFP fusion was localized at the mitochondria. The NAD-ME:GFP fusion was localized in the cytosol and the PEPCK:GFP fusion at the mitochondria. The transcripts level of NAD-ME was extremely low, and PEPCK transcript was significantly induced under the dark, suggesting that PEPCK is involved in the dark metabolism such as respiration and amino acid metabolism in the mitochondria. Treatments of low-CO2grown T. pseudonana cells with inhibitors for PEPCK and PEPC efficiently dissipated the maximum rate of photosynthesis while these treatments did not affect high-affinity photosynthesis. These data strongly suggest that classical C4 enzymes play little role in the CCM in T. pseudonana.
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Affiliation(s)
- Rie Tanaka
- Department of Bioscience, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo, 669-1337, Japan
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Raven JA, Beardall J, Giordano M. Energy costs of carbon dioxide concentrating mechanisms in aquatic organisms. PHOTOSYNTHESIS RESEARCH 2014; 121:111-24. [PMID: 24390639 DOI: 10.1007/s11120-013-9962-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 12/18/2013] [Indexed: 05/19/2023]
Abstract
Minimum energy (as photon) costs are predicted for core reactions of photosynthesis, for photorespiratory metabolism in algae lacking CO2 concentrating mechanisms (CCMs) and for various types of CCMs; in algae, with CCMs; allowance was made for leakage of CO2 from the internal pool. These predicted values are just compatible with the minimum measured photon costs of photosynthesis in microalgae and macroalgae lacking or expressing CCMs. More energy-expensive photorespiration, for example for organisms using Rubiscos with lower CO2-O2 selectivity coefficients, would be less readily accommodated within the lowest measured photon costs of photosynthesis by algae lacking CCMs. The same applies to the cases of CCMs with higher energy costs of active transport of protons or inorganic carbon species, or greater allowance for significant leakage from the accumulated intracellular pool of CO2. High energetic efficiency can involve a higher concentration of catalyst to achieve a given rate of reaction, adding to the resource costs of growth. There are no obvious mechanistic interpretations of the occurrence of CCMs algae adapted to low light and low temperatures using the rationales adopted for the occurrence of C4 photosynthesis in terrestrial flowering plants. There is an exception for cyanobacteria with low-selectivity Form IA or IB Rubiscos, and those dinoflagellates with low-selectivity Form II Rubiscos, for which very few natural environments have high enough CO2:O2 ratios to allow photosynthesis in the absence of CCMs.
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Affiliation(s)
- John A Raven
- Division of Plant Science, University of Dundee at the James Hutton Institute, Invergowrie, Dundee, DD2 5DQ, UK,
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23
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Effect of Lignocellulose Related Compounds on Microalgae Growth and Product Biosynthesis: A Review. ENERGIES 2014. [DOI: 10.3390/en7074446] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Barcelos e Ramos J, Schulz KG, Brownlee C, Sett S, Azevedo EB. Effects of increasing seawater carbon dioxide concentrations on chain formation of the diatom Asterionellopsis glacialis. PLoS One 2014; 9:e90749. [PMID: 24618939 PMCID: PMC3949724 DOI: 10.1371/journal.pone.0090749] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 02/03/2014] [Indexed: 11/18/2022] Open
Abstract
Diatoms can occur as single cells or as chain-forming aggregates. These two strategies affect buoyancy, predator evasion, light absorption and nutrient uptake. Adjacent cells in chains establish connections through various processes that determine strength and flexibility of the bonds, and at distinct cellular locations defining colony structure. Chain length has been found to vary with temperature and nutrient availability as well as being positively correlated with growth rate. However, the potential effect of enhanced carbon dioxide (CO2) concentrations and consequent changes in seawater carbonate chemistry on chain formation is virtually unknown. Here we report on experiments with semi-continuous cultures of the freshly isolated diatom Asterionellopsis glacialis grown under increasing CO2 levels ranging from 320 to 3400 µatm. We show that the number of cells comprising a chain, and therefore chain length, increases with rising CO2 concentrations. We also demonstrate that while cell division rate changes with CO2 concentrations, carbon, nitrogen and phosphorus cellular quotas vary proportionally, evident by unchanged organic matter ratios. Finally, beyond the optimum CO2 concentration for growth, carbon allocation changes from cellular storage to increased exudation of dissolved organic carbon. The observed structural adjustment in colony size could enable growth at high CO2 levels, since longer, spiral-shaped chains are likely to create microclimates with higher pH during the light period. Moreover increased chain length of Asterionellopsis glacialis may influence buoyancy and, consequently, affect competitive fitness as well as sinking rates. This would potentially impact the delicate balance between the microbial loop and export of organic matter, with consequences for atmospheric carbon dioxide.
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Affiliation(s)
- Joana Barcelos e Ramos
- Centre of Climate, Meteorology and Global Change of the University of the Azores and the Research Centre for Agricultural and Environmental Science and Technology of the Azores, Angra do Heroísmo, Azores, Portugal
| | - Kai Georg Schulz
- Centre for Coastal Biogeochemistry, School of Environmental Science and Management, Southern Cross University, Lismore, Australia
| | - Colin Brownlee
- The Marine Biological Association of the United Kingdom, Plymouth, Devon, United Kingdom
| | - Scarlett Sett
- GEOMAR | Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Eduardo Brito Azevedo
- Centre of Climate, Meteorology and Global Change of the University of the Azores and the Research Centre for Agricultural and Environmental Science and Technology of the Azores, Angra do Heroísmo, Azores, Portugal
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Diffusion Limitation and CO2 Concentrating Mechanisms in Bryophytes. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2014. [DOI: 10.1007/978-94-007-6988-5_6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Xu J, Zhang X, Ye N, Zheng Z, Mou S, Dong M, Xu D, Miao J. Activities of principal photosynthetic enzymes in green macroalga Ulva linza: functional implication of C₄ pathway in CO₂ assimilation. SCIENCE CHINA-LIFE SCIENCES 2013; 56:571-80. [PMID: 23737004 DOI: 10.1007/s11427-013-4489-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 04/19/2013] [Indexed: 11/25/2022]
Abstract
The green-tide-forming macroalga Ulva linza was profiled by transcriptome sequencing to ascertain whether the alga carries both C3 and C4 photosynthesis genes. The key enzymes involved in C4 metabolism including pyruvate orthophosphate dikinase (PPDK), phosphoenolpyruvate carboxylase (PEPC), and phosphoenolpyruvate carboxykinase (PCK) were found. When measured under normal and different stress conditions, expression of rbcL was higher under normal conditions and lower under the adverse conditions, whereas that of PPDK was higher under some adverse conditions, namely desiccation, high salinity, and low salinity. Both ribulose-1, 5-biphosphate carboxylase (RuBPCase) and PPDK were found to play a role in carbon fixation, with significantly higher PPDK activity across the stress conditions. These results suggest that elevated PPDK activity alters carbon metabolism in U. linza leading to partial operation of the C4 carbon metabolism, a pathway that, under stress conditions, probably contributes to the hardy character of U. linza and thus to its wide distribution.
