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Kumar M, Tibocha-Bonilla JD, Füssy Z, Lieng C, Schwenck SM, Levesque AV, Al-Bassam MM, Passi A, Neal M, Zuniga C, Kaiyom F, Espinoza JL, Lim H, Polson SW, Allen LZ, Zengler K. Mixotrophic growth of a ubiquitous marine diatom. SCIENCE ADVANCES 2024; 10:eado2623. [PMID: 39018398 PMCID: PMC466952 DOI: 10.1126/sciadv.ado2623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/12/2024] [Indexed: 07/19/2024]
Abstract
Diatoms are major players in the global carbon cycle, and their metabolism is affected by ocean conditions. Understanding the impact of changing inorganic nutrients in the oceans on diatoms is crucial, given the changes in global carbon dioxide levels. Here, we present a genome-scale metabolic model (iMK1961) for Cylindrotheca closterium, an in silico resource to understand uncharacterized metabolic functions in this ubiquitous diatom. iMK1961 represents the largest diatom metabolic model to date, comprising 1961 open reading frames and 6718 reactions. With iMK1961, we identified the metabolic response signature to cope with drastic changes in growth conditions. Comparing model predictions with Tara Oceans transcriptomics data unraveled C. closterium's metabolism in situ. Unexpectedly, the diatom only grows photoautotrophically in 21% of the sunlit ocean samples, while the majority of the samples indicate a mixotrophic (71%) or, in some cases, even a heterotrophic (8%) lifestyle in the light. Our findings highlight C. closterium's metabolic flexibility and its potential role in global carbon cycling.
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Affiliation(s)
- Manish Kumar
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Juan D. Tibocha-Bonilla
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Zoltán Füssy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Chloe Lieng
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Sarah M. Schwenck
- Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Alice V. Levesque
- Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Mahmoud M. Al-Bassam
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Anurag Passi
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Maxwell Neal
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Cristal Zuniga
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Farrah Kaiyom
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Josh L. Espinoza
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, 4120 Capricorn Way, La Jolla, CA 92037, USA
| | - Hyungyu Lim
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Shawn W. Polson
- Department of Computer and Information Sciences, University of Delaware, 18 Amstel Ave., Newark, DE 19716, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, 590 Avenue 1743, Newark, DE 19713, USA
| | - Lisa Zeigler Allen
- Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, 4120 Capricorn Way, La Jolla, CA 92037, USA
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Program in Materials Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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2
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Hamilton M, Ferrer‐González FX, Moran MA. Heterotrophic bacteria trigger transcriptome remodelling in the photosynthetic picoeukaryote Micromonas commoda. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13285. [PMID: 38778545 PMCID: PMC11112143 DOI: 10.1111/1758-2229.13285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
Marine biogeochemical cycles are built on interactions between surface ocean microbes, particularly those connecting phytoplankton primary producers to heterotrophic bacteria. Details of these associations are not well understood, especially in the case of direct influences of bacteria on phytoplankton physiology. Here we catalogue how the presence of three marine bacteria (Ruegeria pomeroyi DSS-3, Stenotrophomonas sp. SKA14 and Polaribacter dokdonensis MED152) individually and uniquely impact gene expression of the picoeukaryotic alga Micromonas commoda RCC 299. We find a dramatic transcriptomic remodelling by M. commoda after 8 h in co-culture, followed by an increase in cell numbers by 56 h compared with the axenic cultures. Some aspects of the algal transcriptomic response are conserved across all three bacterial co-cultures, including an unexpected reduction in relative expression of photosynthesis and carbon fixation pathways. Expression differences restricted to a single bacterium are also observed, with the Flavobacteriia P. dokdonensis uniquely eliciting changes in relative expression of algal genes involved in biotin biosynthesis and the acquisition and assimilation of nitrogen. This study reveals that M. commoda has rapid and extensive responses to heterotrophic bacteria in ways that are generalizable, as well as in a taxon specific manner, with implications for the diversity of phytoplankton-bacteria interactions ongoing in the surface ocean.
