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Xu S, Chen S, Cai J, Yan T, Tu M, Wang R, Hua S, Jiang L. Genomic and transcriptome analyses reveal potential contributors to erucic acid biosynthesis in seeds of rapeseed (Brassica napus). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:129. [PMID: 38740615 DOI: 10.1007/s00122-024-04642-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/29/2024] [Indexed: 05/16/2024]
Abstract
KEY MESSAGE Through comprehensive genomic and transcriptomic analyses, we identified a set of 23 genes that act up- or downstream of erucic acid content (EAC) production in rapeseed seeds. We selected example genes to showcase the distribution of single nucleotide polymorphisms, haplotypes associated with EAC phenotypes, and the creation of molecular markers differentiating low EAC and high EAC genotypes. Erucic acid content (EAC) is a crucial trait in rapeseed, with low LEAC oil recognized for its health benefits and high EA oil holding industrial value. Despite its significance, the genomic consequences of intensive LEAC-cultivar selection and the genetic basis underlying EA regulation remain largely unexplored. To address this knowledge gap, we conducted selective signal analyses, genome-wide association studies (GWAS), and transcriptome analyses. Our investigation unveiled the genetic footprints resulting from LEAC selection in germplasm populations, drawing attention to specific loci that contribute to enriching diversity. By integrating GWAS and transcriptome analyses, we identified a set of 23 genes that play a significant role in determining EAC in seeds or are downstream consequences of EA-level alterations. These genes have emerged as promising candidates for elucidating the potential mechanisms governing EAC in rapeseed. To exemplify the findings, we selected specific genes to demonstrate the distribution of single nucleotide polymorphisms and haplotypes associated with different EAC phenotypes. Additionally, we showcased to develop molecular markers distinguishing between LEAC and high EAC genotypes.
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Affiliation(s)
- Shiqi Xu
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Shan Chen
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Jialing Cai
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Tao Yan
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Mengxin Tu
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Ruisen Wang
- Jaixing Academy of Agricultural Sciences, Jiaxing, 314000, China
| | - Shuijin Hua
- Zhejiang Academy of Agricultural Sciences, Desheng Zhong Road 298, Hangzhou, 310022, China
| | - Lixi Jiang
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China.
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Gong G, Liu L, Wu B, Li J, He M, Hu G. Simultaneous production of algal biomass and lipid by heterotrophic cultivation of linoleic acid-rich oleaginous microalga Chlorella sorokiniana using high acetate dosage. BIORESOURCE TECHNOLOGY 2024; 399:130566. [PMID: 38467262 DOI: 10.1016/j.biortech.2024.130566] [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: 01/08/2024] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/13/2024]
Abstract
The low-cost carbon source, acetate, was utilized to feed a linoleic acid-rich Chlorella sorokiniana for microalgal biomass and lipid accumulation. Remarkably high tolerance capability to high acetate dosage up to 30 g/L was observed, with heterotrophy being the preferred trophic mode for algal growth and lipogenesis when supplemented 20 g/L acetate. Transcriptome analysis revealed a marked activation of pathways involved in acetate bioconversion and lipogenesis upon exposure to high-level of acetate. However, the enhancement of photorespiration inhibited photosynthesis, which ultimately led to a decrease in biomass and lipid under mixotrophy. Heterotrophic acetate-feeding generated more superior amino acid profiling of algal biomass and a predominant linoleic acid content (50 %). Heterotrophic repeat fed-batch strategy in 5 L fermenter significantly increased the growth performance and lipid titer, with the highest levels achieved being 23.4 g/L and 7.0 g/L, respectively. This work provides a viable approach for bio-products production through acetate-based heterotrophic algal cultivation.
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Affiliation(s)
- Guiping Gong
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China.
| | - Linpei Liu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
| | - Bo Wu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
| | - Jianting Li
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
| | - Mingxiong He
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
| | - Guoquan Hu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
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3
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Pan Y, Zhang W, Wang X, Jouhet J, Maréchal E, Liu J, Xia XQ, Hu H. Allele-dependent expression and functionality of lipid enzyme phospholipid:diacylglycerol acyltransferase affect diatom carbon storage and growth. PLANT PHYSIOLOGY 2024; 194:1024-1040. [PMID: 37930282 DOI: 10.1093/plphys/kiad581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/06/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023]
Abstract
In the acyl-CoA-independent pathway of triacylglycerol (TAG) synthesis unique to plants, fungi, and algae, TAG formation is catalyzed by the enzyme phospholipid:diacylglycerol acyltransferase (PDAT). The unique PDAT gene of the model diatom Phaeodactylum tricornutum strain CCMP2561 boasts 47 single nucleotide variants within protein coding regions of the alleles. To deepen our understanding of TAG synthesis, we observed the allele-specific expression of PDAT by the analysis of 87 published RNA-sequencing (RNA-seq) data and experimental validation. The transcription of one of the two PDAT alleles, Allele 2, could be specifically induced by decreasing nitrogen concentrations. Overexpression of Allele 2 in P. tricornutum substantially enhanced the accumulation of TAG by 44% to 74% under nutrient stress; however, overexpression of Allele 1 resulted in little increase of TAG accumulation. Interestingly, a more serious growth inhibition was observed in the PDAT Allele 1 overexpression strains compared with Allele 2 counterparts. Heterologous expression in yeast (Saccharomyces cerevisiae) showed that enzymes encoded by PDAT Allele 2 but not Allele 1 had TAG biosynthetic activity, and 7 N-terminal and 3 C-terminal amino acid variants between the 2 allele-encoded proteins substantially affected enzymatic activity. P. tricornutum PDAT, localized in the innermost chloroplast membrane, used monogalactosyldiacylglycerol and phosphatidylcholine as acyl donors as demonstrated by the increase of the 2 lipids in PDAT knockout lines, which indicated a common origin in evolution with green algal PDATs. Our study reveals unequal roles among allele-encoded PDATs in mediating carbon storage and growth in response to nitrogen stress and suggests an unsuspected strategy toward lipid and biomass improvement for biotechnological purposes.
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Affiliation(s)
- Yufang Pan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wanting Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaofei Wang
- Laboratory for Algae Biotechnology and Innovation, College of Engineering, Peking University, Beijing 100871, China
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire Végétale, Université Grenoble Alpes, CEA, CNRS, INRA, IRIG-LPCV, Grenoble Cedex 9 38054, France
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire Végétale, Université Grenoble Alpes, CEA, CNRS, INRA, IRIG-LPCV, Grenoble Cedex 9 38054, France
| | - Jin Liu
- Laboratory for Algae Biotechnology and Innovation, College of Engineering, Peking University, Beijing 100871, China
| | - Xiao-Qin Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanhua Hu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Huang T, Pan Y, Maréchal E, Hu H. Proteomes reveal the lipid metabolic network in the complex plastid of Phaeodactylum tricornutum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:385-403. [PMID: 37733835 DOI: 10.1111/tpj.16477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 09/05/2023] [Accepted: 09/12/2023] [Indexed: 09/23/2023]
Abstract
Phaeodactylum tricornutum plastid is surrounded by four membranes, and its protein composition and function remain mysterious. In this study, the P. tricornutum plastid-enriched fraction was obtained and 2850 proteins were identified, including 92 plastid-encoded proteins, through label-free quantitative proteomic technology. Among them, 839 nuclear-encoded proteins were further determined to be plastidial proteins based on the BLAST alignments within Plant Proteome DataBase and subcellular localization prediction, in spite of the strong contamination by mitochondria-encoded proteins and putative plasma membrane proteins. According to our proteomic data, we reconstructed the metabolic pathways and highlighted the hybrid nature of this diatom plastid. Triacylglycerol (TAG) hydrolysis and glycolysis, as well as photosynthesis, glycan metabolism, and tocopherol and triterpene biosynthesis, occur in the plastid. In addition, the synthesis of long-chain acyl-CoAs, elongation, and desaturation of fatty acids (FAs), and synthesis of lipids including TAG are confined in the four-layered-membrane plastid based on the proteomic and GFP-fusion localization data. The whole process of generation of docosahexaenoic acid (22:6) from palmitic acid (16:0), via elongation and desaturation of FAs, occurs in the chloroplast endoplasmic reticulum membrane, the outermost membrane of the plastid. Desaturation that generates 16:4 from 16:0 occurs in the plastid stroma and outer envelope membrane. Quantitative analysis of glycerolipids between whole cells and isolated plastids shows similar composition, and the FA profile of TAG was not different. This study shows that the diatom plastid combines functions usually separated in photosynthetic eukaryotes, and differs from green alga and plant chloroplasts by undertaking the whole process of lipid biosynthesis.
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Affiliation(s)
- Teng Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yufang Pan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire Végétale, Université Grenoble Alpes, CEA, CNRS, INRA, IRIG-LPCV, 38054, Grenoble Cedex 9, France
| | - Hanhua Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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5
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Li X, Dong Y, Chen K, Perumal AB, Zhan Z, Gouda M, He Y. 13C-metabolic flux analysis of lipid accumulation in the green microalgae Tetradesmus obliquus under nitrogen deficiency stress. BIORESOURCE TECHNOLOGY 2023; 388:129740. [PMID: 37717702 DOI: 10.1016/j.biortech.2023.129740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/23/2023] [Accepted: 09/06/2023] [Indexed: 09/19/2023]
Abstract
Metabolic fluxes (MF) serve as the functional phenotypes of biochemical processes and are crucial to describe the distribution of precursors within metabolic networks. There is a lack of experimental observations for carbon flux towards lipids, which is important for biodiesel generation. Here, the accumulation of lipid, and MF in Tetradesmus obliquus under nitrogen deficiency stress (NF) using a 13C isotope tracer at different time intervals was investigated. The 13C based MF showed enhanced de novo synthesis of G3P and PEP, indicating increased carbon flux from CO2 into lipid synthesis. An increase in palmitic acid (3500 μmol/mg), linoleic acid (2100 μmol/mg), and oleic acid (2000 μmol/mg) was observed. The accumulation of C16:0 under NF was mainly related to de novo synthesis while C18:3 was accumulated through a non de novo pathway. Under NF stress, T. obliquus had higher flux in PPP and glycolysis pathway, together, it might provide more NADPH and substrate acetyl-CoA for fatty acid synthesis.
