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Zhang Y, Nair S, Zhang Z, Zhao J, Zhao H, Lu L, Chang L, Jiao N. Adverse Environmental Perturbations May Threaten Kelp Farming Sustainability by Exacerbating Enterobacterales Diseases. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:5796-5810. [PMID: 38507562 DOI: 10.1021/acs.est.3c09921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Globally kelp farming is gaining attention to mitigate land-use pressures and achieve carbon neutrality. However, the influence of environmental perturbations on kelp farming remains largely unknown. Recently, a severe disease outbreak caused extensive kelp mortality in Sanggou Bay, China, one of the world's largest high-density kelp farming areas. Here, through in situ investigations and simulation experiments, we find indications that an anomalously dramatic increase in elevated coastal seawater light penetration may have contributed to dysbiosis in the kelp Saccharina japonica's microbiome. This dysbiosis promoted the proliferation of opportunistic pathogenic Enterobacterales, mainly including the genera Colwellia and Pseudoalteromonas. Using transcriptomic analyses, we revealed that high-light conditions likely induced oxidative stress in kelp, potentially facilitating opportunistic bacterial Enterobacterales attack that activates a terrestrial plant-like pattern recognition receptor system in kelp. Furthermore, we uncover crucial genotypic determinants of Enterobacterales dominance and pathogenicity within kelp tissue, including pathogen-associated molecular patterns, potential membrane-damaging toxins, and alginate and mannitol lysis capability. Finally, through analysis of kelp-associated microbiome data sets under the influence of ocean warming and acidification, we conclude that such Enterobacterales favoring microbiome shifts are likely to become more prevalent in future environmental conditions. Our study highlights the need for understanding complex environmental influences on kelp health and associated microbiomes for the sustainable development of seaweed farming.
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Affiliation(s)
- Yongyu Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, Shandong, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao 266101, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, Shandong, China
| | - Shailesh Nair
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, Shandong, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao 266101, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, Shandong, China
| | - Zenghu Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, Shandong, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao 266101, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, Shandong, China
| | - Jiulong Zhao
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, Shandong, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao 266101, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, Shandong, China
| | - Hanshuang Zhao
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, Shandong, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Longfei Lu
- Weihai Changqing Ocean Science Technology Co., Ltd., Rongcheng 264300, China
| | - Lirong Chang
- Weihai Changqing Ocean Science Technology Co., Ltd., Rongcheng 264300, China
| | - Nianzhi Jiao
- Institute of Marine Microbes and Ecospheres, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361100, China
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Lee HK, Woo S, Baek D, Min M, Jung GY, Lim HG. Direct and robust citramalate production from brown macroalgae using fast-growing Vibrio sp. dhg. BIORESOURCE TECHNOLOGY 2024; 394:130304. [PMID: 38211713 DOI: 10.1016/j.biortech.2024.130304] [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: 11/22/2023] [Revised: 12/29/2023] [Accepted: 01/06/2024] [Indexed: 01/13/2024]
Abstract
Brown macroalgae is a promising feedstock for biorefinery owing to its high biomass productivity and contents of carbohydrates such as alginate and mannitol. However, the limited availability of microbial platforms efficiently catabolizing the brown macroalgae sugars has restricted its utilization. In this study, the direct production of citramalate, an important industrial compound, was demonstrated from brown macroalgae by utilizing Vibrio sp. dhg, which has a remarkably efficient catabolism of alginate and mannitol. Specifically, citramalate synthase from Methanocaldococcus jannaschii was synthetically expressed, and competing pathways were removed to maximally redirect the carbon flux toward citramalate production. Notably, a resulting strain, VXHC, produced citramalate up to 9.8 g/L from a 20 g/L mixture of alginate and mannitol regardless of their ratios. Citramalate was robustly produced even when diverse brown macroalgae were provided directly. Collectively, this study showcased the high potential of brown macroalgae biorefinery using Vibrio sp. dhg.
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Affiliation(s)
- Hye Kyung Lee
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Sunghwa Woo
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Dongyeop Baek
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Myeongwon Min
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea; Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea.
| | - Hyun Gyu Lim
- Department of Biological Engineering, Inha University, 100 Inha-Ro, Michuhol-Gu, Incheon 22212, Korea.