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Affiliation(s)
- Maria Hamilton
- Department of Marine SciencesUniversity of GeorgiaAthensGeorgiaUSA
| | | | - Mary Ann Moran
- Department of Marine SciencesUniversity of GeorgiaAthensGeorgiaUSA
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3
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Li Z, Qi L, Cui R, Zhang N, Song C, Li X, Lu X, Fan Y. De novo transcriptome assembly and molecular response mechanism analysis of a diatom Cyclotella meneghiniana Kützing exposed to cadmium. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 272:116020. [PMID: 38306816 DOI: 10.1016/j.ecoenv.2024.116020] [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: 11/11/2023] [Revised: 01/20/2024] [Accepted: 01/24/2024] [Indexed: 02/04/2024]
Abstract
Cadmium is a persistent heavy metal commonly found in aquatic ecosystems and has a strong toxic effect on organisms. The sensitivity of phytoplankton to environmental changes and its role as an indicator of aquatic ecosystem health have been well-established. However, the mechanisms by which phytoplankton respond to cadmium remain incompletely understood. In this study, we chose the typical planktonic diatom Cyclotella meneghiniana Kützing, by integrating physiological-biochemical data and transcriptome analysis, to reveal the molecular mechanisms of C. meneghiniana responing to cadmium. Under cadmium stress, the cell density and chlorophyll-a content of C. meneghiniana significantly decreased, while MDA content and SOD activity gradually increased. At 72 h of cadmium stress, we found that at this time point, cell abundance and physiological variation were very significant, therefore we selected 72 h for subsequent analysis. To better understand the cadmium stress response mechanisms of C. meneghiniana, a de novo transcriptome method was used to analyse C. meneghiniana under cadmium stress for 72 h, and 1704 (M vs. CK) and 4788 (H vs. CK) differentially expressed genes were found. Our results showed that the changes in gene expression were closely correlated to the physiological-biochemical changes. Although cadmium stress could promote the nitrogen metabolism pathway, ROS scavenging system, and photosynthesis. While, C. meneghiniana under medium and high concentrations of cadmium can also limit various intracellular metabolic pathways, such as the MAPK pathway and phosphatidylinositol metabolic pathway, and the degree of inhibition increases with the increase of stress concentration. In present study, the complete molecular mechanism of the planktonic diatom response to cadmium has been established, which provided important information for further studies on heavy metal pollutants and the multiple functional genes responsible for cadmium sensitivity and tolerance in planktonic diatoms.
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Affiliation(s)
- Zhenxiang Li
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Lin Qi
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Runbo Cui
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Nannan Zhang
- Modern Educational Technology and Experiment Center, Harbin Normal University, Harbin 150025, China
| | - Chunhua Song
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China; Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin 150025, China
| | - Xue Li
- Moutai Institute, Zunyi 564507, China
| | - Xinxin Lu
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China; Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin 150025, China.
| | - Yawen Fan
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China; Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin 150025, China.
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4
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Poulsen N, Kröger N. Thalassiosira pseudonana (Cyclotella nana) (Hustedt) Hasle et Heimdal (Bacillariophyceae): A genetically tractable model organism for studying diatom biology, including biological silica formation. JOURNAL OF PHYCOLOGY 2023; 59:809-817. [PMID: 37424141 DOI: 10.1111/jpy.13362] [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: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/11/2023]
Abstract
In 2004, Thalassiosira pseudonana was the first eukaryotic marine alga to have its genome sequenced. Since then, this species has quickly emerged as a valuable model species for investigating the molecular underpinnings of essentially all aspects of diatom life, particularly bio-morphogenesis of the cell wall. An important prerequisite for the model status of T. pseudonana is the ongoing development of increasingly precise tools to study the function of gene networks and their encoded proteins in vivo. Here, we briefly review the current toolbox for genetic manipulation, highlight specific examples of its application in studying diatom metabolism, and provide a peek into the role of diatoms in the emerging field of silica biotechnology.