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Affiliation(s)
- Xiaoli Li
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Yulun Dong
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Kai Chen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Anand Babu Perumal
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.
| | - Zhihao Zhan
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Mostafa Gouda
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China; Department of Nutrition & Food Science, National Research Centre, Dokki, Giza 12622, Egypt
| | - Yong He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
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6
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Yang H, Zhang J, Li H. Strategies of NaCl Tolerance in Saline-Alkali-Tolerant Green Microalga Monoraphidium dybowskii LB50. PLANTS (BASEL, SWITZERLAND) 2023; 12:3495. [PMID: 37836235 PMCID: PMC10575140 DOI: 10.3390/plants12193495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/25/2023] [Accepted: 09/30/2023] [Indexed: 10/15/2023]
Abstract
Studying how freshwater cells modify metabolism and membrane lipids in response to salt stress is important for understanding how freshwater organisms adapt to salt stress and investigating new osmoregulatory ways. Physiological, biochemical, metabolic, and proteomic analyses were applied in a novel saline-alkali-tolerant microalga Monoraphidium dybowskii LB50 under different NaCl concentrations. Cells adopt a variety of strategies to adapt to salt stress, including increasing ion transport and osmolytes, regulating cell cycle and life history, and accumulating triacylglycerol (TAG). A large number of metabolic activities point to TAG accumulation. With increasing NaCl concentration, the C resource for TAG accumulation went from photosynthetically fixed C and a small amount of lipid remodeling to macromolecule degradation and a mass of lipid remodeling, respectively. The energy for TAG accumulation went from linear electron transfer and oxidative phosphate pentose pathway to cyclic electron flow, substrate phosphorylation, oxidation phosphorylation, and FA oxidation. Additionally, digalacturonic acid and amino acids of the N-acetyl group, which usually were the osmotica for marine organisms, were important for M. dybowskii LB50. Freshwater organisms evolved many biological ways to adapt to salt stress. This insight enriches our understanding of the adaptation mechanisms underlying abiotic stress.
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Affiliation(s)
- Haijian Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China;
| | - Jing Zhang
- Analysis and Testing Center of Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Hua Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China;
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7
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Song J, Zhao H, Zhang L, Li Z, Han J, Zhou C, Xu J, Li X, Yan X. The Heat Shock Transcription Factor PtHSF1 Mediates Triacylglycerol and Fucoxanthin Synthesis by Regulating the Expression of GPAT3 and DXS in Phaeodactylum tricornutum. PLANT & CELL PHYSIOLOGY 2023; 64:622-636. [PMID: 36947404 DOI: 10.1093/pcp/pcad023] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 01/31/2023] [Accepted: 03/21/2023] [Indexed: 06/16/2023]
Abstract
In addition to being important primary productive forces in marine ecosystems, diatoms are also rich in bioactive substances such as triacylglycerol and fucoxanthin. However, little is known about the transcriptional mechanisms underlying the biosynthesis of these substances. In this study, we found that the heat shock transcription factor PtHSF1 positively regulated the synthesis of triacylglycerol and fucoxanthin in Phaeodactylum tricornutum. Overexpression of PtHSF1 could increase the contents of triacylglycerol and fucoxanthin and upregulate key enzyme genes involved in the triacylglycerol and fucoxanthin biosynthesis pathways. On the other hand, gene silencing of PtHSF1 reduced the contents of triacylglycerol and fucoxanthin and the expression of the key enzyme genes involved in the triacylglycerol and fucoxanthin biosynthesis pathways. Further biochemical analysis revealed that PtHSF1 upregulated glycerol-2-phosphate acyltransferase 3 (GPAT3) and 1-deoxy-d-xylulose 5-phosphate synthase (DXS) by directly binding to their promoters, while genetic analysis demonstrated that PtHSF1 acted upstream of GPAT3 and DXS to regulate triacylglycerol and fucoxanthin synthesis. Therefore, in addition to elucidating the regulation mechanisms underlying PtHSF1-mediated triacylglycerol and fucoxanthin synthesis, this study also provided a candidate target for metabolic engineering of triacylglycerol and fucoxanthin in P. tricornutum.
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Affiliation(s)
- Jianquan Song
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Hejing Zhao
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315211, China
| | - Linxin Zhang
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315211, China
| | - Zheng Li
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jichang Han
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315211, China
| | - Chengxu Zhou
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315211, China
| | - Jilin Xu
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Xiaohui Li
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315211, China
| | - Xiaojun Yan
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
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Huang W, Krishnan A, Plett A, Meagher M, Linka N, Wang Y, Ren B, Findinier J, Redekop P, Fakhimi N, Kim RG, Karns DA, Boyle N, Posewitz MC, Grossman AR. Chlamydomonas mutants lacking chloroplast TRIOSE PHOSPHATE TRANSPORTER3 are metabolically compromised and light-sensitive. THE PLANT CELL 2023:koad095. [PMID: 36970811 DOI: 10.1093/plcell/koad095] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/08/2023] [Accepted: 03/23/2023] [Indexed: 06/18/2023]
Abstract
Modulation of photoassimilate export from the chloroplast is essential for controlling the distribution of fixed carbon in the cell and maintaining optimum photosynthetic rates. In this study we identified chloroplast TRIOSE PHOSPHATE/PHOSPHATE TRANSLOCATOR2 (CreTPT2) and CreTPT3 in the green alga Chlamydomonas (Chlamydomonas reinhardtii), which exhibit similar substrate specificities but whose encoding genes are differentially expressed over the diurnal cycle. We focused mostly on CreTPT3 because of its high level of expression and the severe phenotype exhibited by tpt3 relative to tpt2 mutants. Null mutants for CreTPT3 had a pleiotropic phenotype that affected growth, photosynthetic activities, metabolite profiles, carbon partitioning, and organelle-specific accumulation of H2O2. These analyses demonstrated that CreTPT3 is a dominant conduit on the chloroplast envelope for the transport of photoassimilates. In addition, CreTPT3 can serve as a safety valve that moves excess reductant out of the chloroplast and appears to be essential for preventing cells from experiencing oxidative stress and accumulating reactive oxygen species, even under low/moderate light intensities. Finally, our studies indicate subfunctionalization of the CreTPT transporters and suggest that there are differences in managing the export of photoassimilates from the chloroplasts of Chlamydomonas and vascular plants.
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Affiliation(s)
- Weichao Huang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Anagha Krishnan
- Department of Chemistry, Colorado School of Mines, Golden, CO 80401, USA
| | - Anastasija Plett
- Institute of Plant Biochemistry, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Michelle Meagher
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO 80401, USA
| | - Nicole Linka
- Institute of Plant Biochemistry, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Yongsheng Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
- School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Bijie Ren
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Justin Findinier
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Petra Redekop
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Neda Fakhimi
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Rick G Kim
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Devin A Karns
- Department of Chemistry, Colorado School of Mines, Golden, CO 80401, USA
| | - Nanette Boyle
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO 80401, USA
| | - Matthew C Posewitz
- Department of Chemistry, Colorado School of Mines, Golden, CO 80401, USA
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
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9
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NmrA acts as a positive regulator of nitrate assimilation in Phaeodactylum tricornutum. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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10
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Yang J, Liu J, Pan Y, Maréchal E, Amato A, Liu M, Gong Y, Li Y, Hu H. PDAT regulates PE as transient carbon sink alternative to triacylglycerol in Nannochloropsis. PLANT PHYSIOLOGY 2022; 189:1345-1362. [PMID: 35385114 PMCID: PMC9237688 DOI: 10.1093/plphys/kiac160] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/14/2022] [Indexed: 05/21/2023]
Abstract
Triacylglycerols (TAGs) are the main storage lipids in photosynthetic organisms under stress. In the oleaginous alga Nannochloropsis oceanica, while multiple acyl CoA:diacylglycerol (DAG) acyltransferases (NoDGATs) are involved in TAG production, the role of the unique phospholipid:DAG acyltransferase (NoPDAT) remains unknown. Here, we performed a functional complementation assay in TAG-deficient yeast (Saccharomyces cerevisiae) and an in vitro assay to probe the acyltransferase activity of NoPDAT. Subcellular localization, overexpression, and knockdown (KD) experiments were also conducted to elucidate the role of NoPDAT in N. oceanica. NoPDAT, residing at the outermost plastid membrane, does not phylogenetically fall into the clades of algae or plants and uses phosphatidylethanolamine (PE) and phosphatidylglycerol with 16:0, 16:1, and 18:1 at position sn-2 as acyl-donors in vivo. NoPDAT KD, not triggering any compensatory mechanism via DGATs, led to an ∼30% decrease of TAG content, accompanied by a vast accumulation of PEs rich in 16:0, 16:1, and 18:1 fatty acids (referred to as "LU-PE") that was positively associated with CO2 availability. We conclude that the NoPDAT pathway is parallel to and independent of the NoDGAT pathway for oil production. LU-PE can serve as an alternative carbon sink for photosynthetically assimilated carbon in N. oceanica when PDAT-mediated TAG biosynthesis is compromised or under stress in the presence of high CO2 levels.
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Affiliation(s)
| | | | - Yufang Pan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire Végétale, Université Grenoble Alpes, CEA, CNRS, INRA, IRIG‐LPCV, 38054 Grenoble Cedex 9, France
| | - Alberto Amato
- Laboratoire de Physiologie Cellulaire Végétale, Université Grenoble Alpes, CEA, CNRS, INRA, IRIG‐LPCV, 38054 Grenoble Cedex 9, France
| | - Meijing Liu
- Laboratory for Algae Biotechnology and Innovation, College of Engineering, Peking University, Beijing 100871, China
| | - Yangmin Gong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Yantao Li
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science and University of Maryland Baltimore County, Baltimore, Maryland 21202, USA
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11
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Cai Y, Chen H, Tang X, Zhao J, Zhang H, Chen YQ, Chen W. The relationship between amino acid and lipid metabolism in oleaginous eukaryotic microorganism. Appl Microbiol Biotechnol 2022; 106:3405-3417. [PMID: 35503470 DOI: 10.1007/s00253-022-11931-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/30/2022]
Abstract
Amino acids are the building blocks of protein, promoting the balance between growth and lipid synthesis. However, the accumulation of microbial lipids involves multiple pathways, which requires the analysis of the global cellular metabolic network in which amino acid metabolism is involved. This review illustrates the dependence patterns of intracellular amino acids and lipids of oleaginous eukaryotic microorganisms in different environments and points out the contribution of amino acid metabolic precursors to the de novo synthesis of fatty acids. We emphasized the key role of amino acid metabolism in lipid remodeling and autophagy behavior and highlighted the regulatory effects of amino acids and their secondary metabolites as signal factors for microbial lipid synthesis. The application prospects of omics technology and genetic engineering technology in the field of microbial lipids are described. KEY POINTS: • Overview of microbial lipid synthesis mediated by amino acid metabolism • Insight into metabolic mechanisms founding multiple regulatory networks is provided • Description of microbial lipid homeostasis mediated by amino acid excitation signal.