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Lu C, Zhang P, Li S, Cheng M, Duan D. Isolation and characterization of glutathione S-transferase genes and their transcripts in Saccharina japonica (Laminariales, Phaeophyceae) during development and under abiotic stress. BMC PLANT BIOLOGY 2023; 23:436. [PMID: 37723443 PMCID: PMC10506224 DOI: 10.1186/s12870-023-04430-5] [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: 02/01/2023] [Accepted: 08/31/2023] [Indexed: 09/20/2023]
Abstract
BACKGROUND Glutathione S-transferase (GST) is a crucial enzyme for metabolism, detoxification, and stress resistance in organisms. Many GSTs have been identified in seaweeds, but the isolation and functional analysis of GSTs in Saccharina japonica have not been completed. RESULT In this study, a total of 32 SjGST genes, localized on 10 scaffolds and 6 contigs, were identified and categorized into three groups. Most of these SjGSTs were presumed to be distributed in the cytoplasm. Tandem duplication had a significant influence on the expansion of the SjGST gene family. Functional analysis of cis-acting elements in the promoter regions demonstrated that SjGSTs enhance the stress resistance of the kelp. Quantitative real-time PCR tests confirmed that SjGSTs positively influence S. japonica sporophytes under stress from low salinity, drought, and high temperature. Recombinant yeast tests further affirmed the role of SjGSTs in stress resistance; SjGSTs improved the growth rate of recombinant yeast under 1.5 M NaCl or 8 mM H2O2. Analysis of biochemical parameters indicated that the optimum temperatures for SjGST20 and SjGST22 were 20 °C, and the optimum pH values were 7.0 and 8.0 for SjGST20 and SjGST22, respectively. The Km values for the substrate 1-chloro-2,4-dinitrobenzene (CDNB) were 2.706 mM and 0.674 mM and were 6.146 mM and 3.559 mM for the substrate glutathione (GSH) for SjGST20 and SjGST22, respectively. CONCLUSION SjGSTs are important stress resistant genes in S. japonica. This research results will enhance our understanding the function of GSTs in brown seaweeds, and explained its functional roles in stress resistance in marine environments.
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Affiliation(s)
- Chang Lu
- Key Lab of Breeding Biotechnology & Sustainable Aquaculture, Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China
- Department of Biological Engineering, College of Life Science, Yantai University, Yantai, 264005, China
| | - Pengyan Zhang
- Functional Lab for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- Division of Mariculture Ecology and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Shuang Li
- Key Lab of Breeding Biotechnology & Sustainable Aquaculture, Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China
- Functional Lab for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Mengzhen Cheng
- Key Lab of Breeding Biotechnology & Sustainable Aquaculture, Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China
- Functional Lab for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Delin Duan
- Key Lab of Breeding Biotechnology & Sustainable Aquaculture, Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China.
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Graf L, Shin Y, Yang JH, Hwang IK, Yoon HS. Transcriptome analysis reveals the spatial and temporal differentiation of gene expression in the sporophyte of Undaria pinnatifida. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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An ML, Miao JL. Genetic and Molecular Characterization of a Dash Cryptochrome Homologous Gene from Antarctic Diatom Phaeodactylum tricornutum ICE-H. Mol Biol 2022. [DOI: 10.1134/s0026893322060024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Shao Z, Duan D. The Cell Wall Polysaccharides Biosynthesis in Seaweeds: A Molecular Perspective. FRONTIERS IN PLANT SCIENCE 2022; 13:902823. [PMID: 35620682 PMCID: PMC9127767 DOI: 10.3389/fpls.2022.902823] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/15/2022] [Indexed: 05/16/2023]
Abstract
Cell wall polysaccharides (CWPS) of seaweeds play crucial roles in mechanical shear resistance, cell-cell adhesion and the interactions with changeable marine environments. They have diverse applications in food, cosmetics, agriculture, pharmaceuticals and therapeutics. The recent boost of multi-omics sequence analysis has rapidly progressed the mining of presumed genes encoding enzymes involved in CWPS biosynthesis pathways. In this review, we summarize the biosynthetic pathways of alginate, fucoidan, agar, carrageenan and ulvan in seaweeds referred to the literatures on published genomes and biochemical characterization of encoded enzymes. Some transcriptomic data were briefly reported to discuss the correlation between gene expression levels and CWPS contents. Mannuronan C-5 epimerase (MC5E) and carbohydrate sulfotransferase (CST) are crucial enzymes for alginate and sulfated CWPS, respectively. Nonetheless, most CWPS-relevant genes were merely investigated by gene mining and phylogenetic analysis. We offer an integrative view of CWPS biosynthesis from a molecular perspective and discuss about the underlying regulation mechanism. However, a clear understanding of the relationship between chemical structure and bioactivities of CWPS is limited, and reverse genetic manipulation and effective gene editing tools need to be developed in future.