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Affiliation(s)
- Nicole Poulsen
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Nils Kröger
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden, Germany
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, Germany
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5
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Guo J, Jian J, Wang L, Xiong L, Lin H, Zhou Z, Sonnenschein EC, Wu W. Genome Sequences of Two Strains of Prototheca wickerhamii Provide Insight Into the Protothecosis Evolution. Front Cell Infect Microbiol 2022; 12:797017. [PMID: 35186789 PMCID: PMC8847788 DOI: 10.3389/fcimb.2022.797017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
The Prototheca alga is the only chlorophyte known to be involved in a series of clinically relevant opportunistic infections in humans and animals, namely, protothecosis. Most pathogenic cases in humans are caused by Prototheca wickerhamii. In order to investigate the evolution of Prototheca and the genetic basis for its pathogenicity, the genomes of two P. wickerhamii strains S1 and S931 were sequenced using Nanopore long-read and Illumina short-read technologies. The mitochondrial, plastid, and nuclear genomes were assembled and annotated including a transcriptomic data set. The assembled nuclear genome size was 17.57 Mb with 19 contigs and 17.45 Mb with 26 contigs for strains S1 and S931, respectively. The number of predicted protein-coding genes was approximately 5,700, and more than 96% of the genes could be annotated with a gene function. A total of 2,798 gene families were shared between the five currently available Prototheca genomes. According to the phylogenetic analysis, the genus of Prototheca was classified in the same clade with A. protothecoides and diverged from Chlorella ~500 million years ago (Mya). A total of 134 expanded genes were enriched in several pathways, mostly in metabolic pathways, followed by biosynthesis of secondary metabolites and RNA transport. Comparative analysis demonstrated more than 96% consistency between the two herein sequenced strains. At present, due to the lack of sufficient understanding of the Prototheca biology and pathogenicity, the diagnosis rate of protothecosis is much lower than the actual infection rate. This study provides an in-depth insight into the genome sequences of two strains of P. wickerhamii isolated from the clinic to contribute to the basic understanding of this alga and explore future prevention and treatment strategies.
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Affiliation(s)
- Jian Guo
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jianbo Jian
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Lili Wang
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lijuan Xiong
- Department of Laboratory Medicine, Guizhou University The Second Affiliated Hospital of Traditional Chinese Medicine, Guizhou, China
| | - Huiping Lin
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ziyi Zhou
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Eva C. Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
- *Correspondence: Wenjuan Wu, ; Eva C. Sonnenschein,
| | - Wenjuan Wu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- *Correspondence: Wenjuan Wu, ; Eva C. Sonnenschein,
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6
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Kong L, Price NM. Transcriptomes of an oceanic diatom reveal the initial and final stages of acclimation to copper deficiency. Environ Microbiol 2021; 24:951-966. [PMID: 34029435 DOI: 10.1111/1462-2920.15609] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/13/2022]
Abstract
Copper (Cu) concentration is greatly reduced in the open sea so that phytoplankton must adjust their uptake systems and acclimate to sustain growth. Acclimation to low Cu involves changes to the photosynthetic apparatus and specific biochemical reactions that use Cu, but little is known how Cu affects cellular metabolic networks. Here we report results of whole transcriptome analysis of a plastocyanin-containing diatom, Thalassiosira oceanica 1005, during its initial stages of acclimation and after long-term adaptation in Cu-deficient seawater. Gene expression profiles, used to identify Cu-regulated metabolic pathways, show downregulation of anabolic and energy-yielding reactions in Cu-limited cells. These include the light reactions of photosynthesis, carbon fixation, nitrogen assimilation and glycolysis. Reduction of these pathways is consistent with reduced growth requirements for C and N caused by slower rates of photosynthetic electron transport. Upregulation of oxidative stress defence systems persists in adapted cells, suggesting cellular damage by increased reactive oxygen species (ROS) occurs even after acclimation. Copper deficiency also alters fatty acid metabolism, possibly in response to an increase in lipid peroxidation and membrane damage driven by ROS. During the initial stages of Cu-limitation the majority of differentially regulated genes are associated with photosynthetic metabolism, highlighting the chloroplast as the primary target of low Cu availability. The results provide insights into the mechanisms of acclimation and adaptation of T. oceanica to Cu deficiency.
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Affiliation(s)
- Liangliang Kong
- Department of Biology, McGill University, Montréal, QC, Canada.,College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
| | - Neil M Price
- Department of Biology, McGill University, Montréal, QC, Canada
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7
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Li Y, Liu X, Zheng X, Yang M, Gao X, Huang J, Zhang L, Fan Z. Toxic effects and mechanisms of PFOA and its substitute GenX on the photosynthesis of Chlorella pyrenoidosa. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 765:144431. [PMID: 33387923 DOI: 10.1016/j.scitotenv.2020.144431] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Perfluorooctanoic acid (PFOA) and its substitute GenX are toxic chemicals that are widespread in the aquatic environment. However, there is little information about their toxicity mechanisms to aquatic organisms. In this study, Chlorella pyrenoidosa (C. pyrenoidosa) was treated with two concentrations (100 ng L-1 and 100 μg L-1) of PFOA or GenX for 12 days. The results showed that these two concentrations of PFOA and GenX began to inhibit the growth of algae after 6 days of treatment, and the Chlorophyll content and photosynthetic activity of C. pyrenoidosa were also negatively affected by these two chemicals. The transcriptomic results indicated that most of the genes related to the photosynthetic metabolism of C. pyrenoidosa were down-regulated (in 100 ng L-1 treatment groups) on the 12th day. Besides, GenX and PFOA showed similar effects on algae photosynthesis including physical damage and metabolic disorders. According to this study, GenX might not be an ideal substitute for PFOA, and more attention should be paid on the management of emerging perfluoroalkyl substances.