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Affiliation(s)
- Jianfang Xu
- Key Laboratory of Marine Bioactive Substance, The First Institute of Oceanography, State Oceanic Administration, Qingdao 266061, China
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Chang KS, Jeon H, Gu MB, Pack SP, Jin E. Conversion of carbon dioxide to oxaloacetate using integrated carbonic anhydrase and phosphoenolpyruvate carboxylase. Bioprocess Biosyst Eng 2013; 36:1923-8. [DOI: 10.1007/s00449-013-0968-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 05/03/2013] [Indexed: 11/29/2022]
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The central carbon and energy metabolism of marine diatoms. Metabolites 2013; 3:325-46. [PMID: 24957995 PMCID: PMC3901268 DOI: 10.3390/metabo3020325] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 04/25/2013] [Accepted: 04/25/2013] [Indexed: 01/27/2023] Open
Abstract
Diatoms are heterokont algae derived from a secondary symbiotic event in which a eukaryotic host cell acquired an eukaryotic red alga as plastid. The multiple endosymbiosis and horizontal gene transfer processes provide diatoms unusual opportunities for gene mixing to establish distinctive biosynthetic pathways and metabolic control structures. Diatoms are also known to have significant impact on global ecosystems as one of the most dominant phytoplankton species in the contemporary ocean. As such their metabolism and growth regulating factors have been of particular interest for many years. The publication of the genomic sequences of two independent species of diatoms and the advent of an enhanced experimental toolbox for molecular biological investigations have afforded far greater opportunities than were previously apparent for these species and re-invigorated studies regarding the central carbon metabolism of diatoms. In this review we discuss distinctive features of the central carbon metabolism of diatoms and its response to forthcoming environmental changes and recent advances facilitating the possibility of industrial use of diatoms for oil production. Although the operation and importance of several key pathways of diatom metabolism have already been demonstrated and determined, we will also highlight other potentially important pathways wherein this has yet to be achieved.
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Yang ZK, Niu YF, Ma YH, Xue J, Zhang MH, Yang WD, Liu JS, Lu SH, Guan Y, Li HY. Molecular and cellular mechanisms of neutral lipid accumulation in diatom following nitrogen deprivation. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:67. [PMID: 23642220 PMCID: PMC3662598 DOI: 10.1186/1754-6834-6-67] [Citation(s) in RCA: 218] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 05/01/2013] [Indexed: 05/03/2023]
Abstract
BACKGROUND Nitrogen limitation can induce neutral lipid accumulation in microalgae, as well as inhibiting their growth. Therefore, to obtain cultures with both high biomass and high lipid contents, and explore the lipid accumulation mechanisms, we implemented nitrogen deprivation in a model diatom Phaeodactylum tricornutum at late exponential phase. RESULTS Neutral lipid contents per cell subsequently increased 2.4-fold, both the number and total volume of oil bodies increased markedly, and cell density rose slightly. Transcriptional profile analyzed by RNA-Seq showed that expression levels of 1213 genes (including key carbon fixation, TCA cycle, glycerolipid metabolism and nitrogen assimilation genes) increased, with a false discovery rate cut-off of 0.001, under N deprivation. However, most light harvesting complex genes were down-regulated, extensive degradation of chloroplast membranes was observed under an electron microscope, and photosynthetic efficiency declined. Further identification of lipid classes showed that levels of MGDG and DGDG, the main lipid components of chloroplast membranes, dramatically decreased and triacylglycerol (TAG) levels significantly rose, indicating that intracellular membrane remodeling substantially contributed to the neutral lipid accumulation. CONCLUSIONS Our findings shed light on the molecular mechanisms of neutral lipid accumulation and the key genes involved in lipid metabolism in diatoms. They also provide indications of possible strategies for improving microalgal biodiesel production.
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Affiliation(s)
- Zhi-Kai Yang
- Key Laboratory of Eutrophication and Prevention of Red Tide of Guangdong Higher Education Institute, College of Life Science, Jinan University, Guangzhou, 510632, China
| | - Ying-Fang Niu
- Key Laboratory of Eutrophication and Prevention of Red Tide of Guangdong Higher Education Institute, College of Life Science, Jinan University, Guangzhou, 510632, China
| | - Yu-Han Ma
- Key Laboratory of Eutrophication and Prevention of Red Tide of Guangdong Higher Education Institute, College of Life Science, Jinan University, Guangzhou, 510632, China
| | - Jiao Xue
- Key Laboratory of Eutrophication and Prevention of Red Tide of Guangdong Higher Education Institute, College of Life Science, Jinan University, Guangzhou, 510632, China
| | - Meng-Han Zhang
- Key Laboratory of Eutrophication and Prevention of Red Tide of Guangdong Higher Education Institute, College of Life Science, Jinan University, Guangzhou, 510632, China
| | - Wei-Dong Yang
- Key Laboratory of Eutrophication and Prevention of Red Tide of Guangdong Higher Education Institute, College of Life Science, Jinan University, Guangzhou, 510632, China
| | - Jie-Sheng Liu
- Key Laboratory of Eutrophication and Prevention of Red Tide of Guangdong Higher Education Institute, College of Life Science, Jinan University, Guangzhou, 510632, China
| | - Song-Hui Lu
- Key Laboratory of Eutrophication and Prevention of Red Tide of Guangdong Higher Education Institute, College of Life Science, Jinan University, Guangzhou, 510632, China
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109, United States of America
| | - Hong-Ye Li
- Key Laboratory of Eutrophication and Prevention of Red Tide of Guangdong Higher Education Institute, College of Life Science, Jinan University, Guangzhou, 510632, China
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Cowling SA. Did early land plants use carbon-concentrating mechanisms? TRENDS IN PLANT SCIENCE 2013; 18:120-124. [PMID: 23102567 DOI: 10.1016/j.tplants.2012.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 09/05/2012] [Accepted: 09/26/2012] [Indexed: 06/01/2023]
Abstract
Carbon-concentrating mechanisms (CCMs) in plants involve actively increasing CO2 concentrations near ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO). The assumption has been that terrestrial plants did not evolve CCMs for well over 300 million years, yet most marine plants probably evolved CCMs at the time when oxygenic photosynthesis first occurred in the Paleozoic. One primary reason for this assumption is that analysis of genetic mutations for phosphoenolpyruvate carboxylase (PEPc; an enzyme required for C4 and CAM photosynthesis) indicate a molecular age of no more than 65 Ma. Could the evolutionary response of both RuBisCO and PEPc to varying concentrations of atmospheric CO2 and O2 over geological time have obscured the real time when land plants first used PEPc during photosynthesis?
