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de Jesús-Campos D, García-Ortega LF, Fimbres-Olivarría D, Herrera-Estrella L, López-Elías JA, Hayano-Kanashiro C. Transcriptomic analysis of Chaetoceros muelleri in response to different nitrogen concentrations reveals the activation of pathways to enable efficient nitrogen uptake. Gene 2024; 924:148589. [PMID: 38777108 DOI: 10.1016/j.gene.2024.148589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/07/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
Nitrogen is the principal nutrient deficiency that increases lipids and carbohydrate content in diatoms but negatively affects biomass production. Marine diatom Chaetoceros muelleri is characterized by lipid and carbohydrate accumulation under low nitrogen concentration without affecting biomass. To elucidate the molecular effects of nitrogen concentrations, we performed an RNA-seq analysis of C. muelleri grown under four nitrogen concentrations (3.53 mM, 1.76 mM, 0.44 mM, and 0.18 mM of NaNO3). This research revealed that changes in global transcription in C. muelleri are differentially expressed by nitrogen concentration. "Energetic metabolism", "Carbohydrate metabolism" and "Lipid metabolism" pathways were identified as the most upregulated by N deficiency. Due to N limitation, alternative pathways to self-supply nitrogen employed by microalgal cells were identified. Additionally, nitrogen limitation decreased chlorophyll content and caused a greater response at the transcriptional level with a higher number of unigenes differentially expressed. By contrast, the highest N concentration (3.53 mM) recorded the lowest number of differentially expressed genes. Amt1, Nrt2, Fad2, Skn7, Wrky19, and Dgat2 genes were evaluated by RT-qPCR. In conclusion, C. muelleri modify their metabolic pathways to optimize nitrogen utilization and minimize nitrogen losses. On the other hand, the assembled transcriptome serves as the basis for metabolic engineering focused on improving the quantity and quality of the diatom for biotechnological applications. However, proteomic and metabolomic analysis is also required to compare gene expression, protein, and metabolite accumulation.
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Affiliation(s)
- Damaristelma de Jesús-Campos
- Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora, Hermosillo-Sonora CP 83000, Mexico
| | - Luis Fernando García-Ortega
- Departamento de Ingeniería Genética, Centro de Investigación y Estudios Avanzados del IPN, Irapuato-Guanajuato Zip Code 36821, Mexico
| | - Diana Fimbres-Olivarría
- Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora, Hermosillo-Sonora CP 83000, Mexico
| | - Luis Herrera-Estrella
- Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, 79409 Lubbock, TX, USA; Unidad de Genómica Avanzada/LANGEBIO, Centro de Investigación y Estudios Avanzados del IPN, Irapuato-Guanajuato Zip Code 36821, Mexico
| | - José Antonio López-Elías
- Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora, Hermosillo-Sonora CP 83000, Mexico.
| | - Corina Hayano-Kanashiro
- Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora, Hermosillo-Sonora CP 83000, Mexico.
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Mariam I, Bettiga M, Rova U, Christakopoulos P, Matsakas L, Patel A. Ameliorating microalgal OMEGA production using omics platforms. TRENDS IN PLANT SCIENCE 2024; 29:799-813. [PMID: 38350829 DOI: 10.1016/j.tplants.2024.01.002] [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: 09/05/2023] [Revised: 12/19/2023] [Accepted: 01/11/2024] [Indexed: 02/15/2024]
Abstract
Over the past decade, the focus on omega (ω)-3 fatty acids from microalgae has intensified due to their diverse health benefits. Bioprocess optimization has notably increased ω-3 fatty acid yields, yet understanding of the genetic architecture and metabolic pathways of high-yielding strains remains limited. Leveraging genomics, transcriptomics, proteomics, and metabolomics tools can provide vital system-level insights into native ω-3 fatty acid-producing microalgae, further boosting production. In this review, we explore 'omics' studies uncovering alternative pathways for ω-3 fatty acid synthesis and genome-wide regulation in response to cultivation parameters. We also emphasize potential targets to fine-tune in order to enhance yield. Despite progress, an integrated omics platform is essential to overcome current bottlenecks in optimizing the process for ω-3 fatty acid production from microalgae, advancing this crucial field.
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Affiliation(s)
- Iqra Mariam
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden
| | - Maurizio Bettiga
- Department of Life Sciences - LIFE, Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; Innovation Unit, Italbiotec Srl Società Benefit, Milan, Italy
| | - Ulrika Rova
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden
| | - Paul Christakopoulos
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden
| | - Leonidas Matsakas
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden
| | - Alok Patel
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden.