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Affiliation(s)
- Yanyao Li
- Department of Environmental Science & Engineering, Fudan University, Shanghai 200438. China
| | - Xianglin Liu
- Department of Environmental Science & Engineering, Fudan University, Shanghai 200438. China
| | - Xiaowei Zheng
- Department of Environmental Science & Engineering, Fudan University, Shanghai 200438. China
| | - Meng Yang
- Department of Environmental Science & Engineering, Fudan University, Shanghai 200438. China
| | - Xutao Gao
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jingling Huang
- Department of Environmental Science & Engineering, Fudan University, Shanghai 200438. China
| | - Liangliang Zhang
- Department of Environmental Science & Engineering, Fudan University, Shanghai 200438. China
| | - Zhengqiu Fan
- Department of Environmental Science & Engineering, Fudan University, Shanghai 200438. China.
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8
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Zheng JW, Mao XT, Ye MH, Li HY, Liu JS, Yang WD. Allelopathy and underlying mechanism of Karenia mikimotoi on the diatom Thalassiosira pseudonana under laboratory condition. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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9
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Thangaraj S, Palanisamy SK, Zhang G, Sun J. Quantitative Proteomic Profiling of Marine Diatom Skeletonema dohrnii in Response to Temperature and Silicate Induced Environmental Stress. Front Microbiol 2021; 11:554832. [PMID: 33519723 PMCID: PMC7841394 DOI: 10.3389/fmicb.2020.554832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 12/23/2020] [Indexed: 11/17/2022] Open
Abstract
Global warming is expected to reduce the nutrient concentration in the upper ocean and affect the physiology of marine diatoms, but the underlying molecular mechanisms controlling these physiological changes are currently unknown. To understand these mechanisms, here we investigated iTRAQ based proteomic profiling of diatom Skeletonema dohrnii in a multifactorial experimental with a combining change of temperature and silicate concentrations. In total, 3369 differently abundant proteins were detected in four different environmental conditions, and the function of all proteins was identified using Gene Ontology and KEGG pathway analysis. For discriminating the proteome variation among samples, multivariate statistical analysis (PCA, PLS-DA) was performed by comparing the protein ratio differences. Further, performing pathway analysis on diatom proteomes, we here demonstrated downregulation of photosynthesis, carbon metabolism, and ribosome biogenesis in the cellular process that leads to decrease the oxidoreductase activity and affects the cell cycle of the diatom. Using PLS-DA VIP score plot analysis, we identified 15 protein biomarkers for discriminating studied samples. Of these, five proteins or gene (rbcL, PRK, atpB, DNA-binding, and signal transduction) identified as key biomarkers, induced by temperature and silicate stress in diatom metabolism. Our results show that proteomic finger-printing of S. dohrnii with different environmental conditions adds biological information that strengthens marine phytoplankton proteome analysis.