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Affiliation(s)
- Sharon A Cowling
- Department of Earth Sciences, University of Toronto, 22 Russell Street, Toronto, Ontario, M5S 3B1, Canada.
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Meyer M, Griffiths H. Origins and diversity of eukaryotic CO2-concentrating mechanisms: lessons for the future. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:769-86. [PMID: 23345319 DOI: 10.1093/jxb/ers390] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The importance of the eukaryotic algal CO(2)-concentrating mechanism (CCM) is considered in terms of global productivity as well as molecular phylogeny and diversity. The three major constituents comprising the CCM in the majority of eukaryotes are described. These include: (i) likely plasma- and chloroplast-membrane inorganic carbon transporters; (ii) a suite of carbonic anhydrase enzymes in strategic locations; and usually (iii) a microcompartment in which most Rubisco aggregates (the chloroplast pyrenoid). The molecular diversity of known CCM components are set against the current green algal model for their probable operation. The review then focuses on the kinetic and cystallographic interactions of Rubisco, which permit pyrenoid formation and CCM function. Firstly, we consider observations that surface residues of the Rubisco small subunit directly condition Rubisco aggregation and pyrenoid formation. Secondly, we reanalyse the phylogenetic progression in green Rubisco kinetic properties, and suggest that Rubisco substrate selectivity (the specificity factor, S(rel), and affinity for CO(2), K(c)) demonstrate a systematic relaxation, which directly relates to the origins and effectiveness of a CCM. Finally, we consider the implications of eukaryotic CCM regulation and minimum components needed for introduction into higher plants as a possible means to enhance crop productivity in the future.
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Affiliation(s)
- Moritz Meyer
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK.
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Alexander H, Jenkins BD, Rynearson TA, Saito MA, Mercier ML, Dyhrman ST. Identifying reference genes with stable expression from high throughput sequence data. Front Microbiol 2012; 3:385. [PMID: 23162540 PMCID: PMC3494082 DOI: 10.3389/fmicb.2012.00385] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 10/16/2012] [Indexed: 11/24/2022] Open
Abstract
Genes that are constitutively expressed across multiple environmental stimuli are crucial to quantifying differentially expressed genes, particularly when employing quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) assays. However, the identification of these potential reference genes in non-model organisms is challenging and is often guided by expression patterns in distantly related organisms. Here, transcriptome datasets from the diatom Thalassiosira pseudonana grown under replete, phosphorus-limited, iron-limited, and phosphorus and iron co-limited nutrient regimes were analyzed through literature-based searches for homologous reference genes, k-means clustering, and analysis of sequence counts (ASC) to identify putative reference genes. A total of 9759 genes were identified and screened for stable expression. Literature-based searches surveyed 18 generally accepted reference genes, revealing 101 homologs in T. pseudonana with variable expression and a wide range of mean tags per million. k-means analysis parsed the whole transcriptome into 15 clusters. The two most stable clusters contained 709 genes, but still had distinct patterns in expression. ASC analyses identified 179 genes that were stably expressed (posterior probability < 0.1 for 1.25 fold change). Genes known to have a stable expression pattern across the test treatments, like actin, were identified in this pool of 179 candidate genes. ASC can be employed on data without biological replicates and was more robust than the k-means approach in isolating genes with stable expression. The intersection of the genes identified through ASC with commonly used reference genes from the literature suggests that actin and ubiquitin ligase may be useful reference genes for T. pseudonana and potentially other diatoms. With the wealth of transcriptome sequence data becoming available, ASC can be easily applied to transcriptome datasets from other phytoplankton to identify reference genes.
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Affiliation(s)
- Harriet Alexander
- MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering Cambridge, MA, USA ; Biology Department, Woods Hole Oceanographic Institution Woods Hole, MA, USA
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Fernie AR, Obata T, Allen AE, Araújo WL, Bowler C. Leveraging metabolomics for functional investigations in sequenced marine diatoms. TRENDS IN PLANT SCIENCE 2012; 17:395-403. [PMID: 22465020 DOI: 10.1016/j.tplants.2012.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 02/13/2012] [Accepted: 02/16/2012] [Indexed: 05/31/2023]
Abstract
Recent years have witnessed the genomic decoding of a wide range of photosynthetic organisms from the model plant Arabidopsis thaliana and the complex genomes of important crop species to single-celled marine phytoplankton. The comparative sequencing of green, red and brown algae has provided considerable insight into a number of important questions concerning their evolution, physiology and metabolism. The combinatorial application of metabolomics has further deepened our understanding both of the function of individual genes and of metabolic processes. Here we discuss the power of utilising metabolomics in conjunction with sequencing data to gain greater insight into the metabolic hierarchies underpinning the function of individual organisms, using unicellular marine diatoms as a case study to exemplify the advantages of this approach.
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Affiliation(s)
- Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany.