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Affiliation(s)
- Yibo Cai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China. .,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China. .,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, People's Republic of China.
| | - Xin Tang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, People's Republic of China.,Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, 214122, People's Republic of China
| | - Yong Q Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, People's Republic of China.,Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 5: , 27127, USA
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, People's Republic of China
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12
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Scarsini M, Thiriet-Rupert S, Veidl B, Mondeguer F, Hu H, Marchand J, Schoefs B. The Transition Toward Nitrogen Deprivation in Diatoms Requires Chloroplast Stand-By and Deep Metabolic Reshuffling. FRONTIERS IN PLANT SCIENCE 2022; 12:760516. [PMID: 35126407 PMCID: PMC8811913 DOI: 10.3389/fpls.2021.760516] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/19/2021] [Indexed: 06/14/2023]
Abstract
Microalgae have adapted to face abiotic stresses by accumulating energy storage molecules such as lipids, which are also of interest to industries. Unfortunately, the impairment in cell division during the accumulation of these molecules constitutes a major bottleneck for the development of efficient microalgae-based biotechnology processes. To address the bottleneck, a multidisciplinary approach was used to study the mechanisms involved in the transition from nitrogen repletion to nitrogen starvation conditions in the marine diatom Phaeodactylum tricornutum that was cultured in a turbidostat. Combining data demonstrate that the different steps of nitrogen deficiency clustered together in a single state in which cells are in equilibrium with their environment. The switch between the nitrogen-replete and the nitrogen-deficient equilibrium is driven by intracellular nitrogen availability. The switch induces a major gene expression change, which is reflected in the reorientation of the carbon metabolism toward an energy storage mode while still operating as a metabolic flywheel. Although the photosynthetic activity is reduced, the chloroplast is kept in a stand-by mode allowing a fast resuming upon nitrogen repletion. Altogether, these results contribute to the understanding of the intricate response of diatoms under stress.
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Affiliation(s)
- Matteo Scarsini
- Metabolism, Bio-Engineering of Microalgal Molecules and Applications (MIMMA), Mer Molécules Santé, IUML—FR 3473 CNRS, Le Mans University, Le Mans, France
| | - Stanislas Thiriet-Rupert
- Metabolism, Bio-Engineering of Microalgal Molecules and Applications (MIMMA), Mer Molécules Santé, IUML—FR 3473 CNRS, Le Mans University, Le Mans, France
- Institut Pasteur, Genetics of Biofilms Laboratory, Paris, France
| | - Brigitte Veidl
- Metabolism, Bio-Engineering of Microalgal Molecules and Applications (MIMMA), Mer Molécules Santé, IUML—FR 3473 CNRS, Le Mans University, Le Mans, France
| | - Florence Mondeguer
- Phycotoxins Laboratory, Institut Français de Recherche pour l'Exploitation de la Mer, Nantes, France
| | - Hanhua Hu
- Key Laboratory of Algal Biology, Chinese Academy of Sciences, Wuhan, China
| | - Justine Marchand
- Metabolism, Bio-Engineering of Microalgal Molecules and Applications (MIMMA), Mer Molécules Santé, IUML—FR 3473 CNRS, Le Mans University, Le Mans, France
| | - Benoît Schoefs
- Metabolism, Bio-Engineering of Microalgal Molecules and Applications (MIMMA), Mer Molécules Santé, IUML—FR 3473 CNRS, Le Mans University, Le Mans, France
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13
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Kato Y, Inabe K, Hidese R, Kondo A, Hasunuma T. Metabolomics-based engineering for biofuel and bio-based chemical production in microalgae and cyanobacteria: A review. BIORESOURCE TECHNOLOGY 2022; 344:126196. [PMID: 34710610 DOI: 10.1016/j.biortech.2021.126196] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Metabolomics, an essential tool in modern synthetic biology based on the design-build-test-learn platform, is useful for obtaining a detailed understanding of cellular metabolic mechanisms through comprehensive analyses of the metabolite pool size and its dynamic changes. Metabolomics is critical to the design of a rational metabolic engineering strategy by determining the rate-limiting reaction and assimilated carbon distribution in a biosynthetic pathway of interest. Microalgae and cyanobacteria are promising photosynthetic producers of biofuels and bio-based chemicals, with high potential for developing a bioeconomic society through bio-based carbon neutral manufacturing. Metabolomics technologies optimized for photosynthetic organisms have been developed and utilized in various microalgal and cyanobacterial species. This review provides a concise overview of recent achievements in photosynthetic metabolomics, emphasizing the importance of microalgal and cyanobacterial cell factories that satisfy industrial requirements.
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Affiliation(s)
- Yuichi Kato
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Kosuke Inabe
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Ryota Hidese
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Tomohisa Hasunuma
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.
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14
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Machado M, Vaz MGMV, Bromke MA, Rosa RM, Covell L, Souza LPD, Rocha DI, Martins MA, Araújo WL, Szymański J, Nunes-Nesi A. Metabolic stability of freshwater Nitzschia palea strains under silicon stress associated with triacylglycerol accumulation. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Fattore N, Bellan A, Pedroletti L, Vitulo N, Morosinotto T. Acclimation of photosynthesis and lipids biosynthesis to prolonged nitrogen and phosphorus limitation in Nannochloropsis gaditana. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102368] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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High-efficiency transformation of a centric diatom Chaetoceros muelleri by electroporation with a variety of selectable markers. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Zhang M, Xing Y, Wang F, Mi T, Zhen Y. Responses of triacylglycerol synthesis in Skeletonema marinoi to nitrogen and phosphate starvations. JOURNAL OF PHYCOLOGY 2020; 56:1505-1520. [PMID: 32602937 DOI: 10.1111/jpy.13044] [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: 02/12/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
Skeletonema marinoi is one of the most widespread marine planktonic diatoms in temperate coastal regions and sometimes can form massive blooms. Yet, the molecular mechanisms of triacylglycerol (TAG) synthesis in nutrient-deficient conditions for this species are still unknown. This study aimed to investigate how the TAG biosynthetic pathway of S. marinoi reacts to the culture age and nitrogen (N) or phosphorus (P) deficiency at molecular levels. Meanwhile, we also described the physiological and biochemical changes of S. marinoi in response to N or P starvation over time. To obtain reliable qRT-PCR data, six putative reference genes were identified for assessing expression stability using geNorm and BestKeeper software, and Actin exhibited the most stable expression across 45 tested S. marinoi samples. We found that the expression of TAG biosynthesis-related genes and ACCase enzyme activity varied in response to the different nutrient conditions and culture age. Taken together, we speculated that the capacity of TAG biosynthesis in S. marinoi is induced by N or P stress, and increases with culture age. Furthermore, TAG biosynthesis appears to respond more strongly to P deficiency than to N deficiency. Our study provides important insights into how diatoms regulate the TAG biosynthetic pathway when stressed by nutrient limitation. Besides, the data obtained from this study also provide useful clues for further exploring genes that can be used for metabolic engineering to enhance lipid production.
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Affiliation(s)
- Mei Zhang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, 266100, China
| | - Yongze Xing
- Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, 536002, China
| | - Fuwen Wang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, 266100, China
| | - Tiezhu Mi
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, 266100, China
| | - Yu Zhen
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, 266100, China
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18
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Sulochana SB, Arumugam M. Targeted Metabolomic and Biochemical Changes During Nitrogen Stress Mediated Lipid Accumulation in Scenedesmus quadricauda CASA CC202. Front Bioeng Biotechnol 2020; 8:585632. [PMID: 33195150 PMCID: PMC7604524 DOI: 10.3389/fbioe.2020.585632] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/28/2020] [Indexed: 01/08/2023] Open
Abstract
Scenedesmus quadricauda CASA CC202, a potent freshwater microalga is being used as a biofuel feedstock, which accumulates 2.27 fold lipid during nitrogen stress induction. Upon nitrogen starvation, S. quadricauda undergoes biochemical and metabolic changes that perturb the cell to cope up the stress condition. The nitrogen stress-induced biochemical changes in mitochondrion exhibits due to the oxidative stress-induced Reactive Oxygen species (ROS) generation at high membrane potential (Δψm). The predominant ROS generated during nitrogen starvation was H2O2, OH–, O2⋅− and to suppress them, scavenging enzymes such as peroxidase and catalase increased to about 23.16 and 0.79 U/ml as compared to control (20.2, 0.19 U/ml). The targeted metabolic analysis showed, stress-related non-proteinogenic amino acids and energy equivalents elevated during the initial hours of nitrogen starvation. The nitrogen stress-triggered biochemical and metabolic changes along with other cellular events eventually lead to lipid accumulation in S. quadricauda.
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Affiliation(s)
- Sujitha Balakrishnan Sulochana
- Microbial Processes and Technology Division, Council of Scientific and Industrial Research - National Institute for Interdisciplinary Science and Technology, Trivandrum, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Muthu Arumugam
- Microbial Processes and Technology Division, Council of Scientific and Industrial Research - National Institute for Interdisciplinary Science and Technology, Trivandrum, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
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19
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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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20
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Yang H, Hu C. Regulation and remodeling of intermediate metabolite and membrane lipid during NaCl-induced stress in freshwater microalga Micractinium sp. XJ-2 for biofuel production. Biotechnol Bioeng 2020; 117:3727-3738. [PMID: 32749671 DOI: 10.1002/bit.27528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/25/2020] [Accepted: 08/03/2020] [Indexed: 01/23/2023]
Abstract
Microalgae can accumulate a large fraction of reduced carbon as lipids under NaCl stress. This study investigated the mechanism of carbon allocation and reduction and triacylglycerol (TAG) accumulation in microalgae under NaCl-induced stress. Micractinium sp. XJ-2 was exposed to NaCl stress and cells were subjected to physiological, biochemical, and metabolic analyses to elucidate the stress-responsive mechanism. Lipid increased with NaCl concentration after 0-12 hr, then stabilized after 12-48 hr, and finally decreased after 48-72 hr, whereas TAG increased (0-48 hr) and then decreased (48-72 hr). Under NaCl-induced stress at lower concentrations, TAG accumulation, at first, mainly shown to rely on the carbon fixation through photosynthetic fixation, carbohydrate degradation, and membrane lipids remodeling. Moreover, carbon compounds generated by the degradation of some amino acids were reallocated and enhanced fatty acid synthesis. The remodeling of the membrane lipids of NaCl-induced microalgae relied on the following processes: (a) Increase in the amount of phospholipids and reduction in the amount of glycolipids and (b) extension of long-chain fatty acids. This study enhances our understanding of TAG production under NaCl stress and thus will provide a theoretical basis for the industrial application of NaCl-induced in the microalgal biodiesel industry.
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Affiliation(s)
- Haijian Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chunxiang Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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21
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Huang B, Mimouni V, Lukomska E, Morant-Manceau A, Bougaran G. Carbon Partitioning and Lipid Remodeling During Phosphorus and Nitrogen Starvation in the Marine Microalga Diacronema lutheri (Haptophyta). JOURNAL OF PHYCOLOGY 2020; 56:908-922. [PMID: 32215912 DOI: 10.1111/jpy.12995] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 03/03/2020] [Indexed: 06/10/2023]
Abstract
The domesticated marine microalga Diacronema lutheri is of great interest for producing various highly valuable molecules like lipids, particularly long-chain polyunsaturated fatty acids (LC-PUFA). In this study, we investigated the impact of phosphorus (P) and nitrogen (N) starvation on growth, carbon fixation (photosynthetic activity) and partitioning, and membrane lipid remodeling in this alga during batch culture. Our results show that the photosynthetic machinery was similarly affected by P and N stress. Under N starvation, we observed a much lower photosynthetic rate and biomass productivity. The degradation and re-use of cellular N-containing compounds contributed to triacylglycerol (TAG) accumulation. On the other hand, P-starved cells maintained pigment content and a carbon partitioning pattern more similar to the control, ensuring a high biomass. Betaine lipids constitute the major compounds of non-plastidial membranes, which are rich in eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids. Under P and N starvations, EPA was transferred from the recycling of membrane polar lipids, most likely contributing to TAG accumulation.