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Affiliation(s)
| | - Satheesh Kumar Palanisamy
- Department of Zoology, School of Natural Science, Ryan Institute, National University of Ireland, Galway, Ireland
| | - Guicheng Zhang
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, Tianjin, China
| | - Jun Sun
- College of Marine Science and Technology, China University of Geosciences, Wuhan, China
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10
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Zhao Y, Tang X, Lv M, Liu Q, Li J, Zhang B, Li L, Zhang X, Zhao Y. The molecular response mechanisms of a diatom Thalassiosira pseudonana to the toxicity of BDE-47 based on whole transcriptome analysis. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2020; 229:105669. [PMID: 33142158 DOI: 10.1016/j.aquatox.2020.105669] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/16/2020] [Accepted: 10/21/2020] [Indexed: 06/11/2023]
Abstract
Polybrominated diphenyl ethers (PBDEs) are ubiquitously distributed persistent organic pollutants (POPs) in marine environments. Phytoplankton are the entrance of PBDEs entering to biotic environments from abiotic environments, while the responding mechanisms of phytoplankton to PBDEs have not been full established. Therefore, we chose the model diatom Thalassiosira pseudonana in this study, by integrating whole transcriptome analysis with physiological-biochemical data, to reveal the molecular responding mechanisms of T. pseudonana to the toxicity of BDE-47. Our results indicated the changes of genes expressions correlated to the physiological-biochemical changes, and there were multiple molecular mechanisms of T. pseudonana responding to the toxicity of BDE-47: Gene expressions evidence explained the suppression of light reaction and proved the occurrence of cellular oxidative stress; In the meanwhile, up-regulations of genes in pathways involving carbon metabolisms happened, including the Calvin cycle, glycolysis, TCA cycle, fatty acid synthesis, and triacylglycerol synthesis; Lastly, DNA damage was found and three outcome including DNA repair, cell cycle arrest and programmed cell death (PCD) happened, which could finally inhibit the cell division and population growth of T. pseudonana. This study presented the most complete molecular responding mechanisms of phytoplankton cells to PBDEs, and provided valuable information of various PBDEs-sensitive genes with multiple functions for further research involving organic pollutants and phytoplankton.
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Affiliation(s)
- Yirong Zhao
- College of Marine Life Sciences, Department of Marine Ecology, Ocean University of China, Qingdao, 266003, China
| | - Xuexi Tang
- College of Marine Life Sciences, Department of Marine Ecology, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
| | - Mengchen Lv
- College of Marine Life Sciences, Department of Marine Ecology, Ocean University of China, Qingdao, 266003, China
| | - Qian Liu
- College of Marine Life Sciences, Department of Marine Ecology, Ocean University of China, Qingdao, 266003, China
| | - Jun Li
- College of Marine Life Sciences, Department of Marine Ecology, Ocean University of China, Qingdao, 266003, China
| | - Bihan Zhang
- College of Marine Life Sciences, Department of Marine Ecology, Ocean University of China, Qingdao, 266003, China
| | - Luying Li
- College of Marine Life Sciences, Department of Marine Ecology, Ocean University of China, Qingdao, 266003, China
| | - Xinxin Zhang
- College of Marine Life Sciences, Department of Marine Ecology, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Yan Zhao
- College of Marine Life Sciences, Department of Marine Ecology, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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11
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Kumar G, Shekh A, Jakhu S, Sharma Y, Kapoor R, Sharma TR. Bioengineering of Microalgae: Recent Advances, Perspectives, and Regulatory Challenges for Industrial Application. Front Bioeng Biotechnol 2020; 8:914. [PMID: 33014997 PMCID: PMC7494788 DOI: 10.3389/fbioe.2020.00914] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/15/2020] [Indexed: 01/14/2023] Open
Abstract
Microalgae, due to their complex metabolic capacity, are being continuously explored for nutraceuticals, pharmaceuticals, and other industrially important bioactives. However, suboptimal yield and productivity of the bioactive of interest in local and robust wild-type strains are of perennial concerns for their industrial applications. To overcome such limitations, strain improvement through genetic engineering could play a decisive role. Though the advanced tools for genetic engineering have emerged at a greater pace, they still remain underused for microalgae as compared to other microorganisms. Pertaining to this, we reviewed the progress made so far in the development of molecular tools and techniques, and their deployment for microalgae strain improvement through genetic engineering. The recent availability of genome sequences and other omics datasets form diverse microalgae species have remarkable potential to guide strategic momentum in microalgae strain improvement program. This review focuses on the recent and significant improvements in the omics resources, mutant libraries, and high throughput screening methodologies helpful to augment research in the model and non-model microalgae. Authors have also summarized the case studies on genetically engineered microalgae and highlight the opportunities and challenges that are emerging from the current progress in the application of genome-editing to facilitate microalgal strain improvement. Toward the end, the regulatory and biosafety issues in the use of genetically engineered microalgae in commercial applications are described.