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Valenzuela J, Mazurie A, Carlson RP, Gerlach R, Cooksey KE, Peyton BM, Fields MW. Potential role of multiple carbon fixation pathways during lipid accumulation in Phaeodactylum tricornutum. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:40. [PMID: 22672912 PMCID: PMC3457861 DOI: 10.1186/1754-6834-5-40] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 06/06/2012] [Indexed: 05/04/2023]
Abstract
BACKGROUND Phaeodactylum tricornutum is a unicellular diatom in the class Bacillariophyceae. The full genome has been sequenced (<30 Mb), and approximately 20 to 30% triacylglyceride (TAG) accumulation on a dry cell basis has been reported under different growth conditions. To elucidate P. tricornutum gene expression profiles during nutrient-deprivation and lipid-accumulation, cell cultures were grown with a nitrate to phosphate ratio of 20:1 (N:P) and whole-genome transcripts were monitored over time via RNA-sequence determination. RESULTS The specific Nile Red (NR) fluorescence (NR fluorescence per cell) increased over time; however, the increase in NR fluorescence was initiated before external nitrate was completely exhausted. Exogenous phosphate was depleted before nitrate, and these results indicated that the depletion of exogenous phosphate might be an early trigger for lipid accumulation that is magnified upon nitrate depletion. As expected, many of the genes associated with nitrate and phosphate utilization were up-expressed. The diatom-specific cyclins cyc7 and cyc10 were down-expressed during the nutrient-deplete state, and cyclin B1 was up-expressed during lipid-accumulation after growth cessation. While many of the genes associated with the C3 pathway for photosynthetic carbon reduction were not significantly altered, genes involved in a putative C4 pathway for photosynthetic carbon assimilation were up-expressed as the cells depleted nitrate, phosphate, and exogenous dissolved inorganic carbon (DIC) levels. P. tricornutum has multiple, putative carbonic anhydrases, but only two were significantly up-expressed (2-fold and 4-fold) at the last time point when exogenous DIC levels had increased after the cessation of growth. Alternative pathways that could utilize HCO3- were also suggested by the gene expression profiles (e.g., putative propionyl-CoA and methylmalonyl-CoA decarboxylases). CONCLUSIONS The results indicate that P. tricornutum continued carbon dioxide reduction when population growth was arrested and different carbon-concentrating mechanisms were used dependent upon exogenous DIC levels. Based upon overall low gene expression levels for fatty acid synthesis, the results also suggest that the build-up of precursors to the acetyl-CoA carboxylases may play a more significant role in TAG synthesis rather than the actual enzyme levels of acetyl-CoA carboxylases per se. The presented insights into the types and timing of cellular responses to inorganic carbon will help maximize photoautotrophic carbon flow to lipid accumulation.
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Affiliation(s)
- Jacob Valenzuela
- Department of Biochemistry and Chemistry, Bozeman, USA
- Center for Biofilm Engineering, Bozeman, USA
| | - Aurelien Mazurie
- Department of Microbiology, Bozeman, USA
- Bioinformatics Core, Bozeman, USA
| | - Ross P Carlson
- Center for Biofilm Engineering, Bozeman, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, 59717, USA
| | - Robin Gerlach
- Center for Biofilm Engineering, Bozeman, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, 59717, USA
| | | | - Brent M Peyton
- Center for Biofilm Engineering, Bozeman, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, 59717, USA
| | - Matthew W Fields
- Center for Biofilm Engineering, Bozeman, USA
- Department of Microbiology, Bozeman, USA
- Center for Biofilm Engineering, 366 EPS Building, Montana State University, Bozeman, MT, 59717, USA
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Xu J, Fan X, Zhang X, Xu D, Mou S, Cao S, Zheng Z, Miao J, Ye N. Evidence of coexistence of C₃ and C₄ photosynthetic pathways in a green-tide-forming alga, Ulva prolifera. PLoS One 2012; 7:e37438. [PMID: 22616009 PMCID: PMC3353924 DOI: 10.1371/journal.pone.0037438] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 04/22/2012] [Indexed: 11/19/2022] Open
Abstract
Ulva prolifera, a typical green-tide-forming alga, can accumulate a large biomass in a relatively short time period, suggesting that photosynthesis in this organism, particularly its carbon fixation pathway, must be very efficient. Green algae are known to generally perform C₃ photosynthesis, but recent metabolic labeling and genome sequencing data suggest that they may also perform C₄ photosynthesis, so C₄ photosynthesis might be more wide-spread than previously anticipated. Both C₃ and C₄ photosynthesis genes were found in U. prolifera by transcriptome sequencing. We also discovered the key enzymes of C₄ metabolism based on functional analysis, such as pyruvate orthophosphate dikinase (PPDK), phosphoenolpyruvate carboxylase (PEPC), and phosphoenolpyruvate carboxykinase (PCK). To investigate whether the alga operates a C₄-like pathway, the expression of rbcL and PPDK and their enzyme activities were measured under various forms and intensities of stress (differing levels of salinity, light intensity, and temperature). The expression of rbcL and PPDK and their enzyme activities were higher under adverse circumstances. However, under conditions of desiccation, the expression of rbcL and ribulose-1, 5-biphosphate carboxylase (RuBPCase) activity was lower, whereas that of PPDK was higher. These results suggest that elevated PPDK activity may alter carbon metabolism and lead to a partial operation of C₄-type carbon metabolism in U. prolifera, probably contributing to its wide distribution and massive, repeated blooms in the Yellow Sea.