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Affiliation(s)
- Zhanru Shao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Delin Duan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- State Key Laboratory of Bioactive Seaweed Substances, Qingdao Bright Moon Seaweed Group Co., Ltd., Qingdao, China
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Zhang C, Ren H, Yao X, Wang K, Chang J. Comparative Transcriptome Analysis Reveals Differential Regulation of Flavonoids Biosynthesis Between Kernels of Two Pecan Cultivars. FRONTIERS IN PLANT SCIENCE 2022; 13:804968. [PMID: 35283902 PMCID: PMC8914201 DOI: 10.3389/fpls.2022.804968] [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: 10/29/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Flavonoids influence the flavor and nutritional value of pecan nuts. However, limited information is available regarding the molecular mechanisms underlying pecan flavonoid biosynthesis. Here, we used a high ("YLC28") and a low ("Oconee") flavonoid content cultivar as the research objects. The changes in flavonoid content and the gene transcription patterns during kernel development were identified. Different accumulation patterns of total flavonoids (TF) and condensed tannins (CT) were observed between the two cultivars. The contents of TF and CT in "YLC28" were 1.76- and 2.67-fold higher levels than that of "Oconee" on 150 days after full bloom of female flowers, respectively. In total, 30 RNA-Seq libraries were constructed and sequenced. The upregulated genes in "YLC28" were highly enriched in flavonoid-related pathways. Thirty-three structural genes were identified, and the expression of two phenylalanine ammonia lyases, one chalcone synthase, one flavonoid 3',5'-hydroxylase, and one flavonol synthase exhibited high correlation (r ≥ 0.7, p < 0.01) with the condensed tannin content in "YLC28." A putative MYB transcription factor, CIL1093S0100, might act as a flavonoid biosynthesis repressor during kernel development. Altogether, these results will be useful for uncovering the molecular mechanisms of flavonoid biosynthesis and subsequently accelerating quality pecan breeding.
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Fournier GP, Parsons CW, Cutts EM, Tamre E. Standard Candles for Dating Microbial Lineages. Methods Mol Biol 2022; 2569:41-74. [PMID: 36083443 DOI: 10.1007/978-1-0716-2691-7_3] [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] [Indexed: 05/24/2023]
Abstract
Molecular clock analyses are challenging for microbial phylogenies, due to a lack of fossil calibrations that can reliably provide absolute time constraints. An alternative source of temporal constraints for microbial groups is provided by the inheritance of proteins that are specific for the utilization of eukaryote-derived substrates, which have often been dispersed across the Tree of Life via horizontal gene transfer. In particular, animal, algal, and plant-derived substrates are often produced by groups with more precisely known divergence times, providing an older-bound on their availability within microbial environments. Therefore, these ages can serve as "standard candles" for dating microbial groups across the Tree of Life, expanding the reach of informative molecular clock investigations. Here, we formally develop the concept of substrate standard candles and describe how they can be propagated and applied using both microbial species trees and individual gene family phylogenies. We also provide detailed evaluations of several candidate standard candles and discuss their suitability in light of their often complex evolutionary and metabolic histories.