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Affiliation(s)
- Gulshan Kumar
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Ajam Shekh
- Plant Cell Biotechnology Department, CSIR-Central Food Technological Research Institute (CFTRI), Mysuru, India
| | - Sunaina Jakhu
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Yogesh Sharma
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Ritu Kapoor
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Tilak Raj Sharma
- Division of Crop Science, Indian Council of Agricultural Research, New Delhi, India
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12
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Thangaraj S, Giordano M, Sun J. Comparative Proteomic Analysis Reveals New Insights Into the Common and Specific Metabolic Regulation of the Diatom Skeletonema dohrnii to the Silicate and Temperature Availability. FRONTIERS IN PLANT SCIENCE 2020; 11:578915. [PMID: 33224167 PMCID: PMC7674209 DOI: 10.3389/fpls.2020.578915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/28/2020] [Indexed: 05/12/2023]
Abstract
Silicate (Si) and temperature are essential drivers for diatom growth and development in the ocean. Response of diatoms to these particular stress has been investigated; however, their common and specific responses to regulate intracellular development and growth are not known. Here, we investigated the combination of physiological characteristics and comparative proteomics of the diatom Skeletonema dohrnii grown in silicate- and temperature-limited conditions. Results show that cell carbon and lipid quotas were higher at lower-temperature cells, whereas cellular phosphate was higher in cells grown with lower Si. In silicate-limited cells, nitrate transporters were downregulated and resulted in lower nitrate assimilation, whereas the phosphate transporters and its assimilation were reduced in lower-temperature conditions. In photosynthesis, lower silicate caused impact in the linear electron flow and NADPH production, whereas cycling electron transport and ATP production were affected by the lower temperature. Concerning cell cycle, imbalances in the translation process were observed in lower-silicate cells, whereas impact in the transcription mechanism was observed in lower-temperature cells. However, proteins associated with carbon fixation and photorespiration were downregulated in both stress conditions, while the carbohydrate and lipid synthesis proteins were upregulated. Our results showed new insights into the common and specific responses on the proteome and physiology of S. dohrnii to silicate and temperature limitation, providing particular nutrient (Si)- and temperature-dependent mechanisms in diatoms.
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Affiliation(s)
- Satheeswaran Thangaraj
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan, China
| | - Mario Giordano
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Jun Sun
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan, China
- *Correspondence: Jun Sun,
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Telussa I, Rusnadi, Zeily Nurachman. Dynamics of β-carotene and fucoxanthin of tropical marine Navicula sp. as a response to light stress conditions. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101530] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Thangaraj S, Shang X, Sun J, Liu H. Quantitative Proteomic Analysis Reveals Novel Insights into Intracellular Silicate Stress-Responsive Mechanisms in the Diatom Skeletonema dohrnii. Int J Mol Sci 2019; 20:E2540. [PMID: 31126124 PMCID: PMC6566588 DOI: 10.3390/ijms20102540] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/19/2019] [Accepted: 05/20/2019] [Indexed: 01/04/2023] Open
Abstract
Diatoms are a successful group of marine phytoplankton that often thrives under adverse environmental stress conditions. Members of the Skeletonema genus are ecologically important which may subsist during silicate stress and form a dense bloom following higher silicate concentration. However, our understanding of diatoms' underlying molecular mechanism involved in these intracellular silicate stress-responses are limited. Here an iTRAQ-based proteomic method was coupled with multiple physiological techniques to explore distinct cellular responses associated with oxidative stress in the diatom Skeletonema dohrnii to the silicate limitation. In total, 1768 proteins were detected; 594 proteins were identified as differentially expressed (greater than a two-fold change; p < 0.05). In Si-limited cells, downregulated proteins were mainly related to photosynthesis metabolism, light-harvesting complex, and oxidative phosphorylation, corresponding to inducing oxidative stress, and ROS accumulation. None of these responses were identified in Si-limited cells; in comparing with other literature, Si-stress cells showed that ATP-limited diatoms are unable to rely on photosynthesis, which will break down and reshuffle carbon metabolism to compensate for photosynthetic carbon fixation losses. Our findings have a good correlation with earlier reports and provides a new molecular level insight into the systematic intracellular responses employed by diatoms in response to silicate stress in the marine environment.
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Affiliation(s)
- Satheeswaran Thangaraj
- Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, No 29, 13th Avenue, TEDA, Tianjin 300457, China.
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, No 29, 13th Avenue, TEDA, Tianjin 300457, China.
- Faculty of Food Engineering and Biotechnology, Tianjin University of Science and Technology, No 29, 13th Avenue, TEDA, Tianjin 300457, China.
| | - Xiaomei Shang
- Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, No 29, 13th Avenue, TEDA, Tianjin 300457, China.