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Affiliation(s)
- Bing Huang
- Laboratoire Mer, Molécules, Santé (IUML - FR 3473 CNRS), UFR Sciences et Techniques, Le Man Université, Avenue Olivier Messiaen, 72085, Le Mans Cedex 09, France
| | - Virginie Mimouni
- Laboratoire Mer, Molécules, Santé (IUML - FR 3473 CNRS), IUT de Laval, Département Génie Biologique, Le Mans Université, 52 rue des Docteurs Calmette et Guérin, 53020, Laval Cedex 9, France
| | - Ewa Lukomska
- Laboratoire Physiologie et Biotechnologie des Algues, IFREMER, rue de l'Ile d'Yeu, BP 21105, 44311, Nantes Cedex 03, France
| | - Annick Morant-Manceau
- Laboratoire Mer, Molécules, Santé (IUML - FR 3473 CNRS), UFR Sciences et Techniques, Le Man Université, Avenue Olivier Messiaen, 72085, Le Mans Cedex 09, France
| | - Gaël Bougaran
- Laboratoire Physiologie et Biotechnologie des Algues, IFREMER, rue de l'Ile d'Yeu, BP 21105, 44311, Nantes Cedex 03, France
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22
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Shi TQ, Wang LR, Zhang ZX, Sun XM, Huang H. Stresses as First-Line Tools for Enhancing Lipid and Carotenoid Production in Microalgae. Front Bioeng Biotechnol 2020; 8:610. [PMID: 32850686 PMCID: PMC7396513 DOI: 10.3389/fbioe.2020.00610] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 05/18/2020] [Indexed: 12/30/2022] Open
Abstract
Microalgae can produce high-value-added products such as lipids and carotenoids using light or sugars, and their biosynthesis mechanism can be triggered by various stress conditions. Under nutrient deprivation or environmental stresses, microalgal cells accumulate lipids as an energy-rich carbon storage battery and generate additional amounts of carotenoids to alleviate the oxidative damage induced by stress conditions. Though stressful conditions are unfavorable for biomass accumulation and can induce oxidative damage, stress-based strategies are widely used in this field due to their effectiveness and economy. For the overproduction of different target products, it is required and meaningful to deeply understand the effects and mechanisms of various stress conditions so as to provide guidance on choosing the appropriate stress conditions. Moreover, the underlying molecular mechanisms under stress conditions can be clarified by omics technologies, which exhibit enormous potential in guiding rational genetic engineering for improving lipid and carotenoid biosynthesis.
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Affiliation(s)
- Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Ling-Ru Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Zi-Xu Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
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23
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Butler T, Kapoore RV, Vaidyanathan S. Phaeodactylum tricornutum: A Diatom Cell Factory. Trends Biotechnol 2020; 38:606-622. [PMID: 31980300 DOI: 10.1016/j.tibtech.2019.12.023] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 01/12/2023]
Abstract
A switch from a petroleum-based to a biobased economy requires the capacity to produce both high-value low-volume and low-value high-volume products. Recent evidence supports the development of microalgae-based microbial cell factories with the objective of establishing environmentally sustainable manufacturing solutions. Diatoms display rich diversity and potential in this regard. We focus on Phaeodactylum tricornutum, a pennate diatom that is commonly found in marine ecosystems, and discuss recent trends in developing the diatom chassis for the production of a suite of natural and genetically engineered products. Both upstream and downstream developments are reviewed for the commercial development of P. tricornutum as a cell factory for a spectrum of marketable products.
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Affiliation(s)
- Thomas Butler
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, S1 3JD, UK
| | - Rahul Vijay Kapoore
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, S1 3JD, UK; Present address: Department of Biosciences, College of Science, Swansea University, Swansea, SA2 8PP, UK
| | - Seetharaman Vaidyanathan
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, S1 3JD, UK.
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24
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Lu H, Chen H, Tang X, Yang Q, Zhang H, Chen YQ, Chen W. Time-resolved multi-omics analysis reveals the role of nutrient stress-induced resource reallocation for TAG accumulation in oleaginous fungus Mortierella alpina. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:116. [PMID: 32625246 PMCID: PMC7328260 DOI: 10.1186/s13068-020-01757-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 06/23/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Global resource reallocation is an established critical strategy through which organisms deal with environmental stress. The regulation of intracellular lipid storage or utilization is one of the most important strategies for maintaining energy homeostasis and optimizing growth. Oleaginous microorganisms respond to nitrogen deprivation by inducing lipid hyper accumulation; however, the associations between resource allocation and lipid accumulation are poorly understood. RESULTS Here, the time-resolved metabolomics, lipidomics, and proteomics data were generated in response to nutrient availability to examine how metabolic alternations induced by nitrogen deprivation drive the triacylglycerols (TAG) accumulation in M. alpina. The subsequent accumulation of TAG under nitrogen deprivation was a consequence of the reallocation of carbon, nitrogen sources, and lipids, rather than an up-regulation of TAG biosynthesis genes. On one hand, nitrogen deprivation induced the down-regulation of isocitrate dehydrogenase level in TCA cycle and redirected glycolytic flux of carbon from amino acid biosynthesis into fatty acids' synthesis; on the other hand, nitrogen deprivation induced the up-regulation of cell autophagy and ubiquitin-mediated protein proteolysis which resulted in a recycling of preformed protein nitrogen and carbon. Combining with the up-regulation of glutamate decarboxylase and succinic semialdehyde dehydrogenase in GABA shunt, and the phosphoenolpyruvate carboxykinase in the central hub involving pyruvate/phosphoenolpyruvate/oxaloacetate, the products from nitrogen-containing compounds degradation were recycled to be intermediates of TCA cycle and be shunted toward de novo biosynthesis of fatty acids. We found that nitrogen deprivation increased the protein level of phospholipase C/D that contributes to degradation of phosphatidylcholine and phosphatidylethanolamine, and supplied acyl chains for TAG biosynthesis pathway. In addition, ATP from substrate phosphorylation was presumed to be a critical factor regulation of the global resource allocation and fatty acids' synthesis rate. CONCLUSIONS The present findings offer a panoramic view of resource allocation by M. alpina in response to nutrient stress and revealed a set of intriguing associations between resource reallocation and TAG accumulation. This system-level insight provides a rich resource with which to explore in-depth functional characterization and gain information about the strategic combination of strain development and process integration to achieve optimal lipid productivity under nutrient stress.
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Affiliation(s)
- Hengqian Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Ave, Wuxi, 214122 Jiangsu People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Ave, Wuxi, 214122 Jiangsu People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122 Jiangsu China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, 225004 China
| | - Xin Tang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Ave, Wuxi, 214122 Jiangsu People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Qin Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Ave, Wuxi, 214122 Jiangsu People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Ave, Wuxi, 214122 Jiangsu People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, 225004 China
| | - Yong Q. Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Ave, Wuxi, 214122 Jiangsu People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122 Jiangsu China
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC USA
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Ave, Wuxi, 214122 Jiangsu People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122 Jiangsu China
- Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048 China
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Pan Y, Hu F, Yu C, Li C, Huang T, Hu H. Amino Acid Catabolism During Nitrogen Limitation in Phaeodactylum tricornutum. FRONTIERS IN PLANT SCIENCE 2020; 11:589026. [PMID: 33408729 PMCID: PMC7780933 DOI: 10.3389/fpls.2020.589026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/23/2020] [Indexed: 05/08/2023]
Abstract
Diatoms can accumulate high levels of triacylglycerols (TAGs) under nitrogen depletion and have attracted increasing attention as a potential system for biofuel production. In Phaeodactylum tricornutum, a model diatom, about 40% of lipid is synthesized from the breakdown of cellular components under nitrogen starvation. Our previous studies indicated that carbon skeletons from enhanced branched-chain amino acid (BCAA) degradation under nitrogen deficiency contribute to TAG biosynthesis in P. tricornutum. In this review, we outlined the catabolic pathways of all 20 amino acids based on the genome, transcriptome, proteome, and metabolome data. The contribution of these amino acid catabolic pathways to TAG accumulation was also analyzed.
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Affiliation(s)
- Yufang Pan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Fan Hu
- School of Foreign Languages, China University of Geosciences, Wuhan, China
| | - Chen Yu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chenjie Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Teng Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hanhua Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- *Correspondence: Hanhua Hu,
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He Y, Li R, Lin F, Xiong Y, Wang L, Wang B, Guo J, Hu C. Transcriptome Changes Induced by Different Potassium Levels in Banana Roots. PLANTS (BASEL, SWITZERLAND) 2019; 9:E11. [PMID: 31861661 PMCID: PMC7020221 DOI: 10.3390/plants9010011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/14/2019] [Accepted: 12/16/2019] [Indexed: 12/14/2022]
Abstract
Potassium plays an important role in enhancing plant resistance to biological and abiotic stresses and improving fruit quality. To study the effect of potassium nutrient levels on banana root growth and its regulation mechanism, four potassium concentrations were designed to treat banana roots from no potassium to high potassium. The results indicated that K2 (3 mmol/L K2SO4) treatment was a relatively normal potassium concentration for the growth of banana root, and too high or too low potassium concentration was not conducive to the growth of banana root. By comparing the transcriptome data in each treatment in pairs, 4454 differentially expressed genes were obtained. There were obvious differences in gene function enrichment in root systems treated with different concentrations of potassium. Six significant expression profiles (profile 0, 1, 2, 7, 9 and 13) were identified by STEM analysis. The hub genes were FKF1, HsP70-1, NRT1/PTR5, CRY1, and ZIP11 in the profile 0; CYP51 in profile 1; SOS1 in profile 7; THA, LKR/SDH, MCC, C4H, CHI, F3'H, 2 PR1s, BSP, TLP, ICS, RO, chitinase and peroxidase in profile 9. Our results provide a comprehensive and systematic analysis of the gene regulation network in banana roots under different potassium stress.
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Affiliation(s)
- Yingdui He
- College of Resource and Environment, Huazhong Agricultural University, Wuhan 430070, China;
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (F.L.); (Y.X.); (L.W.); (B.W.)
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Ruimei Li
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
| | - Fei Lin
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (F.L.); (Y.X.); (L.W.); (B.W.)
| | - Ying Xiong
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (F.L.); (Y.X.); (L.W.); (B.W.)