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Affiliation(s)
- Gregory P Fournier
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Chris W Parsons
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Elise M Cutts
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Erik Tamre
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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Pengyan Z, Chang L, Zhanru S, Fuli L, Jianting Y, Delin D. Genome-wide transcriptome profiling and characterization of mannuronan C5-epimerases in Saccharina japonica. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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Yang X, Wang X, Yao J, Duan D. Genome-Wide Mapping of Cytosine Methylation Revealed Dynamic DNA Methylation Patterns Associated with Sporophyte Development of Saccharina japonica. Int J Mol Sci 2021; 22:9877. [PMID: 34576045 PMCID: PMC8472486 DOI: 10.3390/ijms22189877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/27/2021] [Accepted: 09/08/2021] [Indexed: 02/04/2023] Open
Abstract
Cytosine methylation plays vital roles in regulating gene expression and plant development. However, the function of DNA methylation in the development of macroalgae remains unclear. Through the genome-wide bisulfite sequencing of cytosine methylation in holdfast, stipe and blade, we obtained the complete 5-mC methylation landscape of Saccharina japonica sporophyte. Our results revealed that the total DNA methylation level of sporophyte was less than 0.9%, and the content of CHH contexts was dominant. Moreover, the distribution of CHH methylation within the genes exhibited exon-enriched characteristics. Profiling of DNA methylation in three parts revealed the diverse methylation pattern of sporophyte development. These pivotal DMRs were involved in cell motility, cell cycle and cell wall/membrane biogenesis. In comparison with stipe and blade, hypermethylation of mannuronate C5-epimerase in holdfast decreased the transcript abundance, which affected the synthesis of alginate, the key component of cell walls. Additionally, 5-mC modification participated in the regulation of blade and holdfast development by the glutamate content respectively via glutamine synthetase and amidophosphoribosyl transferase, which may act as the epigenetic regulation signal. Overall, our study revealed the global methylation characteristics of the well-defined holdfast, stipe and blade, and provided evidence for epigenetic regulation of sporophyte development in brown macroalgae.
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Affiliation(s)
- Xiaoqi Yang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Y.); (X.W.); (J.Y.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiuliang Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Y.); (X.W.); (J.Y.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Jianting Yao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Y.); (X.W.); (J.Y.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Delin Duan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Y.); (X.W.); (J.Y.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
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Role and Evolution of the Extracellular Matrix in the Acquisition of Complex Multicellularity in Eukaryotes: A Macroalgal Perspective. Genes (Basel) 2021; 12:genes12071059. [PMID: 34356075 PMCID: PMC8307928 DOI: 10.3390/genes12071059] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/05/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022] Open
Abstract
Multicellular eukaryotes are characterized by an expanded extracellular matrix (ECM) with a diversified composition. The ECM is involved in determining tissue texture, screening cells from the outside medium, development, and innate immunity, all of which are essential features in the biology of multicellular eukaryotes. This review addresses the origin and evolution of the ECM, with a focus on multicellular marine algae. We show that in these lineages the expansion of extracellular matrix played a major role in the acquisition of complex multicellularity through its capacity to connect, position, shield, and defend the cells. Multiple innovations were necessary during these evolutionary processes, leading to striking convergences in the structures and functions of the ECMs of algae, animals, and plants.
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Dai Y, Sun X, Wang C, Li F, Zhang S, Zhang H, Li G, Yuan L, Chen G, Sun R, Zhang S. Gene co-expression network analysis reveals key pathways and hub genes in Chinese cabbage (Brassica rapa L.) during vernalization. BMC Genomics 2021; 22:236. [PMID: 33823810 PMCID: PMC8022416 DOI: 10.1186/s12864-021-07510-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 03/05/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Vernalization is a type of low temperature stress used to promote rapid bolting and flowering in plants. Although rapid bolting and flowering promote the reproduction of Chinese cabbages (Brassica rapa L. ssp. pekinensis), this process causes their commercial value to decline. Clarifying the mechanisms of vernalization is essential for its further application. We performed RNA sequencing of gradient-vernalization in order to explore the reasons for the different bolting process of two Chinese cabbage accessions during vernalization. RESULTS There was considerable variation in gene expression between different-bolting Chinese cabbage accessions during vernalization. Comparative transcriptome analysis and weighted gene co-expression network analysis (WGCNA) were performed for different-bolting Chinese cabbage during different vernalization periods. The biological function analysis and hub gene annotation of highly relevant modules revealed that shoot system morphogenesis and polysaccharide and sugar metabolism caused early-bolting 'XBJ' to bolt and flower faster; chitin, ABA and ethylene-activated signaling pathways were enriched in late-bolting 'JWW'; and leaf senescence and carbohydrate metabolism enrichment were found in the two Chinese cabbage-related modules, indicating that these pathways may be related to bolting and flowering. The high connectivity of hub genes regulated vernalization, including MTHFR2, CPRD49, AAP8, endoglucanase 10, BXLs, GATLs, and WRKYs. Additionally, five genes related to flower development, BBX32 (binds to the FT promoter), SUS1 (increases FT expression), TSF (the closest homologue of FT), PAO and NAC029 (plays a role in leaf senescence), were expressed in the two Chinese cabbage accessions. CONCLUSION The present work provides a comprehensive overview of vernalization-related gene networks in two different-bolting Chinese cabbages during vernalization. In addition, the candidate pathways and hub genes related to vernalization identified here will serve as a reference for breeders in the regulation of Chinese cabbage production.