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Lu H, Liu K, Zhang H, Xie X, Ge Y, Chi Z, Xue S, Kong F, Ohama T. Enhanced triacyclglycerols and starch synthesis in Chlamydomonas stimulated by the engineered biodegradable nanoparticles. Appl Microbiol Biotechnol 2023; 107:971-983. [PMID: 36622426 DOI: 10.1007/s00253-023-12366-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 10/17/2022] [Accepted: 01/03/2023] [Indexed: 01/10/2023]
Abstract
Microalgae are promising feedstock for renewable fuels. The accumulation of oils in microalgae can be enhanced by nanoparticle exposure. However, the nanoparticles employed in previous studies are mostly non-biodegradable, which hinders nanoparticles developing as promising approach for biofuel production. We recently reported the engineered resin nanoparticles (iBCA-NPs), which were found to be biodegradable in this study. When the cells of green microalga Chlamydomonas reinhardtii were exposed to the iBCA-NPs for 1 h, the cellular triacyclglycerols (TAG) and starch contents increased by 520% and 60% than that in the control. The TAG production improved by 1.8-fold compared to the control without compromised starch production. Additionally, the content of total fatty acids increased by 1.3-fold than that in control. Furthermore, we found that the iBCA-NPs addition resulted in increased cellular reactive oxygen species (ROS) content and upregulated the activities of antioxidant enzymes. The relative expressions of the key genes involved in TAG and starch biosynthesis were also upregulated. Overall, our results showed that short exposure of the iBCA-NPs dramatically enhances TAG and starch accumulation in Chlamydomonas, which probably resulted from prompt upregulated expression of the key genes in lipid and starch metabolic pathways that were triggered by over-accumulated ROS. This study reported a useful approach to enhance energy-rich reserve accumulation in microalgae. KEY POINTS: 1. The first attempt to increase oil and starch in microalgae by biodegradable NPs. 2. The biodegradability of iBCA-NPs by the BOD test was more than 50% after 28 days. 3. The iBCA-NPs induce more energy reserves than that of previously reported NPs.
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Affiliation(s)
- Han Lu
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Keqing Liu
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Hao Zhang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Xi Xie
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Yunlong Ge
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Zhanyou Chi
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Song Xue
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Fantao Kong
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.
| | - Takeshi Ohama
- School of Environmental Science and Engineering, Kochi University of Technology, 185 Miyanokuchi, Tosayamada, Kami-City, 782-8502, Japan
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Wang R, Miao X. Lipid turnover and SQUAMOSA promoter-binding proteins mediate variation in fatty acid desaturation under early nitrogen deprivation revealed by lipidomic and transcriptomic analyses in Chlorella pyrenoidosa. FRONTIERS IN PLANT SCIENCE 2022; 13:987354. [PMID: 36247620 PMCID: PMC9558234 DOI: 10.3389/fpls.2022.987354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/06/2022] [Indexed: 06/16/2023]
Abstract
Nitrogen deprivation induces variations in fatty acid desaturation in microalgae, which determines the performance of biodiesel and the nutritional value of bioproducts. However, the detailed scenario and the underlying regulatory mechanism remain unclear. In this study, we attempt to outline these scenario and mechanisms by performing biochemical, lipidomic, and transcriptomic analyses in Chlorella pyrenoidosa and functional characterization of transcription factors in Yarrowia lipolytica. We found that early nitrogen deprivation dramatically reduced fatty acid desaturation without increasing lipid content. The contents of palmitic acid (16:0) and oleic acid (18:1) dramatically increased to 2.14 and 2.87 times that of nitrogen repletion on the second day, respectively. Lipidomic analysis showed the transfer of polyunsaturated fatty acids from phospholipids and glycolipids to triacylglycerols, and an increase in lipid species with 16:0 or 18:1 under nitrogen deprivation conditions. Upregulated stearoyl-ACP desaturase and oleyl-ACP thioesterase promoted the synthesis of 18:1, but restricted acetyl-CoA supply revealed that it was the intensive lipid turnover instead of an attenuated Kennedy pathway that played an important role in the variation in fatty acid composition under early nitrogen deprivation. Finally, two differentially expressed SQUAMOSA promoter-binding proteins (SBPs) were heterologously expressed in Y. lipolytica, demonstrating their role in promoting the accumulation of total fatty acid and the reduction in fatty acid desaturation. These results revealed the crucial role of lipid turnover and SBPs in determining fatty acid desaturation under early nitrogen deprivation, opening new avenues for the metabolic engineering of fatty acid desaturation in microalgae.