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Lixia Wang
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (F.L.); (Y.X.); (L.W.); (B.W.)
| | - Bizun Wang
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (F.L.); (Y.X.); (L.W.); (B.W.)
| | - Jianchun Guo
- College of Resource and Environment, Huazhong Agricultural University, Wuhan 430070, China;
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Chengxiao Hu
- College of Resource and Environment, Huazhong Agricultural University, Wuhan 430070, China;
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Ran W, Wang H, Liu Y, Qi M, Xiang Q, Yao C, Zhang Y, Lan X. Storage of starch and lipids in microalgae: Biosynthesis and manipulation by nutrients. BIORESOURCE TECHNOLOGY 2019; 291:121894. [PMID: 31387839 DOI: 10.1016/j.biortech.2019.121894] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 05/28/2023]
Abstract
Microalgae accumulate starch and lipid as storage metabolites under nutrient depletion, which can be used as sustainable feedstock for biorefinery. Omics analysis coupled with enzymatic and genetic verifications uncovered a partial picture of pathways and important enzymes or regulators related to starch and lipid biosynthesis as well as the carbon partitioning between them under nutrient depletion conditions. Depletion of macronutrients (N, P, and S) resulted in considerable enhancement of starch and/or lipid content in microalgae, but the accompanying declined photosynthesis hampered the achievements of high concentrations. This review summarized the current knowledge on the pathways and the committed steps as well as their carbon allocation involved in starch and lipid biosynthesis, and focused on the manipulation of different nutrients and the alleviation of oxidative stress for enhanced storage metabolites production. The biological and engineering approaches to cope with the conflict between biomass production and storage metabolites accumulation are proposed.
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Affiliation(s)
- Wenyi Ran
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Haitao Wang
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning 116034, China
| | - Yinghui Liu
- Information Management Center of Sichuan University, Chengdu, Sichuan 610065, China
| | - Man Qi
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Qi Xiang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Changhong Yao
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, China.
| | - Yongkui Zhang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Xianqiu Lan
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, China
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Venuleo M, Giordano M. Different Nutritional Histories Affect the Susceptibility of Algae to Grazing. JOURNAL OF PHYCOLOGY 2019; 55:997-1010. [PMID: 31309551 DOI: 10.1111/jpy.12901] [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: 11/20/2018] [Accepted: 06/11/2019] [Indexed: 06/10/2023]
Abstract
We hypothesize that algae with different cell compositions are differently perceived by their predators and consequently subjected to selective grazing. Five populations of the diatom Phaeodactylum tricornutum that differed in organic and elemental composition, but were otherwise identical, were generated by acclimation to distinct growth regimes. The different populations were then mixed in pairs and subjected to predation by either the rotifer Brachionus plicatilis or the copepod Acartia tonsa. The presence of rotifers had no impact on the ratio between any two algal populations. The presence of copepods, however, affected the ratio between algae previously acclimated to a medium containing 1 mM NH4+ and algae acclimated to 0.5 mM NO3- , and to either a lower irradiance or a higher CO2 concentration. We discuss the possible reason for the influence of different nutritional histories on the vulnerability of algae to predators. The differential impact of grazers on the growth of algae with different nutritional histories may result from direct selective grazing (i.e., grazers can detect algae with the most palatable cell composition), alone or combined to an asymmetric utilization of the nutrients regenerated after predation by co-existing algal populations. Our results strongly suggest that the nutritional history of algae can influence the relationships between phytoplankton and grazers and hint at the possibility that algal cell composition is potentially subject to natural selection, because it influences the probability that algae survive predation.
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Affiliation(s)
- Marianna Venuleo
- Laboratory of Algal and Plant Physiology, Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Mario Giordano
- Laboratory of Algal and Plant Physiology, Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
- STU-UNIVPM Joint Algal Research Center, Marine Biology Institute, College of Sciences, Shantou University, Shantou, Guangdong, 515063, China
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Algatech, Trebon, Czech Republic
- National Research Council, Institute of Marine Science ISMAR, Venezia, Italy
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Wu S, Gu W, Huang A, Li Y, Kumar M, Lim PE, Huan L, Gao S, Wang G. Elevated CO 2 improves both lipid accumulation and growth rate in the glucose-6-phosphate dehydrogenase engineered Phaeodactylum tricornutum. Microb Cell Fact 2019; 18:161. [PMID: 31547820 PMCID: PMC6757359 DOI: 10.1186/s12934-019-1214-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 09/17/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Numerous studies have shown that stress induction and genetic engineering can effectively increase lipid accumulation, but lead to a decrease of growth in the majority of microalgae. We previously found that elevated CO2 concentration increased lipid productivity as well as growth in Phaeodactylum tricornutum, along with an enhancement of the oxidative pentose phosphate pathway (OPPP) activity. The purpose of this work directed toward the verification of the critical role of glucose-6-phosphate dehydrogenase (G6PDH), the rate-limiting enzyme in the OPPP, in lipid accumulation in P. tricornutum and its simultaneous rapid growth rate under high-CO2 (0.15%) cultivation. RESULTS In this study, G6PDH was identified as a target for algal strain improvement, wherein G6PDH gene was successfully overexpressed and antisense knockdown in P. tricornutum, and systematic comparisons of the photosynthesis performance, algal growth, lipid content, fatty acid profiles, NADPH production, G6PDH activity and transcriptional abundance were performed. The results showed that, due to the enhanced G6PDH activity, transcriptional abundance and NAPDH production, overexpression of G6PDH accompanied by high-CO2 cultivation resulted in a much higher of both lipid content and growth in P. tricornutum, while knockdown of G6PDH greatly decreased algal growth as well as lipid accumulation. In addition, the total proportions of saturated and unsaturated fatty acid, especially the polyunsaturated fatty acid eicosapentaenoic acid (EPA; C20:5, n-3), were highly increased in high-CO2 cultivated G6PDH overexpressed strains. CONCLUSIONS The successful of overexpression and antisense knockdown of G6PDH well demonstrated the positive influence of G6PDH on algal growth and lipid accumulation in P. tricornutum. The improvement of algal growth, lipid content as well as polyunsaturated fatty acids in high-CO2 cultivated G6PDH overexpressed P. tricornutum suggested this G6PDH overexpression-high CO2 cultivation pattern provides an efficient and economical route for algal strain improvement to develop algal-based biodiesel production.
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Affiliation(s)
- Songcui Wu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, People's Republic of China
| | - Wenhui Gu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, People's Republic of China
| | - Aiyou Huang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, People's Republic of China
| | - Yuanxiang Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, People's Republic of China
| | - Manoj Kumar
- Climate Change Cluster, Faculty of Science, University of Technology Sydney (UTS), Sydney, NSW, Australia
| | - Phaik Eem Lim
- Institute of Ocean and Earth Sciences (IOES), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Li Huan
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, People's Republic of China
| | - Shan Gao
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, People's Republic of China
| | - Guangce Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China. .,Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, People's Republic of China.
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Metabolic Innovations Underpinning the Origin and Diversification of the Diatom Chloroplast. Biomolecules 2019; 9:biom9080322. [PMID: 31366180 PMCID: PMC6723447 DOI: 10.3390/biom9080322] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 12/13/2022] Open
Abstract
Of all the eukaryotic algal groups, diatoms make the most substantial contributions to photosynthesis in the contemporary ocean. Understanding the biological innovations that have occurred in the diatom chloroplast may provide us with explanations to the ecological success of this lineage and clues as to how best to exploit the biology of these organisms for biotechnology. In this paper, we use multi-species transcriptome datasets to compare chloroplast metabolism pathways in diatoms to other algal lineages. We identify possible diatom-specific innovations in chloroplast metabolism, including the completion of tocopherol synthesis via a chloroplast-targeted tocopherol cyclase, a complete chloroplast ornithine cycle, and chloroplast-targeted proteins involved in iron acquisition and CO2 concentration not shared between diatoms and their closest relatives in the stramenopiles. We additionally present a detailed investigation of the chloroplast metabolism of the oil-producing diatom Fistulifera solaris, which is of industrial interest for biofuel production. These include modified amino acid and pyruvate hub metabolism that might enhance acetyl-coA production for chloroplast lipid biosynthesis and the presence of a chloroplast-localised squalene synthesis pathway unknown in other diatoms. Our data provides valuable insights into the biological adaptations underpinning an ecologically critical lineage, and how chloroplast metabolism can change even at a species level in extant algae.
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Huang B, Marchand J, Thiriet-Rupert S, Carrier G, Saint-Jean B, Lukomska E, Moreau B, Morant-Manceau A, Bougaran G, Mimouni V. Betaine lipid and neutral lipid production under nitrogen or phosphorus limitation in the marine microalga Tisochrysis lutea (Haptophyta). ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101506] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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32
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Broddrick JT, Du N, Smith SR, Tsuji Y, Jallet D, Ware MA, Peers G, Matsuda Y, Dupont CL, Mitchell BG, Palsson BO, Allen AE. Cross-compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum. THE NEW PHYTOLOGIST 2019; 222:1364-1379. [PMID: 30636322 PMCID: PMC6594073 DOI: 10.1111/nph.15685] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 12/20/2018] [Indexed: 05/07/2023]
Abstract
Photoacclimation consists of short- and long-term strategies used by photosynthetic organisms to adapt to dynamic light environments. Observable photophysiology changes resulting from these strategies have been used in coarse-grained models to predict light-dependent growth and photosynthetic rates. However, the contribution of the broader metabolic network, relevant to species-specific strategies and fitness, is not accounted for in these simple models. We incorporated photophysiology experimental data with genome-scale modeling to characterize organism-level, light-dependent metabolic changes in the model diatom Phaeodactylum tricornutum. Oxygen evolution and photon absorption rates were combined with condition-specific biomass compositions to predict metabolic pathway usage for cells acclimated to four different light intensities. Photorespiration, an ornithine-glutamine shunt, and branched-chain amino acid metabolism were hypothesized as the primary intercompartment reductant shuttles for mediating excess light energy dissipation. Additionally, simulations suggested that carbon shunted through photorespiration is recycled back to the chloroplast as pyruvate, a mechanism distinct from known strategies in photosynthetic organisms. Our results suggest a flexible metabolic network in P. tricornutum that tunes intercompartment metabolism to optimize energy transport between the organelles, consuming excess energy as needed. Characterization of these intercompartment reductant shuttles broadens our understanding of energy partitioning strategies in this clade of ecologically important primary producers.