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Affiliation(s)
- Yun Dai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Changjiang West Road, NO.130, Hefei, 230036, Anhui, China
| | - Xiao Sun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chenggang Wang
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Changjiang West Road, NO.130, Hefei, 230036, Anhui, China
| | - Fei Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shifan Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guoliang Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lingyun Yuan
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Changjiang West Road, NO.130, Hefei, 230036, Anhui, China
| | - Guohu Chen
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Changjiang West Road, NO.130, Hefei, 230036, Anhui, China
| | - Rifei Sun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shujiang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Zhang X, Fan X, Wang Y, Xu D, Zhang J, Ye N. Exploring Core Response Mechanisms to Multiple Environmental Stressors Via A Genome-Wide Study in the Brown Alga Saccharina japonica (Laminariales, Phaeophyceae). JOURNAL OF PHYCOLOGY 2021; 57:345-354. [PMID: 33211355 DOI: 10.1111/jpy.13108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 09/22/2020] [Accepted: 10/23/2020] [Indexed: 06/11/2023]
Abstract
Saccharina japonica is an important large brown alga and a major component of productive beds on the northwest coast of the Pacific Ocean. Abiotic stress response mechanisms are receiving considerable attention because global climate change is increasing their abiotic stress levels. However, our knowledge of how S. japonica broadly responds to stress is limited. In this study, we investigated the S. japonica responsive genes underlying acclimation to diverse stressors of acidification, high light, high temperature, hypersalinity, and hyposalinity and identified 408 core genes constantly and differentially expressed in response to all stressors. Our results confirm that stressors had strong effects on genes participating in photosynthesis, amino acid metabolism, carbohydrate metabolism, halogen metabolism, and reactive oxygen species defense. These findings will improve our understanding of brown algal response mechanisms linked to environmental stress and provide a list of candidate genes for improving algal stress tolerance in light of environmental stress in future studies.
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Affiliation(s)
- Xiaowen Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China
| | - Xiao Fan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China
| | - Yitao Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China
| | - Dong Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China
| | - Jian Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China
| | - Naihao Ye
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China
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14
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Guzinski J, Ruggeri P, Ballenghien M, Mauger S, Jacquemin B, Jollivet C, Coudret J, Jaugeon L, Destombe C, Valero M. Seascape Genomics of the Sugar Kelp Saccharina latissima along the North Eastern Atlantic Latitudinal Gradient. Genes (Basel) 2020; 11:E1503. [PMID: 33322137 PMCID: PMC7763533 DOI: 10.3390/genes11121503] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 12/23/2022] Open
Abstract
Temperature is one of the most important range-limiting factors for many seaweeds. Driven by the recent climatic changes, rapid northward shifts of species' distribution ranges can potentially modify the phylogeographic signature of Last Glacial Maximum. We explored this question in detail in the cold-tolerant kelp species Saccharina latissima, using microsatellites and double digest restriction site-associated DNA sequencing ( ddRAD-seq) derived single nucleotide polymorphisms (SNPs) to analyze the genetic diversity and structure in 11 sites spanning the entire European Atlantic latitudinal range of this species. In addition, we checked for statistical correlation between genetic marker allele frequencies and three environmental proxies (sea surface temperature, salinity, and water turbidity). Our findings revealed that genetic diversity was significantly higher for the northernmost locality (Spitsbergen) compared to the southern ones (Northern Iberia), which we discuss in light of the current state of knowledge on phylogeography of S. latissima and the potential influence of the recent climatic changes on the population structure of this species. Seven SNPs and 12 microsatellite alleles were found to be significantly associated with at least one of the three environmental variables. We speculate on the putative adaptive functions of the genes associated with the outlier markers and the importance of these markers for successful conservation and aquaculture strategies for S. latissima in this age of rapid global change.