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Affiliation(s)
- Jianfang Xu
- Key Laboratory of Marine Bioactive substance, The First Institute of Oceanography, State Oceanic Administration, Qingdao, China
| | - Xiao Fan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiaowen Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Dong Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Shanli Mou
- Key Laboratory of Marine Bioactive substance, The First Institute of Oceanography, State Oceanic Administration, Qingdao, China
| | - Shaona Cao
- Qingdao Agricultural University, Qingdao, China
| | - Zhou Zheng
- Key Laboratory of Marine Bioactive substance, The First Institute of Oceanography, State Oceanic Administration, Qingdao, China
| | - Jinlai Miao
- Key Laboratory of Marine Bioactive substance, The First Institute of Oceanography, State Oceanic Administration, Qingdao, China
| | - Naihao Ye
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
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37
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Comparative analysis of diatom genomes reveals substantial differences in the organization of carbon partitioning pathways. ALGAL RES 2012. [DOI: 10.1016/j.algal.2012.04.003] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Allen AE, Moustafa A, Montsant A, Eckert A, Kroth PG, Bowler C. Evolution and functional diversification of fructose bisphosphate aldolase genes in photosynthetic marine diatoms. Mol Biol Evol 2011; 29:367-79. [PMID: 21903677 PMCID: PMC3245544 DOI: 10.1093/molbev/msr223] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Diatoms and other chlorophyll-c containing, or chromalveolate, algae are among the most productive and diverse phytoplankton in the ocean. Evolutionarily, chlorophyll-c algae are linked through common, although not necessarily monophyletic, acquisition of plastid endosymbionts of red as well as most likely green algal origin. There is also strong evidence for a relatively high level of lineage-specific bacterial gene acquisition within chromalveolates. Therefore, analyses of gene content and derivation in chromalveolate taxa have indicated particularly diverse origins of their overall gene repertoire. As a single group of functionally related enzymes spanning two distinct gene families, fructose 1,6-bisphosphate aldolases (FBAs) illustrate the influence on core biochemical pathways of specific evolutionary associations among diatoms and other chromalveolates with various plastid-bearing and bacterial endosymbionts. Protein localization and activity, gene expression, and phylogenetic analyses indicate that the pennate diatom Phaeodactylum tricornutum contains five FBA genes with very little overall functional overlap. Three P. tricornutum FBAs, one class I and two class II, are plastid localized, and each appears to have a distinct evolutionary origin as well as function. Class I plastid FBA appears to have been acquired by chromalveolates from a red algal endosymbiont, whereas one copy of class II plastid FBA is likely to have originated from an ancient green algal endosymbiont. The other copy appears to be the result of a chromalveolate-specific gene duplication. Plastid FBA I and chromalveolate-specific class II plastid FBA are localized in the pyrenoid region of the chloroplast where they are associated with β-carbonic anhydrase, which is known to play a significant role in regulation of the diatom carbon concentrating mechanism. The two pyrenoid-associated FBAs are distinguished by contrasting gene expression profiles under nutrient limiting compared with optimal CO2 fixation conditions, suggestive of a distinct specialized function for each. Cytosolically localized FBAs in P. tricornutum likely play a role in glycolysis and cytoskeleton function and seem to have originated from the stramenopile host cell and from diatom-specific bacterial gene transfer, respectively.
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Affiliation(s)
- Andrew E Allen
- Environmental and Evolutionary Genomics Section, Institut de Biologie de l'Ecole Normale Supéreure, CNRS UMR8186 INSERM U1024, Ecole Normale Supérieure, Paris, France
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39
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Matsuda Y, Nakajima K, Tachibana M. Recent progresses on the genetic basis of the regulation of CO2 acquisition systems in response to CO2 concentration. PHOTOSYNTHESIS RESEARCH 2011; 109:191-203. [PMID: 21287273 DOI: 10.1007/s11120-011-9623-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 01/06/2011] [Indexed: 05/24/2023]
Abstract
Marine diatoms, the major primary producer in ocean environment, are known to take up both CO(2) and HCO(3)(-) in seawater and efficiently concentrate them intracellularly, which enable diatom cells to perform high-affinity photosynthesis under limiting CO(2). However, mechanisms so far proposed for the inorganic carbon acquisition in marine diatoms are significantly diverse despite that physiological studies on this aspect have been done with only limited number of species. There are two major hypotheses about this; that is, they take up and concentrate both CO(2) and HCO(3)(-) as inorganic forms, and efficiently supply CO(2) to Rubisco by an aid of carbonic anhydrases (biophysical CO(2)-concentrating mechanism: CCM); and as the other hypothesis, biochemical conversion of HCO(3)(-) into C(4) compounds may play a major role to supply concentrated CO(2) to Rubisco. At moment however, physiological evidence for these hypotheses were not related well to molecular level evidence. In this study, recent progresses in molecular studies on diatom-carbon-metabolism genes were related to the physiological aspects of carbon acquisition. Furthermore, we discussed the mechanisms regulating CO(2) acquisition systems in response to changes in pCO(2). Recent findings about the participation of cAMP in the signaling pathway of CO(2) concentration strongly suggested the occurrences of mammalian-type-signaling pathways in diatoms to respond to changes in pCO(2). In fact, there were considerable numbers of putative adenylyl cyclases, which may take part in the processes of CO(2) signal capturing.
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Affiliation(s)
- Yusuke Matsuda
- Department of Bioscience, Research Center for Environmental Bioscience, Kwansei-Gakuin University, Sanda, Hyogo, Japan.
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40
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Mercado JM, Gordillo FJL. Inorganic carbon acquisition in algal communities: are the laboratory data relevant to the natural ecosystems? PHOTOSYNTHESIS RESEARCH 2011; 109:257-267. [PMID: 21445608 DOI: 10.1007/s11120-011-9646-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 03/14/2011] [Indexed: 05/30/2023]
Abstract
Most of the experimental work on the effects of ocean acidification on the photosynthesis of algae has been performed in the laboratory using monospecific cultures. It is frequently assumed that the information obtained from these cultures can be used to predict the acclimation response in the natural environment. CO(2) concentration is known to regulate the expression and functioning of the CCMs in the natural communities; however, ambient CO(2) can become quite variable in the marine ecosystems even in the short- to mid-term. We propose that the degree of saturation of the photosynthesis for a given algal community should be defined in relation to the particular characteristics of its habitat, and not only in relation to its taxonomic composition. The convenience of high CO(2) experiments to infer the degree of photosynthesis saturation by CO(2) in the natural algal communities under the present ocean conditions, as well as its trend in a coming future is discussed taking into account other factors such as the availability of light and nutrients, and seasonality.
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Affiliation(s)
- Jesús M Mercado
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Fuengirola, Málaga, Spain.