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Affiliation(s)
- Rui Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
- Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoling Miao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
- Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai, China
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Shi M, Yu L, Shi J, Liu J. A conserved MYB transcription factor is involved in regulating lipid metabolic pathways for oil biosynthesis in green algae. THE NEW PHYTOLOGIST 2022; 235:576-594. [PMID: 35342951 DOI: 10.1111/nph.18119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
Green algae can accumulate high levels of triacylglycerol (TAG), yet knowledge remains fragmented on the regulation of lipid metabolic pathways by transcription factors (TFs). Here, via bioinformatics and in vitro and in vivo analyses, we revealed the roles of a myeloblastosis (MYB) TF in regulating TAG accumulation in green algae. CzMYB1, an R2R3-MYB from Chromochloris zofingiensis, was transcriptionally upregulated upon TAG-inducing conditions and correlated well with many genes involved in the de novo fatty acid synthesis, fatty acid activation and desaturation, membrane lipid turnover, and TAG assembly. Most promoters of these genes were transactivated by CzMYB1 in the yeast one-hybrid assay and contained the binding elements CNGTTA that were recognized by CzMYB1 through the electrophoretic mobility shift assay. CrMYB1, a close homologue of CzMYB1 from Chlamydomonas reinhardtii that recognized similar elements for binding, also transcriptionally correlated with many lipid metabolic genes. Insertional disruption of CrMYB1 severely suppressed the transcriptional expression of CrMYB1, as well as of key lipogenic genes, and impaired TAG level considerably under stress conditions. Our results reveal that this MYB, conserved in green algae, is involved in regulating global lipid metabolic pathways for TAG biosynthesis and accumulation.
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Affiliation(s)
- Meicheng Shi
- Laboratory for Algae Biotechnology & Innovation, College of Engineering, Peking University, Beijing, 100871, China
| | - Lihua Yu
- Laboratory for Algae Biotechnology & Innovation, College of Engineering, Peking University, Beijing, 100871, China
| | - Jianan Shi
- Laboratory for Algae Biotechnology & Innovation, College of Engineering, Peking University, Beijing, 100871, China
| | - Jin Liu
- Laboratory for Algae Biotechnology & Innovation, College of Engineering, Peking University, Beijing, 100871, China
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Lin Y, Dai Y, Xu W, Wu X, Li Y, Zhu H, Zhou H. The Growth, Lipid Accumulation and Fatty Acid Profile Analysis by Abscisic Acid and Indol-3-Acetic Acid Induced in Chlorella sp. FACHB-8. Int J Mol Sci 2022; 23:ijms23074064. [PMID: 35409427 PMCID: PMC8999460 DOI: 10.3390/ijms23074064] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/22/2022] [Accepted: 04/04/2022] [Indexed: 02/05/2023] Open
Abstract
Microalgae are considered a promising source for biodiesel. The addition of plant hormone can exert a significant impact on the production of microalgae biomass and lipid accumulation. Nevertheless, the response of microalgae cells to hormones is species- or strain-dependent. It remains controversial which genes involved in strong increase of fatty acids production in response to abscisic acid (ABA) in Chlorella sp. FACHB-8 strain. We investigated cell growth, lipid accumulation, and fatty acid composition when ABA and indol-3-acetic acid (IAA) were used in the growth medium of Chlorella sp. FACHB-8. The four treatments, including 5 mg/L IAA (E1), 10 mg/L IAA (E2), 10 mg/L ABA (E3), the combination of 5 mg/L IAA and 5 mg/L ABA (E4), were found to increase cell growth, but only 10 mg/L ABA treatment could enhance the lipid accumulation. The fatty acid profile was changed by the addition of ABA, making fatty acids afflux from polyunsaturated fatty acids to monounsaturated and saturated fatty acids, which were suitable for diesel application. Furthermore, a transcriptome analysis was conducted, unraveling the differentially expressed genes enriched in fatty acid biosynthesis, fatty acid metabolism, and biosynthesis of the unsaturated fatty acid pathway in response to ABA. Our results clarified the correlation of fatty acid synthesis-related genes and fatty acid profiles, helping understand the potential response mechanism of Chlorella sp. FACHB-8 strain respond to ABA treatment.
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Affiliation(s)
- Yihua Lin
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (Y.L.); (W.X.); (X.W.); (Y.L.)
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (Y.D.); (H.Z.)
| | - Yue Dai
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (Y.D.); (H.Z.)
| | - Weinan Xu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (Y.L.); (W.X.); (X.W.); (Y.L.)
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (Y.D.); (H.Z.)
| | - Xiaobin Wu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (Y.L.); (W.X.); (X.W.); (Y.L.)
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (Y.D.); (H.Z.)
| | - Yanyan Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (Y.L.); (W.X.); (X.W.); (Y.L.)
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (Y.D.); (H.Z.)
| | - Hongmei Zhu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (Y.D.); (H.Z.)
| | - Hantao Zhou
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (Y.L.); (W.X.); (X.W.); (Y.L.)
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (Y.D.); (H.Z.)
- Correspondence:
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