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Affiliation(s)
- Jared T. Broddrick
- Division of Biological SciencesUC San DiegoLa JollaCA92093USA
- Department of BioengineeringUC San DiegoLa JollaCA92093USA
| | - Niu Du
- Scripps Institution of OceanographyUC San DiegoLa JollaCA92093USA
- J. Craig Venter InstituteLa JollaCA92037USA
| | | | - Yoshinori Tsuji
- Department of Environmental BioscienceKwansei Gakuin UniversitySanda669‐1337Japan
| | - Denis Jallet
- Department of BiologyColorado State UniversityFort CollinsCO80523USA
| | - Maxwell A. Ware
- Department of BiologyColorado State UniversityFort CollinsCO80523USA
| | - Graham Peers
- Department of BiologyColorado State UniversityFort CollinsCO80523USA
| | - Yusuke Matsuda
- Department of Environmental BioscienceKwansei Gakuin UniversitySanda669‐1337Japan
| | | | - B. Greg Mitchell
- Scripps Institution of OceanographyUC San DiegoLa JollaCA92093USA
| | | | - Andrew E. Allen
- Scripps Institution of OceanographyUC San DiegoLa JollaCA92093USA
- J. Craig Venter InstituteLa JollaCA92037USA
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Liang Y, Kong F, Torres-Romero I, Burlacot A, Cuine S, Légeret B, Billon E, Brotman Y, Alseekh S, Fernie AR, Beisson F, Peltier G, Li-Beisson Y. Branched-Chain Amino Acid Catabolism Impacts Triacylglycerol Homeostasis in Chlamydomonas reinhardtii. PLANT PHYSIOLOGY 2019; 179:1502-1514. [PMID: 30728273 PMCID: PMC6446750 DOI: 10.1104/pp.18.01584] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 01/30/2019] [Indexed: 05/05/2023]
Abstract
Nitrogen (N) starvation-induced triacylglycerol (TAG) synthesis, and its complex relationship with starch metabolism in algal cells, has been intensively studied; however, few studies have examined the interaction between amino acid metabolism and TAG biosynthesis. Here, via a forward genetic screen for TAG homeostasis, we isolated a Chlamydomonas (Chlamydomonas reinhardtii) mutant (bkdE1α) that is deficient in the E1α subunit of the branched-chain ketoacid dehydrogenase (BCKDH) complex. Metabolomics analysis revealed a defect in the catabolism of branched-chain amino acids in bkdE1α Furthermore, this mutant accumulated 30% less TAG than the parental strain during N starvation and was compromised in TAG remobilization upon N resupply. Intriguingly, the rate of mitochondrial respiration was 20% to 35% lower in bkdE1α compared with the parental strains. Three additional knockout mutants of the other components of the BCKDH complex exhibited phenotypes similar to that of bkdE1α Transcriptional responses of BCKDH to different N status were consistent with its role in TAG homeostasis. Collectively, these results indicate that branched-chain amino acid catabolism contributes to TAG metabolism by providing carbon precursors and ATP, thus highlighting the complex interplay between distinct subcellular metabolisms for oil storage in green microalgae.
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Affiliation(s)
- Yuanxue Liang
- Aix-Marseille University, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Commissariat à l'Energie Atomique Cadarache, Saint-Paul-lez Durance F-13108, France
| | - Fantao Kong
- Aix-Marseille University, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Commissariat à l'Energie Atomique Cadarache, Saint-Paul-lez Durance F-13108, France
| | - Ismael Torres-Romero
- Aix-Marseille University, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Commissariat à l'Energie Atomique Cadarache, Saint-Paul-lez Durance F-13108, France
| | - Adrien Burlacot
- Aix-Marseille University, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Commissariat à l'Energie Atomique Cadarache, Saint-Paul-lez Durance F-13108, France
| | - Stéphan Cuine
- Aix-Marseille University, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Commissariat à l'Energie Atomique Cadarache, Saint-Paul-lez Durance F-13108, France
| | - Bertrand Légeret
- Aix-Marseille University, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Commissariat à l'Energie Atomique Cadarache, Saint-Paul-lez Durance F-13108, France
| | - Emmanuelle Billon
- Aix-Marseille University, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Commissariat à l'Energie Atomique Cadarache, Saint-Paul-lez Durance F-13108, France
| | - Yariv Brotman
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Fred Beisson
- Aix-Marseille University, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Commissariat à l'Energie Atomique Cadarache, Saint-Paul-lez Durance F-13108, France
| | - Gilles Peltier
- Aix-Marseille University, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Commissariat à l'Energie Atomique Cadarache, Saint-Paul-lez Durance F-13108, France
| | - Yonghua Li-Beisson
- Aix-Marseille University, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Commissariat à l'Energie Atomique Cadarache, Saint-Paul-lez Durance F-13108, France
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Lu H, Chen H, Tang X, Yang Q, Zhang H, Chen YQ, Chen W. Evaluation of metabolome sample preparation and extraction methodologies for oleaginous filamentous fungi Mortierella alpina. Metabolomics 2019; 15:50. [PMID: 30900034 DOI: 10.1007/s11306-019-1506-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 03/04/2019] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Metabolomics has been successfully applied to guide the rational engineering of industrial strains and improve the performance of bioprocesses. Mortierella alpina has traditionally been one of the most popular industrial strains for the production of polyunsaturated fatty acids. However, a systematic comparison and optimisation of the metabolomic analysis methods of M. alpina has not yet been reported. OBJECTIVE We sought to identify potential weaknesses that are important for accurate metabolomic analysis. We also aimed to determine an efficient sample preparation protocol for metabolomics studies in the oleaginous filamentous fungus M. alpina. METHODS In this study, using GC-MS, we evaluated three sample preparation protocols and five solvent mixtures by assessment of the metabolite profile differences, the sum of peak intensities and the reproducibility of metabolite quantification. RESULTS The freeze-dried biomass had better reproducibility and recovery than fresh biomass for metabolite extraction and data normalisation that is part of a metabolomics analysis of filamentous fungi M. alpina. Methanol:water (1:1) was superior for the profiling of metabolites in oleaginous fungi M. alpina. The unbiased metabolite profiling difference between the growth phase and lipids synthesis phase revealed that the degradation of amino acids were critical nodes for the efficient synthesis of lipids in M. alpina. CONCLUSION The use of freeze-dried biomass for metabolite extraction and data normalisation was more efficient at measuring the active state of the intracellular metabolites in M. alpina. We recommend extracting the intracellular metabolites with methanol:water (1:1). An important role of amino acid oxidation in the nitrogen limitation-mediated lipid accumulation was found.
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Affiliation(s)
- Hengqian Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, 214122, China.
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, 225004, China.
| | - Xin Tang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Qin Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, 225004, China
| | - Yong Q Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, 214122, China
- Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048, China
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Wierzbicki MP, Maloney V, Mizrachi E, Myburg AA. Xylan in the Middle: Understanding Xylan Biosynthesis and Its Metabolic Dependencies Toward Improving Wood Fiber for Industrial Processing. FRONTIERS IN PLANT SCIENCE 2019; 10:176. [PMID: 30858858 PMCID: PMC6397879 DOI: 10.3389/fpls.2019.00176] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 02/04/2019] [Indexed: 05/14/2023]
Abstract
Lignocellulosic biomass, encompassing cellulose, lignin and hemicellulose in plant secondary cell walls (SCWs), is the most abundant source of renewable materials on earth. Currently, fast-growing woody dicots such as Eucalyptus and Populus trees are major lignocellulosic (wood fiber) feedstocks for bioproducts such as pulp, paper, cellulose, textiles, bioplastics and other biomaterials. Processing wood for these products entails separating the biomass into its three main components as efficiently as possible without compromising yield. Glucuronoxylan (xylan), the main hemicellulose present in the SCWs of hardwood trees carries chemical modifications that are associated with SCW composition and ultrastructure, and affect the recalcitrance of woody biomass to industrial processing. In this review we highlight the importance of xylan properties for industrial wood fiber processing and how gaining a greater understanding of xylan biosynthesis, specifically xylan modification, could yield novel biotechnology approaches to reduce recalcitrance or introduce novel processing traits. Altering xylan modification patterns has recently become a focus of plant SCW studies due to early findings that altered modification patterns can yield beneficial biomass processing traits. Additionally, it has been noted that plants with altered xylan composition display metabolic differences linked to changes in precursor usage. We explore the possibility of using systems biology and systems genetics approaches to gain insight into the coordination of SCW formation with other interdependent biological processes. Acetyl-CoA, s-adenosylmethionine and nucleotide sugars are precursors needed for xylan modification, however, the pathways which produce metabolic pools during different stages of fiber cell wall formation still have to be identified and their co-regulation during SCW formation elucidated. The crucial dependence on precursor metabolism provides an opportunity to alter xylan modification patterns through metabolic engineering of one or more of these interdependent pathways. The complexity of xylan biosynthesis and modification is currently a stumbling point, but it may provide new avenues for woody biomass engineering that are not possible for other biopolymers.
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Affiliation(s)
| | | | | | - Alexander A. Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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Huang R, Ding J, Gao K, Cruz de Carvalho MH, Tirichine L, Bowler C, Lin X. A Potential Role for Epigenetic Processes in the Acclimation Response to Elevated pCO 2 in the Model Diatom Phaeodactylum tricornutum. Front Microbiol 2019; 9:3342. [PMID: 30692981 PMCID: PMC6340190 DOI: 10.3389/fmicb.2018.03342] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 12/27/2018] [Indexed: 12/24/2022] Open
Abstract
Understanding of the molecular responses underpinning diatom responses to ocean acidification is fundamental for predicting how important primary producers will be shaped by the continuous rise in atmospheric CO2. In this study, we have analyzed global transcriptomic changes of the model diatom Phaeodactylum tricornutum following growth for 15 generations in elevated pCO2 by strand-specific RNA sequencing (ssRNA-seq). Our results indicate that no significant effects of elevated pCO2 and associated carbonate chemistry changes on the physiological performance of the cells were observed after 15 generations whereas the expression of genes encoding histones and other genes involved in chromatin structure were significantly down-regulated, while the expression of transposable elements (TEs) and genes encoding histone acetylation enzymes were significantly up-regulated. Furthermore, we identified a series of long non-protein coding RNAs (lncRNAs) specifically responsive to elevated pCO2, suggesting putative regulatory roles for these largely uncharacterized genome components. Taken together, our integrative analyses reveal that epigenetic elements such as TEs, histone modifications and lncRNAs may have important roles in the acclimation of diatoms to elevated pCO2 over short time scales and thus may influence longer term adaptive processes in response to progressive ocean acidification.
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Affiliation(s)
- Ruiping Huang
- State Key Laboratory of Marine Environmental Science,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Jiancheng Ding
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Kunshan Gao
- State Key Laboratory of Marine Environmental Science,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Maria Helena Cruz de Carvalho
- Ecology and Evolutionary Biology Section, Institut de Biologie de l’École Normale Supérieure (IBENS), Département de Biologie, Ecole Normale Supérieure, CNRS UMR8197, Inserm U1024, PSL Research University, Paris, France
- Faculté des Sciences et Technologie, Université Paris Est-Créteil, Créteil, France
| | - Leila Tirichine
- Faculté des Sciences et Techniques, Université de Nantes, CNRS UMR6286, UFIP, Nantes, France
| | - Chris Bowler
- Ecology and Evolutionary Biology Section, Institut de Biologie de l’École Normale Supérieure (IBENS), Département de Biologie, Ecole Normale Supérieure, CNRS UMR8197, Inserm U1024, PSL Research University, Paris, France
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
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Heydarizadeh P, Veidl B, Huang B, Lukomska E, Wielgosz-Collin G, Couzinet-Mossion A, Bougaran G, Marchand J, Schoefs B. Carbon Orientation in the Diatom Phaeodactylum tricornutum: The Effects of Carbon Limitation and Photon Flux Density. FRONTIERS IN PLANT SCIENCE 2019; 10:471. [PMID: 31057578 PMCID: PMC6477932 DOI: 10.3389/fpls.2019.00471] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/28/2019] [Indexed: 05/03/2023]
Abstract
Diatoms adapt to changing environmental conditions in very efficient ways. Among the mechanisms that can be activated, the reorientation of carbon metabolism is crucial because it allows the storage of energy into energy-dense molecules, typically lipids. Beside their roles in physiology, lipids are commercially interesting compounds. Therefore studies dealing with this topic are relevant for both basic and applied science. Although the molecular mechanisms involved in the reorientation of carbon metabolism as a response to a deficiency in nutrients such as nitrogen or phosphorus has been partially elucidated, the impacts of carbon availability on the implementation of the reorientation mechanisms remain unclear. Indeed, it has not been determined if the same types of mechanisms are activated under carbon and other nutrient deficiencies or limitations. The first aim of this work was to get insights into the physiological, biological and molecular processes triggered by progressive carbon starvation in the model diatom Phaeodactylum tricornutum. The second aim was to investigate the effects of the growth light intensity on these processes. For such a purpose three different photon flux densities 30, 300, and 1000 μmol photons m-2 s-1 were used. The results presented here demonstrate that under carbon limitation, diatom cells still reorient carbon metabolism toward either phosphoenolpyruvate or pyruvate, which serves as a hub for the production of more complex molecules. The distribution of carbon atoms between the different pathways was partially affected by the growth photon flux density because low light (LL) provides conditions for the accumulation of chrysolaminarin, while medium light mostly stimulated lipid synthesis. A significant increase in the amount of proteins was observed under high light (HL).