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41
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Tachibana M, Allen AE, Kikutani S, Endo Y, Bowler C, Matsuda Y. Localization of putative carbonic anhydrases in two marine diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana. PHOTOSYNTHESIS RESEARCH 2011; 109:205-21. [PMID: 21365259 DOI: 10.1007/s11120-011-9634-4] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 02/13/2011] [Indexed: 05/12/2023]
Abstract
It is believed that intracellular carbonic anhydrases (CAs) are essential components of carbon concentrating mechanisms in microalgae. In this study, putative CA-encoding genes were identified in the genome sequences of the marine diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. Subsequently, the subcellular localizations of the encoded proteins were determined. Nine and thirteen CA sequences were found in the genomes of P. tricornutum and T. pseudonana, respectively. Two of the β-CA genes in P. tricornutum corresponded to ptca1 and ptca2 identified previously. Immunostaining transmission electron microscopy of a PtCA1:YFP fusion expressed in the cells of P. tricornutum clearly showed the localization of PtCA1 within the central part of the pyrenoid structure in the chloroplast. Besides these two β-CA genes, P. tricornutum likely contains five α- and two γ-CA genes, whereas T. pseudonana has three α-, five γ-, four δ-, and one ζ-CA genes. Semi-quantitative reverse transcription PCR performed on mRNA from the two diatoms grown in changing light and CO(2) conditions revealed that levels of six putative α- and γ-CA mRNAs in P. tricornutum did not change between cells grown in air-level CO(2) and 5% CO(2). However, mRNA levels of one putative α-CA gene, CA-VII in P. tricornutum, were reduced in the dark compared to that in the light. In T. pseudonana, mRNA accumulation levels of putative α-CA (CA-1), ζ-CA (CA-3) and δ-CA (CA-7) were analyzed and all levels found to be significantly reduced when cells were grown in 0.16% CO(2). Intercellular localizations of eight putative CAs were analyzed by expressing GFP fusion in P. tricornutum and T. pseudonana. In P. tricornutum, CA-I and II localized in the periplastidial compartment, CA-III, VI, VII were found in the chloroplast endoplasmic reticulum, and CA-VIII was localized in the mitochondria. On the other hand, T. pseudonana CA-1 localized in the stroma and CA-3 was found in the periplasm. These results suggest that CAs are constitutively present in the four chloroplastic membrane systems in P. tricornutum and that CO(2) responsive CAs occur in the pyrenoid of P. tricornutum, and in the stroma and periplasm of T. pseudonana.
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Affiliation(s)
- Masaaki Tachibana
- Department of Bioscience, School of Science and Technology, Kwansei Gakuin University,Sanda, Hyogo, Japan
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42
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McGinn PJ, Dickinson KE, Bhatti S, Frigon JC, Guiot SR, O'Leary SJB. Integration of microalgae cultivation with industrial waste remediation for biofuel and bioenergy production: opportunities and limitations. PHOTOSYNTHESIS RESEARCH 2011; 109:231-247. [PMID: 21461850 DOI: 10.1007/s11120-011-9638-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Accepted: 02/16/2011] [Indexed: 05/30/2023]
Abstract
There is currently a renewed interest in developing microalgae as a source of renewable energy and fuel. Microalgae hold great potential as a source of biomass for the production of energy and fungible liquid transportation fuels. However, the technologies required for large-scale cultivation, processing, and conversion of microalgal biomass to energy products are underdeveloped. Microalgae offer several advantages over traditional 'first-generation' biofuels crops like corn: these include superior biomass productivity, the ability to grow on poor-quality land unsuitable for agriculture, and the potential for sustainable growth by extracting macro- and micronutrients from wastewater and industrial flue-stack emissions. Integrating microalgal cultivation with municipal wastewater treatment and industrial CO(2) emissions from coal-fired power plants is a potential strategy to produce large quantities of biomass, and represents an opportunity to develop, test, and optimize the necessary technologies to make microalgal biofuels more cost-effective and efficient. However, many constraints on the eventual deployment of this technology must be taken into consideration and mitigating strategies developed before large scale microalgal cultivation can become a reality. As a strategy for CO(2) biomitigation from industrial point source emitters, microalgal cultivation can be limited by the availability of land, light, and other nutrients like N and P. Effective removal of N and P from municipal wastewater is limited by the processing capacity of available microalgal cultivation systems. Strategies to mitigate against the constraints are discussed.
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Affiliation(s)
- Patrick J McGinn
- Institute for Marine Biosciences, National Research Council of Canada, Halifax, NS, Canada.
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43
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Cock JM, Coelho SM. Algal models in plant biology. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:2425-2430. [PMID: 21576398 DOI: 10.1093/jxb/err117] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Affiliation(s)
- J Mark Cock
- UPMC Univ. Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Place Georges Teissier, F-29682 Roscoff, France.
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44
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Abstract
C4 photosynthesis is an adaptation that evolved to alleviate the detrimental effects of photorespiration as a result of the gradual decline in atmospheric carbon dioxide levels. In most C4 plants, two cell types, bundle sheath and mesophyll, cooperate in carbon fixation, and, in so doing, are able to alleviate photorespiratory losses. Although much of the biochemistry is well characterized, little is known about the genetic mechanisms underlying the cell-type specificity driving C4 . However, several studies have shown that regulation acts at multiple levels, including transcriptional, post-transcriptional, post-translational and epigenetic. One example of such a regulatory mechanism is the cell-specific accumulation of major photorespiratory transcripts/proteins in bundle sheath cells, where ribulose-1,5-bisphosphate carboxylase/oxygenase is localized. Although many of the genes are expressed in the bundle sheath, some are expressed in both cell types, implicating post-transcriptional control mechanisms. Recently, ultra-high-throughput sequencing techniques and sophisticated mass spectrometry instrumentation have provided new opportunities to further our understanding of C4 regulation. Computational pipelines are being developed to accommodate the mass of data associated with these techniques. Finally, we discuss a readily transformable C4 grass--Setaria viridis--that has great potential to serve as a model for the genetic dissection of C4 photosynthesis in the grasses.
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Affiliation(s)
- Lin Wang
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14850, USA
| | - Richard B Peterson
- Department of Biochemistry & Genetics, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Thomas P Brutnell
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14850, USA
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45
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Reinfelder JR. Carbon concentrating mechanisms in eukaryotic marine phytoplankton. ANNUAL REVIEW OF MARINE SCIENCE 2011; 3:291-315. [PMID: 21329207 DOI: 10.1146/annurev-marine-120709-142720] [Citation(s) in RCA: 230] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The accumulation of inorganic carbon from seawater by eukaryotic marine phytoplankton is limited by the diffusion of carbon dioxide (CO2) in water and the dehydration kinetics of bicarbonate to CO2 and by ribulose-1,5-bisphosphate carboxylase/oxygenase's (RubisCO) low affinity for its inorganic carbon substrate, CO2. Nearly all marine phytoplankton have adapted to these limitations and evolved inorganic carbon (or CO2) concentrating mechanisms (CCMs) to support photosynthetic carbon fixation at the concentrations of CO2 present in ocean surface waters (< 10-30 microM). The biophysics and biochemistry of CCMs vary within and among the three dominant groups of eukaryotic marine phytoplankton and may involve the activity of external or intracellular carbonic anhydrase, HCO3- transport, and perhaps a C4 carbon pump. In general, coccolithophores have low-efficiency CCMs, and diatoms and the haptophyte genus Phaeocystis have high-efficiency CCMs. Dinoflagellates appear to possess moderately efficient CCMs, which may be necessitated by the very low CO2 affinity of their form II RubisCO. The energetic and nutrient costs of CCMs may modulate how variable CO2 affects primary production, element composition, and species composition of phytoplankton in the ocean.