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Affiliation(s)
- Jaromir Guzinski
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone KT15 3NB, Surrey, UK
| | - Paolo Ruggeri
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
- Xelect ltd, Horizon House, Abbey Walk, St Andrews KY16 9LB, Scotland, UK
| | - Marion Ballenghien
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
- UMR 7144, Adaptation et Diversité en Milieu Marin, CNRS, Sorbonne Université, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France
| | - Stephane Mauger
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
| | - Bertrand Jacquemin
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
- CEVA, 83 Presqu’île de Pen Lan, 22610 Pleubian, France
| | - Chloe Jollivet
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
- Ecole polytechnique de Lausanne (EPFL), SV-IBI UPOATES, Route cantonale, CH-1015 Lausanne, Switzerland
| | - Jerome Coudret
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
| | - Lucie Jaugeon
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
| | - Christophe Destombe
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
| | - Myriam Valero
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
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15
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Zhang L, Cao Z, Liang G, Li X, Wu H, Yang G. Comparative Transcriptome Analysis Reveals Candidate Genes Related to Structural and Storage Carbohydrate Biosynthesis in Kelp Saccharina japonica (Laminariales, Phaeophyceae). JOURNAL OF PHYCOLOGY 2020; 56:1168-1183. [PMID: 32408392 DOI: 10.1111/jpy.13016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
Saccharina japonica is a brown macroalga that has been commercially cultivated in China for almost a century. As a natural raw material, it is widely used in the food and pharmaceutical industries, and it may potentially be useful for biofuel production. However, little is known about the genes involved in carbohydrate biosynthesis, and their regulation is less understood. In this study, the analysis of growth traits and alginate and mannitol contents suggested that sporophyte development could be divided into four stages. Accordingly, we performed transcriptome analysis of the S. japonica sporophyte. In total, 589 million clean reads were generated, and 4,514 novel genes were identified. Gene expression analysis revealed that 2,542 genes were differentially expressed. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis indicated that these genes were significantly enriched in "Carbon metabolism," "Photosynthesis," and "Photosynthesis-antenna proteins" pathways, which are important for metabolism of various carbohydrates during sporophyte development. Systematic analysis identified the genes encoding enzymes for the biosynthesis of cell wall carbohydrates (including alginate, fucoidan, and cellulose) and cytoplasm storage carbohydrates (mannitol, laminarin, and trehalose). Among them, some key genes associated with carbohydrate content were further identified based on detailed expression profiling, representing good candidates for further functional studies. This study provides a global view of the carbohydrate metabolism process and an important resource for functional genomics studies in S. japonica. The results obtained lay the basis for elucidating the molecular mechanism of carbohydrate biosynthesis and for genetic breeding of carbohydrates-related traits in kelp.
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Affiliation(s)
- Linan Zhang
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Zengmei Cao
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd., Yantai, 264003, China
| | - Guangjin Liang
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd., Yantai, 264003, China
| | - Xiaojie Li
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd., Yantai, 264003, China
| | - Hao Wu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Guanpin Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
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Landi S, Esposito S. Bioinformatic Characterization of Sulfotransferase Provides New Insights for the Exploitation of Sulfated Polysaccharides in Caulerpa. Int J Mol Sci 2020; 21:ijms21186681. [PMID: 32932673 PMCID: PMC7554865 DOI: 10.3390/ijms21186681] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/01/2020] [Accepted: 09/11/2020] [Indexed: 12/19/2022] Open
Abstract
Caulerpa is an unusual algal genus from Caulerpaceae (Chlorophyta, Bryopsidales). Species from this family produce a wide range of metabolites suitable for biotechnology applications. Among these, sulfated polysaccharides (SPs) are often highly desirable for pharmaceutical and nutraceutical applications. Here, we provide a classification of sulfotransferases from Caulerpa; these important enzymes catalyze the nodal step for the biosynthesis of SPs. For this, we performed phylogenetic, genomic, expression analyses and prediction of the protein structure on sulfotransferases from Caulerpa. Sequences, domains and structures of sulfotransferases generally shared common characteristics with other plants and algae. However, we found an extensive duplication of sulfotransferase gene family, which is unique among the green algae. Expression analysis revealed specific transcript abundance in the pinnae and rachis of the alga. The unique genomic features could be utilized for the production of complex SPs, which require multiple and specific sulfation reactions. The expansion of this gene family in Caulerpaceae would have resulted in a number of proteins characterizing the unique SPs found in these algae. We provide a putative biosynthetic pathway of SPs, indicating the unique characteristics of this pathway in Caulerpa species. These data may help in the future selection of Caulerpa species for both commercial applications and genetic studies to improve the synthesis of valuable products from Caulerpa.