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Affiliation(s)
- Parisa Heydarizadeh
- Metabolism, Bioengineering of Microalgal Molecules and Applications, Mer Molécule Santé, Le Mans University, IUML FR 3473 CNRS, Le Mans, France
| | - Brigitte Veidl
- Metabolism, Bioengineering of Microalgal Molecules and Applications, Mer Molécule Santé, Le Mans University, IUML FR 3473 CNRS, Le Mans, France
| | - Bing Huang
- Metabolism, Bioengineering of Microalgal Molecules and Applications, Mer Molécule Santé, Le Mans University, IUML FR 3473 CNRS, Le Mans, France
| | - Ewa Lukomska
- Physiology and Biotechnology of Algae Laboratory, IFREMER, Nantes, France
| | | | | | - Gaël Bougaran
- Physiology and Biotechnology of Algae Laboratory, IFREMER, Nantes, France
| | - Justine Marchand
- Metabolism, Bioengineering of Microalgal Molecules and Applications, Mer Molécule Santé, Le Mans University, IUML FR 3473 CNRS, Le Mans, France
| | - Benoît Schoefs
- Metabolism, Bioengineering of Microalgal Molecules and Applications, Mer Molécule Santé, Le Mans University, IUML FR 3473 CNRS, Le Mans, France
- *Correspondence: Benoît Schoefs,
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Remmers IM, D'Adamo S, Martens DE, de Vos RC, Mumm R, America AH, Cordewener JH, Bakker LV, Peters SA, Wijffels RH, Lamers PP. Orchestration of transcriptome, proteome and metabolome in the diatom Phaeodactylum tricornutum during nitrogen limitation. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.08.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Xue J, Chen TT, Zheng JW, Balamurugan S, Cai JX, Liu YH, Yang WD, Liu JS, Li HY. The role of diatom glucose-6-phosphate dehydrogenase on lipogenic NADPH supply in green microalgae through plastidial oxidative pentose phosphate pathway. Appl Microbiol Biotechnol 2018; 102:10803-10815. [PMID: 30349933 DOI: 10.1007/s00253-018-9415-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 08/23/2018] [Accepted: 09/20/2018] [Indexed: 11/27/2022]
Abstract
Commercial production of biofuel from oleaginous microalgae is often impeded by their slow growth rate than other fast-growing algal species. A promising strategy is to genetically engineer the fast-growing algae to accumulate lipids by expressing key lipogenic genes from oleaginous microalgae. However, lacking of strong expression cassette to transform most of the algal species and potential metabolic target to engineer lipid metabolism has hindered its biotechnological applications. In this study, we engineered the oxidative pentose phosphate pathway (PPP) of green microalga Chlorella pyrenoidosa for lipid enhancement by expressing a glucose-6-phosphate dehydrogenase (G6PD) from oleaginous diatom Phaeodactylum tricornutum. Molecular characterization of transformed lines revealed that heterologous PtG6PD was transcribed and expressed successfully. Interestingly, subcellular localization analyses revealed that PtG6PD was targeted to chloroplasts of C. pyrenoidosa. PtG6PD expression remarkably elevated NADPH content and consequently enhanced the lipid content without affecting growth rate. Collectively, this report represents a promising candidate to engineer lipid biosynthesis in heterologous hosts with notable commercial significance, and it highlights the potential role of plastidial PPP in supplying lipogenic NADPH in microalgae.
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Affiliation(s)
- Jiao Xue
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Ting-Ting Chen
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Jian-Wei Zheng
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Srinivasan Balamurugan
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Jia-Xi Cai
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Yu-Hong Liu
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Wei-Dong Yang
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Jie-Sheng Liu
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Hong-Ye Li
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
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Yang M, Lin X, Liu X, Zhang J, Ge F. Genome Annotation of a Model Diatom Phaeodactylum tricornutum Using an Integrated Proteogenomic Pipeline. MOLECULAR PLANT 2018; 11:1292-1307. [PMID: 30176371 DOI: 10.1016/j.molp.2018.08.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/26/2018] [Accepted: 08/28/2018] [Indexed: 06/08/2023]
Abstract
Diatoms comprise a diverse and ecologically important group of eukaryotic phytoplankton that significantly contributes to marine primary production and global carbon cycling. Phaeodactylum tricornutum is commonly used as a model organism for studying diatom biology. Although its genome was sequenced in 2008, a high-quality genome annotation is still not available for this diatom. Here we report the development of an integrated proteogenomic pipeline and its application for improved annotation of P. tricornutum genome using mass spectrometry (MS)-based proteomics data. Our proteogenomic analysis unambiguously identified approximately 8300 genes and revealed 606 novel proteins, 506 revised genes, 94 splice variants, 58 single amino acid variants, and a holistic view of post-translational modifications in P. tricornutum. We experimentally confirmed a subset of novel events and obtained MS evidence for more than 200 micropeptides in P. tricornutum. These findings expand the genomic landscape of P. tricornutum and provide a rich resource for the study of diatom biology. The proteogenomic pipeline we developed in this study is applicable to any sequenced eukaryote and thus represents a significant contribution to the toolset for eukaryotic proteogenomic analysis. The pipeline and its source code are freely available at https://sourceforge.net/projects/gapeproteogenomic.
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Affiliation(s)
- Mingkun Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaohuang Lin
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xin Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jia Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China.
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41
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Li X, Pan Y, Hu H. Identification of the triacylglycerol lipase in the chloroplast envelope of the diatom Phaeodactylum tricornutum. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.06.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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42
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Abbriano R, Vardar N, Yee D, Hildebrand M. Manipulation of a glycolytic regulator alters growth and carbon partitioning in the marine diatom Thalassiosira pseudonana. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.03.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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43
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Arora N, Pienkos PT, Pruthi V, Poluri KM, Guarnieri MT. Leveraging algal omics to reveal potential targets for augmenting TAG accumulation. Biotechnol Adv 2018; 36:1274-1292. [PMID: 29678388 DOI: 10.1016/j.biotechadv.2018.04.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 04/11/2018] [Accepted: 04/15/2018] [Indexed: 02/08/2023]
Abstract
Ongoing global efforts to commercialize microalgal biofuels have expedited the use of multi-omics techniques to gain insights into lipid biosynthetic pathways. Functional genomics analyses have recently been employed to complement existing sequence-level omics studies, shedding light on the dynamics of lipid synthesis and its interplay with other cellular metabolic pathways, thus revealing possible targets for metabolic engineering. Here, we review the current status of algal omics studies to reveal potential targets to augment TAG accumulation in various microalgae. This review specifically aims to examine and catalog systems level data related to stress-induced TAG accumulation in oleaginous microalgae and inform future metabolic engineering strategies to develop strains with enhanced bioproductivity, which could pave a path for sustainable green energy.
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Affiliation(s)
- Neha Arora
- Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Philip T Pienkos
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Vikas Pruthi
- Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Krishna Mohan Poluri
- Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Michael T Guarnieri
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA.
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Maeda Y, Nojima D, Yoshino T, Tanaka T. Structure and properties of oil bodies in diatoms. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0408. [PMID: 28717018 DOI: 10.1098/rstb.2016.0408] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2017] [Indexed: 01/23/2023] Open
Abstract
Diatoms accumulate triacylglycerols in spherical organelles called oil bodies when exposed to nutrient deprivation conditions. Oil body biology in diatoms has attracted significant attention due to the complexity of the intracellular organelles and the unique combination of genes generated by the evolutionary history of secondary endosymbiosis. The demand for biofuel production has further increased the interest in and importance of a better understanding of oil body biology in diatoms, because it could provide targets for genetic engineering to further enhance their promising lipid accumulation. This review describes recent progress in studies of the structure and properties of diatom oil bodies. Firstly, the general features of diatom oil bodies are described, in particular, their number, size and morphology, as well as the quantity and quality of lipids they contain. Subsequently, the diatom oil body-associated proteins, which were recently discovered through oil body proteomics, are introduced. Then, the metabolic pathways responsible for the biogenesis and degradation of diatom oil bodies are summarized. During biogenesis and degradation, oil bodies interact with other organelles, including chloroplasts, the endoplasmic reticulum and mitochondria, suggesting their dynamic nature in response to environmental changes. Finally, the functions of oil bodies in diatoms are discussed.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'.
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Affiliation(s)
- Yoshiaki Maeda
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Daisuke Nojima
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Tomoko Yoshino
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Tsuyoshi Tanaka
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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Pan Y, Yang J, Gong Y, Li X, Hu H. 3-Hydroxyisobutyryl-CoA hydrolase involved in isoleucine catabolism regulates triacylglycerol accumulation in Phaeodactylum tricornutum. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0409. [PMID: 28717019 DOI: 10.1098/rstb.2016.0409] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2017] [Indexed: 11/12/2022] Open
Abstract
Since methylmalonyl-CoA epimerase appears to be absent in the majority of photosynthetic organisms, including diatoms, (S)-methylmalonyl-CoA, the intermediate of isoleucine (Ile) catabolism, cannot be metabolized to (R)-methylmalonyl-CoA then to succinyl-CoA. In this study, propionyl-CoA carboxylase (PCC) RNAi silenced strains and 3-hydroxyisobutyryl-CoA hydrolase (HIBCH) overexpression strains were constructed to elucidate the Ile degradation pathway and its influence on lipid accumulation in Phaeodactylum tricornutum based on growth, neutral lipid content and metabolite profile analysis. Knockdown of PCC disturbed the metabolism of Ile through propionyl-CoA to methylmalonyl-CoA, as illustrated by much higher Ile content at day 6. However, Ile decreased to comparable levels to the wild-type at day 10. PCC silencing redirected propionyl-CoA to acetyl-CoA via a modified β-oxidation pathway, and transcript levels for some branched-chain amino acid (BCAA) degradation-related genes, especially HIBCH, significantly upregulated in the PCC mutant, which enhanced the BCAA degradations and thus resulted in higher triacylglycerol (TAG) content. Overexpression of HIBCH accelerates Ile degradation and results in a lowered Ile content in the overexpression strains, thus enhancing carbon skeletons to the tricarboxylic acid cycle and giving rise to increasing TAG accumulation. Our study provides a good strategy to obtain high-lipid-yield transgenic diatoms by modifying the propionyl-CoA metabolism.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'.