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Affiliation(s)
- John R Reinfelder
- Department of Environmental Sciences, Rutgers University, New Brunswick, New Jersey 08901, USA.
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46
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Raven JA. Inorganic carbon acquisition by eukaryotic algae: four current questions. PHOTOSYNTHESIS RESEARCH 2010; 106:123-34. [PMID: 20524069 DOI: 10.1007/s11120-010-9563-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2010] [Accepted: 05/17/2010] [Indexed: 05/18/2023]
Abstract
The phylogenetically and morphologically diverse eukaryotic algae are typically oxygenic photolithotrophs. They have a diversity of incompletely understood mechanisms of inorganic carbon acquisition: this article reviews four areas where investigations continue. The first topic is diffusive CO(2) entry. Most eukaryotic algae, like all cyanobacteria, have inorganic carbon concentrating mechanisms (CCMs). The ancestral condition was presumably the absence of a CCM, i.e. diffusive CO(2) entry, as found in a small minority of eukaryotic algae today; however, it is likely that, as is found in several cases, this condition is due to a loss of a CCM. There are a number of algae which are in various respects intermediate between diffusive CO(2) entry and occurrence of a CCM: further study is needed on this aspect. A second topic is the nature of cyanelles and their role in inorganic carbon assimilation. The cyanelles (plastids) of the euglyphid amoeba Paulinella have been acquired relatively recently by endosymbiosis with genetic integration of an α-cyanobacterium with a Form 1A Rubisco. The α-carboxysomes in the cyanelles are presumably involved in a CCM, but further investigation is needed.Also called cyanelles are the plastids of glaucocystophycean algae, but is it now clear that these were derived from the β-cyanobacterial ancestor of all plastids other than that of Paulinella. The resemblances of the central body of the cyanelles of glaucocystophycean algae to carboxysomes may not reflect derivation from cyanobacterial β-carboxysomes; although it is clear that these algae have CCMs but these are now well characterized. The other two topics concern CCMs in other eukaryotic algae; these CCMs arose polyphyletically and independently of the cyanobacterial CCMs. It is generally believed that eukaryotic algal, like cyanobacterial, CCMs are based on active transport of an inorganic carbon species and/or protons, and they have C(3) biochemistry. This is the case for the organism considered as the third topic, i.e. Chlamydomonas reinhardtii, the eukaryotic alga with the best understood CCM. This CCM involves HCO(3)(-) conversion to CO(2) in the thylakoid lumen so the external inorganic carbon must cross four membranes in series with a final CO(2) effux from the thylakoid. More remains to be investigated about this CCM. The final topic is that of the occurrence of C(4)-like metabolism in the CCMs of marine diatoms. Different conclusions have been reached depending on the organism investigated and the techniques used, and several aspects require further study.
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Affiliation(s)
- John A Raven
- Division of Plant Sciences, College of Life Sciences, University of Dundee at SCRI, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK.
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47
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Finazzi G, Moreau H, Bowler C. Genomic insights into photosynthesis in eukaryotic phytoplankton. TRENDS IN PLANT SCIENCE 2010; 15:565-572. [PMID: 20800533 DOI: 10.1016/j.tplants.2010.07.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 07/21/2010] [Accepted: 07/22/2010] [Indexed: 05/29/2023]
Abstract
The evolution of photosynthesis completely altered the biogeochemistry of our planet and permitted the evolution of more complex multicellular organisms. Curiously, terrestrial photosynthesis is carried out largely by green algae and their descendents the higher plants, whereas in the ocean the most abundant photosynthetic eukaryotes are microscopic and have red algal affiliations. Although primary productivity is approximately equal between the land and the ocean, the marine microbes represent less than 1% of the photosynthetic biomass found on land. This review focuses on this highly successful and diverse group of organisms collectively known as phytoplankton and reviews how insights from whole genome analyses have improved our understanding of the novel innovations employed by them to maximize photosynthetic efficiency in variable light environments.
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Affiliation(s)
- Giovanni Finazzi
- Laboratoire de Physiologie Vegetale et Cellulaire, UMR 5168 Centre National de la Recherche Scientifique/Commissariat à l'énergie atomique et aux énergies alternatives/Université Joseph Fourier, CEA Grenoble, 17 rue des Martyrs, 38054 Grenoble, France
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48
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Bowler C, Vardi A, Allen AE. Oceanographic and biogeochemical insights from diatom genomes. ANNUAL REVIEW OF MARINE SCIENCE 2010; 2:333-65. [PMID: 21141668 DOI: 10.1146/annurev-marine-120308-081051] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Diatoms are the most successful group of eukaryotic phytoplankton in the modern ocean and have risen to dominance relatively quickly over the last 100 million years. Recently completed whole genome sequences from two species of diatom, Thalassiosira pseudonana and Phaeodactylum tricornutum, have revealed a wealth of information about the evolutionary origins and metabolic adaptations that have led to their ecological success. A major finding is that they have incorporated genes both from their endosymbiotic ancestors and by horizontal gene transfer from marine bacteria. This unique melting pot of genes encodes novel capacities for metabolic management, for example, allowing the integration of a urea cycle into a photosynthetic cell. In this review we show how genome-enabled approaches are being leveraged to explore major phenomena of oceanographic and biogeochemical relevance, such as nutrient assimilation and life histories in diatoms. We also discuss how diatoms may be affected by climate change-induced alterations in ocean processes.
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Affiliation(s)
- Chris Bowler
- CNRS UMR8186, Department of Biology, Ecole Normale Supérieure, Paris, France.