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Lu C, Shao Z, Zhang P, Duan D. Genome-wide analysis of the Saccharina japonica sulfotransferase genes and their transcriptional profiles during whole developmental periods and under abiotic stresses. BMC PLANT BIOLOGY 2020; 20:271. [PMID: 32527219 PMCID: PMC7291590 DOI: 10.1186/s12870-020-02422-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/29/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND As a unique sulfated polysaccharide, fucoidan is an important component of cell wall in brown seaweeds. Its biochemical properties are determined by the positions and quantity of sulfate groups. Sulfotransferases (STs) catalyze the sulfation process, which transfer the sulfuryl groups to carbohydrate backbones and are crucial for fucoidan biosynthesis. Nevertheless, the structures and functions of STs in brown seaweeds are rarely investigated. RESULTS There are a total of 44 ST genes identified from our genome and transcriptome analysis of Saccharina japonica, which were located in the 17 scaffolds and 11 contigs. The S. japonica ST genes have abundant introns and alternative splicing sites, and five tandem duplicated gene clusters were identified. Generally, the ST genes could be classified into five groups (Group I ~ V) based on phylogenetic analysis. Accordingly, the ST proteins, which were encoded by genes within the same group, contained similar conserved motifs. Members of the S. japonica ST gene family show various expression patterns in different tissues and developmental stages. Transcriptional profiles indicate that the transcriptional levels of more than half of the ST genes are higher in kelp basal blades than in distal blades. Except for ST5 and ST28, most ST genes are down-regulated with the kelp development stages. The expression levels of nine ST genes were detected by real-time quantitative PCR, which demonstrates that they responded to low salinity and drought stresses. CONCLUSIONS Various characteristics of the STs allow the feasibilities of S. japonica to synthesize fucoidans with different sulfate groups. This enables the kelp the potential to adapt to the costal environments and meet the needs of S. japonica growth.
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Affiliation(s)
- Chang Lu
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 P. R. China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049 P. R. China
| | - Zhanru Shao
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 P. R. China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 P. R. China
| | - Pengyan Zhang
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 P. R. China
- Division of Mariculture Ecology and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071 China
| | - Delin Duan
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 P. R. China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 P. R. China
- State Key Laboratory of Bioactive Seaweed Substances, Qingdao Bright Moon Seaweed Group Co Ltd, Qingdao, 266400 P. R. China
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Zayed A, Ulber R. Fucoidans: Downstream Processes and Recent Applications. Mar Drugs 2020; 18:E170. [PMID: 32197549 PMCID: PMC7142712 DOI: 10.3390/md18030170] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/14/2020] [Accepted: 03/15/2020] [Indexed: 02/06/2023] Open
Abstract
Fucoidans are multifunctional marine macromolecules that are subjected to numerous and various downstream processes during their production. These processes were considered the most important abiotic factors affecting fucoidan chemical skeletons, quality, physicochemical properties, biological properties and industrial applications. Since a universal protocol for fucoidans production has not been established yet, all the currently used processes were presented and justified. The current article complements our previous articles in the fucoidans field, provides an updated overview regarding the different downstream processes, including pre-treatment, extraction, purification and enzymatic modification processes, and shows the recent non-traditional applications of fucoidans in relation to their characters.
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Affiliation(s)
- Ahmed Zayed
- Institute of Bioprocess Engineering, Technical University of Kaiserslautern, Gottlieb-Daimler-Straße 49, 67663 Kaiserslautern, Germany;
- Department of Pharmacognosy, Tanta University, College of Pharmacy, El Guish Street, Tanta 31527, Egypt
| | - Roland Ulber
- Institute of Bioprocess Engineering, Technical University of Kaiserslautern, Gottlieb-Daimler-Straße 49, 67663 Kaiserslautern, Germany;
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