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Affiliation(s)
- Yufang Pan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, People's Republic of China
| | - Juan Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yangmin Gong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, People's Republic of China
| | - Xiaolong Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, People's Republic of China
| | - Hanhua Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, People's Republic of China
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Gan Q, Jiang J, Han X, Wang S, Lu Y. Engineering the Chloroplast Genome of Oleaginous Marine Microalga Nannochloropsis oceanica. FRONTIERS IN PLANT SCIENCE 2018; 9:439. [PMID: 29696028 PMCID: PMC5904192 DOI: 10.3389/fpls.2018.00439] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 03/21/2018] [Indexed: 05/21/2023]
Abstract
Plastid engineering offers an important tool to fill the gap between the technical and the enormous potential of microalgal photosynthetic cell factory. However, to date, few reports on plastid engineering in industrial microalgae have been documented. This is largely due to the small cell sizes and complex cell-wall structures which make these species intractable to current plastid transformation methods (i.e., biolistic transformation and polyethylene glycol-mediated transformation). Here, employing the industrial oleaginous microalga Nannochloropsis oceanica as a model, an electroporation-mediated chloroplast transformation approach was established. Fluorescent microscopy and laser confocal scanning microscopy confirmed the expression of the green fluorescence protein, driven by the endogenous plastid promoter and terminator. Zeocin-resistance selection led to an acquisition of homoplasmic strains of which a stable and site-specific recombination within the chloroplast genome was revealed by sequencing and DNA gel blotting. This demonstration of electroporation-mediated chloroplast transformation opens many doors for plastid genome editing in industrial microalgae, particularly species of which the chloroplasts are recalcitrant to chemical and microparticle bombardment transformation.
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Affiliation(s)
- Qinhua Gan
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou, China
| | - Jiaoyun Jiang
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou, China
| | - Xiao Han
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou, China
| | - Shifan Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou, China
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Hainan University, Haikou, China
| | - Yandu Lu
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou, China
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Hainan University, Haikou, China
- *Correspondence: Yandu Lu
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Hao X, Luo L, Jouhet J, Rébeillé F, Maréchal E, Hu H, Pan Y, Tan X, Chen Z, You L, Chen H, Wei F, Gong Y. Enhanced triacylglycerol production in the diatom Phaeodactylum tricornutum by inactivation of a Hotdog-fold thioesterase gene using TALEN-based targeted mutagenesis. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:312. [PMID: 30455741 PMCID: PMC6231261 DOI: 10.1186/s13068-018-1309-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 10/30/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND In photosynthetic oleaginous microalgae, acyl-CoA molecules are used as substrates for the biosynthesis of membrane glycerolipids, triacylglycerol (TAG) and other acylated molecules. Acyl-CoA can also be directed to beta-oxidative catabolism. They can be utilized by a number of lipid metabolic enzymes including endogenous thioesterases, which catalyze their hydrolysis to release free fatty acids. Acyl-CoA availability thus plays fundamental roles in determining the quantity and composition of membrane lipids and storage lipids. RESULTS Here, we have engineered the model diatom Phaeodactylum tricornutum to produce significantly increased TAGs by disruption of the gene encoding a Hotdog-fold thioesterase involved in acyl-CoA hydrolysis (ptTES1). This plastidial thioesterase can hydrolyze both medium- and long-chain fatty acyl-CoAs, but has the highest activity toward long-chain saturated and monounsaturated fatty acyl-CoAs. The maximum rate was found with oleoyl-CoA, which is hydrolyzed at 50 nmol/min/mg protein. The stable and targeted interruption of acyl-CoA thioesterase gene was achieved using a genome editing technique, transcription activator-like effector nucleases (TALENs). Disruption of native ptTES1 gene resulted in a 1.7-fold increase in TAG content when algal strains were grown in nitrogen-replete media for 8 days, whereas the content of other lipid classes, including phosphoglycerolipids and galactoglycerolipids, remained almost unchanged. The engineered algal strain also exhibited a marked change in fatty acid profile, including a remarkable increase in 16:0 and 16:1 and a decrease in 20:5. Nitrogen deprivation for 72 h further increased TAG content and titer of the engineered strain, reaching 478 μg/109 cells and 4.8 mg/L, respectively. Quantitative determination of in vivo acyl-CoAs showed that the total acyl-CoA pool size was significantly higher in the engineered algal strain than that in the wild type. CONCLUSIONS This study supports the role of ptTES1 in free fatty acid homeostasis in the plastid of Phaeodactylum and demonstrates the potential of TALEN-based genome editing technique to generate an enhanced lipid-producing algal strain through blocking acyl-CoA catabolism.
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Affiliation(s)
- Xiahui Hao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, No. 2 Xudong Second Road, Wuhan, 430062 People’s Republic of China
- Hubei Key Laboratory of Lipid Chemistry and Nutrition, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Ling Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, No. 2 Xudong Second Road, Wuhan, 430062 People’s Republic of China
- Hubei Key Laboratory of Lipid Chemistry and Nutrition, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire et Végétale, Centre National de la Recherche Scientifique, Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut National de la Recherche Agronomique, Université Grenoble Alpes, UMR 5168, 38041 Grenoble, France
| | - Fabrice Rébeillé
- Laboratoire de Physiologie Cellulaire et Végétale, Centre National de la Recherche Scientifique, Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut National de la Recherche Agronomique, Université Grenoble Alpes, UMR 5168, 38041 Grenoble, France
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale, Centre National de la Recherche Scientifique, Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut National de la Recherche Agronomique, Université Grenoble Alpes, UMR 5168, 38041 Grenoble, France
| | - Hanhua Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 China
| | - Yufang Pan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 China
| | - Xiaoming Tan
- Hubei Collaborative Innovation Center for Green Transformation of Bioresources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Zhuo Chen
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Science, Shandong Normal University, Jinan, 250014 China
| | - Lingjie You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, No. 2 Xudong Second Road, Wuhan, 430062 People’s Republic of China
- Hubei Key Laboratory of Lipid Chemistry and Nutrition, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Hong Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, No. 2 Xudong Second Road, Wuhan, 430062 People’s Republic of China
- Hubei Key Laboratory of Lipid Chemistry and Nutrition, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Fang Wei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, No. 2 Xudong Second Road, Wuhan, 430062 People’s Republic of China
- Hubei Key Laboratory of Lipid Chemistry and Nutrition, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Yangmin Gong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, No. 2 Xudong Second Road, Wuhan, 430062 People’s Republic of China
- Hubei Key Laboratory of Lipid Chemistry and Nutrition, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
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Rocha RP, Machado M, Vaz MGMV, Vinson CC, Leite M, Richard R, Mendes LBB, Araujo WL, Caldana C, Martins MA, Williams TC, Nunes-Nesi A. Exploring the metabolic and physiological diversity of native microalgal strains (Chlorophyta) isolated from tropical freshwater reservoirs. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.10.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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49
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Chen B, Wan C, Mehmood MA, Chang JS, Bai F, Zhao X. Manipulating environmental stresses and stress tolerance of microalgae for enhanced production of lipids and value-added products-A review. BIORESOURCE TECHNOLOGY 2017; 244:1198-1206. [PMID: 28601395 DOI: 10.1016/j.biortech.2017.05.170] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/25/2017] [Accepted: 05/26/2017] [Indexed: 05/12/2023]
Abstract
Microalgae have promising potential to produce lipids and a variety of high-value chemicals. Suitable stress conditions such as nitrogen starvation and high salinity could stimulate synthesis and accumulation of lipids and high-value products by microalgae, therefore, various stress-modification strategies were developed to manipulate and optimize cultivation processes to enhance bioproduction efficiency. On the other hand, advancements in omics-based technologies have boosted the research to globally understand microalgal gene regulation under stress conditions, which enable further improvement of production efficiency via genetic engineering. Moreover, integration of multi-omics data, synthetic biology design, and genetic engineering manipulations exhibits a tremendous potential in the betterment of microalgal biorefinery. This review discusses the process manipulation strategies and omics studies on understanding the regulation of metabolite biosynthesis under various stressful conditions, and proposes genetic engineering of microalgae to improve bioproduction via manipulating stress tolerance.
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Affiliation(s)
- Bailing Chen
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chun Wan
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Muhammad Aamer Mehmood
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Bioenergy Research Centre, Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng Kung University, Taiwan; Research Center for Energy Technology and Strategy, National Cheng Kung University, Taiwan
| | - Fengwu Bai
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinqing Zhao
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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50
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Chen Z, Luo L, Chen R, Hu H, Pan Y, Jiang H, Wan X, Jin H, Gong Y. Acetylome Profiling Reveals Extensive Lysine Acetylation of the Fatty Acid Metabolism Pathway in the Diatom Phaeodactylum tricornutum. Mol Cell Proteomics 2017; 17:399-412. [PMID: 29093020 DOI: 10.1074/mcp.ra117.000339] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Indexed: 02/05/2023] Open
Abstract
Nε-lysine acetylation represents a highly dynamic and reversibly regulated post-translational modification widespread in almost all organisms, and plays important roles for regulation of protein function in diverse metabolic pathways. However, little is known about the role of lysine acetylation in photosynthetic eukaryotic microalgae. We integrated proteomic approaches to comprehensively characterize the lysine acetylome in the model diatom Phaeodactylum tricornutum In total, 2324 acetylation sites from 1220 acetylated proteins were identified, representing the largest data set of the lysine acetylome in plants to date. Almost all enzymes involved in fatty acid synthesis were found to be lysine acetylated. Six putative lysine acetylation sites were identified in a plastid-localized long-chain acyl-CoA synthetase. Site-directed mutagenesis and site-specific incorporation of N-acetyllysine in acyl-CoA synthetase show that acetylation at K407 and K425 increases its enzyme activity. Moreover, the nonenzymatically catalyzed overall hyperacetylation of acyl-CoA synthetase by acetyl-phosphate can be effectively deacetylated and reversed by a sirtuin-type NAD+-dependent deacetylase with subcellular localization of both the plastid and nucleus in Phaeodactylum This work indicates the regulation of acyl-CoA synthetase activity by site-specific lysine acetylation and highlights the potential regulation of fatty acid metabolism by lysine actetylation in the plastid of the diatom Phaeodactylum.
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Affiliation(s)
- Zhuo Chen
- From the ‡Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China.,§Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan 250014, Shandong, China
| | - Ling Luo
- From the ‡Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Runfa Chen
- From the ‡Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Hanhua Hu
- ¶Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yufang Pan
- ¶Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Haibo Jiang
- ‖School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, China
| | - Xia Wan
- From the ‡Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Hu Jin
- ¶Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yangmin Gong
- From the ‡Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China;
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