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49
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Maberly SC, Ball LA, Raven JA, Sültemeyer D. INORGANIC CARBON ACQUISITION BY CHRYSOPHYTES(1). JOURNAL OF PHYCOLOGY 2009; 45:1052-61. [PMID: 27032350 DOI: 10.1111/j.1529-8817.2009.00734.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Twelve species, representing 12 families of the chrysophytes sensu lato, were tested for their ability to take up inorganic carbon. Using the pH-drift technique, CO2 compensation points generally varied between 1 and 20 μmol · L(-1) with a mean concentration of 5 μmol · L(-1) . Neither pH nor alkalinity affected the CO2 compensation point. The concentration of oxygen had a relatively minor effect on CO2 -uptake kinetics, and the mean CO2 compensation point calculated from the kinetic curves was 3.6 μmol · L(-1) at 10-15 kPa starting oxygen partial pressure and 3.8 μmol · L(-1) at atmospheric starting oxygen partial pressure (21 kPa). Similarly, uptake kinetics were not affected by alkalinity, and hence concentration of bicarbonate. Membrane inlet mass spectrometry (MIMS) in the presence and absence of acetazolamide suggested that external carbonic anhydrase in Dinobryon sertularia Ehrenb. and Synura petersenii Korschikov was either very low or absent. Rates of net HCO3 (-) uptake were very low (∼5% of oxygen evolution) using MIMS and decreased rather than increased with increasing HCO3 (-) concentration, suggesting that it was not a real uptake. The CO2 compensation points determined by MIMS for CO2 uptake and oxygen evolution were similar to those determined in pH-drift and were >1 μmol · L(-1) . Overall, the results suggest that chrysophytes as a group lack a carbon-concentrating mechanism (CCM), or an ability to make use of bicarbonate as an alternative source of inorganic carbon. The possible evolutionary and ecological consequences of this are briefly discussed.
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Affiliation(s)
- Stephen C Maberly
- Centre for Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP, UKThe Freshwater Biological Association, The Ferry Landing, Far Sawrey, Ambleside, Cumbria, LA22 0LP, UKDivision of Plant Sciences, The University of Dundee at SCRI, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UKFachbereich Biologie, Technische Universität Kaiserslautern, D-67663 Kaiserslautner, Germany
| | - Lucy A Ball
- Centre for Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP, UKThe Freshwater Biological Association, The Ferry Landing, Far Sawrey, Ambleside, Cumbria, LA22 0LP, UKDivision of Plant Sciences, The University of Dundee at SCRI, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UKFachbereich Biologie, Technische Universität Kaiserslautern, D-67663 Kaiserslautner, Germany
| | - John A Raven
- Centre for Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP, UKThe Freshwater Biological Association, The Ferry Landing, Far Sawrey, Ambleside, Cumbria, LA22 0LP, UKDivision of Plant Sciences, The University of Dundee at SCRI, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UKFachbereich Biologie, Technische Universität Kaiserslautern, D-67663 Kaiserslautner, Germany
| | - Dieter Sültemeyer
- Centre for Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP, UKThe Freshwater Biological Association, The Ferry Landing, Far Sawrey, Ambleside, Cumbria, LA22 0LP, UKDivision of Plant Sciences, The University of Dundee at SCRI, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UKFachbereich Biologie, Technische Universität Kaiserslautern, D-67663 Kaiserslautner, Germany
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50
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Granum E, Roberts K, Raven JA, Leegood RC. PRIMARY CARBON AND NITROGEN METABOLIC GENE EXPRESSION IN THE DIATOM THALASSIOSIRA PSEUDONANA (BACILLARIOPHYCEAE): DIEL PERIODICITY AND EFFECTS OF INORGANIC CARBON AND NITROGEN(1). JOURNAL OF PHYCOLOGY 2009; 45:1083-92. [PMID: 27032353 DOI: 10.1111/j.1529-8817.2009.00728.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Diel periodicity and effects of inorganic carbon (Ci ) and NO3 (-) on the expression of 11 key genes for primary carbon and nitrogen metabolism, including potential C4 photosynthesis, in the marine diatom Thalassiosira pseudonana Hasle et Heimdal were investigated. Target gene transcripts were measured by quantitative reverse transcriptase-PCR, and some of the gene-encoded proteins were analyzed by Western blotting. The diatom was grown with a 12 h photoperiod at two different Ci concentrations maintained by air-equilibration with either 380 μL · L(-1) (near-ambient) or 100 μL · L(-1) (low) CO2 . Transcripts of the principal Ci and NO3 (-) assimilatory genes RUBISCO LSU (rbcL) and nitrate reductase displayed very strong diel oscillations with peaks at the end of the scotophase. Considerable diel periodicities were also exhibited by the β-carboxylase genes phosphoenolpyruvate carboxylase (PEPC1 and PEPC2) and phosphoenolpyruvate carboxykinase (PEPCK), and the Benson-Calvin cycle gene sedoheptulose-bisphosphatase (SBPase), with peaks during mid- to late scotophase. In accordance with the transcripts, there were substantial diel periodicities in PEPC1, PEPC2, PEPCK, and especially rbcL proteins, although they peaked during early to mid-photophase. Inorganic carbon had some transient effects on the β-carboxylase transcripts, and glycine decarboxylase P subunit was highly up-regulated by low Ci concentration, indicating increased capacity for photorespiration. Nitrogen-starved cells had reduced amounts of carbon metabolic gene transcripts, but the PEPC1, PEPC2, PEPCK, and rbcL transcripts increased rapidly when NO3 (-) was replenished. The results suggest that the β-carboxylases in T. pseudonana play key anaplerotic roles but show no clear support for C4 photosynthesis.
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Affiliation(s)
- Espen Granum
- Robert Hill Institute and Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UKDivision of Plant Sciences, University of Dundee at Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UKRobert Hill Institute and Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Karen Roberts
- Robert Hill Institute and Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UKDivision of Plant Sciences, University of Dundee at Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UKRobert Hill Institute and Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - John A Raven
- Robert Hill Institute and Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UKDivision of Plant Sciences, University of Dundee at Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UKRobert Hill Institute and Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Richard C Leegood
- Robert Hill Institute and Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UKDivision of Plant Sciences, University of Dundee at Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UKRobert Hill Institute and Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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