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, No 29, 13th Avenue, TEDA, Tianjin 300457, China.
| | - Jun Sun
- Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, No 29, 13th Avenue, TEDA, Tianjin 300457, China.
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, No 29, 13th Avenue, TEDA, Tianjin 300457, China.
| | - Haijiao Liu
- Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, No 29, 13th Avenue, TEDA, Tianjin 300457, China.
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, No 29, 13th Avenue, TEDA, Tianjin 300457, China.
- Institute of Marine Science and Technology, Shandong University, No 27, Shanda Nan Road, Jinan 250110, China.
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Dong C, Zhang H, Yang Y, He X, Liu L, Fu J, Shi J, Wu Z. Physiological and transcriptomic analyses to determine the responses to phosphorus utilization in Nostoc sp. HARMFUL ALGAE 2019; 84:10-18. [PMID: 31128794 DOI: 10.1016/j.hal.2019.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 03/05/2019] [Accepted: 03/08/2019] [Indexed: 05/05/2023]
Abstract
Phosphorus (P) is an important factor driving algal growth in aquatic ecosystems. In the present study, the growth, P uptake and utilization, photosynthesis, and transcriptome profile of Nostoc sp. were measured when Nostoc sp. cultured in media containing β-glycerol phosphate (β-gly, containing COP bonds), 2-aminoethylphosphonic acid (2-amin, containing CP bonds), or orthophosphate (K2HPO4), and in P-free (NP) medium. The results revealed that NP treatment adversely affected the growth and photosynthesis of Nostoc sp. and significantly down-regulated the expression of genes related to nutrient transport and material metabolism. Furthermore, 2-amin treatment reduced the growth of Nostoc sp. but did not significantly reduce photosynthesis, and the treatments of NP and 2-amin up-regulated the expressions of genes related antioxidation and stress. Additionally, there were no obvious differences in growth, photosynthesis, and phosphorus utilization between the β-gly and K2HPO4 treatments. These results suggested that Nostoc had a flexible ability to utilize P, which might play an important role in its widespread distribution in the environment.
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Affiliation(s)
- Congcong Dong
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, PR China
| | - Hongbo Zhang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, PR China
| | - Yanjun Yang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, PR China
| | - Xinyu He
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, PR China
| | - Li Liu
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, PR China
| | - Junke Fu
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, PR China
| | - Junqiong Shi
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, PR China
| | - Zhongxing Wu
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, PR China.
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Alipanah L, Winge P, Rohloff J, Najafi J, Brembu T, Bones AM. Molecular adaptations to phosphorus deprivation and comparison with nitrogen deprivation responses in the diatom Phaeodactylum tricornutum. PLoS One 2018; 13:e0193335. [PMID: 29474408 PMCID: PMC5825098 DOI: 10.1371/journal.pone.0193335] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 02/08/2018] [Indexed: 01/12/2023] Open
Abstract
Phosphorus, an essential element for all living organisms, is a limiting nutrient in many regions of the ocean due to its fast recycling. Changes in phosphate (Pi) availability in aquatic systems affect diatom growth and productivity. We investigated the early adaptive mechanisms in the marine diatom Phaeodactylum tricornutum to P deprivation using a combination of transcriptomics, metabolomics, physiological and biochemical experiments. Our analysis revealed strong induction of gene expression for proteins involved in phosphate acquisition and scavenging, and down-regulation of processes such as photosynthesis, nitrogen assimilation and nucleic acid and ribosome biosynthesis. P deprivation resulted in alterations of carbon allocation through the induction of the pentose phosphate pathway and cytosolic gluconeogenesis, along with repression of the Calvin cycle. Reorganization of cellular lipids was indicated by coordinated induced expression of phospholipases, sulfolipid biosynthesis enzymes and a putative betaine lipid biosynthesis enzyme. A comparative analysis of nitrogen- and phosphorus-deprived P. tricornutum revealed both common and distinct regulation patterns in response to phosphate and nitrate stress. Regulation of central carbon metabolism and amino acid metabolism was similar, whereas unique responses were found in nitrogen assimilation and phosphorus scavenging in nitrogen-deprived and phosphorus-deprived cells, respectively.
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Affiliation(s)
- Leila Alipanah
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Per Winge
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jens Rohloff
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Javad Najafi
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Tore Brembu
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Atle M. Bones
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
- * E-mail:
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