Comparative omics study of Spirulinaplatensis mutants based on ARTP mutagenesis breeding system

doi:10.11949/0438-1157.20211340

CIESC Journal ›› 2021, Vol. 72 ›› Issue (12): 6298-6310.DOI: 10.11949/0438-1157.20211340

• Biochemical engineering and technology • Previous Articles Next Articles

Comparative omics study of Spirulinaplatensis mutants based on ARTP mutagenesis breeding system

Nan SU¹(),Yinan WU¹(),Yinyee TAN¹,Lihua JIN²,Chong ZHANG¹,Aikawa SHIMPEI³,Hasunuma TOMOHISA³,Kondo AKIHIKO³,Xinhui XING^1,^4,⁵()

^1.Institute of Biochemical Engineering, Department of Chemical Engineering, Key Laboratory for Industrial Biocatalysis, Ministry of Education, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
^2.Department of Biotechnology, Beijing Electronic Science and Technology Vocational College, Beijing 100029, China
^3.Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Japan
^4.Institute of Biomedicine and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong, China
^5.Medical and Health Technology and Engineering Institute, Shenzhen Bay Laboratory, Shenzhen 518055, Guangdong, China

Received:2021-09-16 Revised:2021-11-23 Online:2021-12-22 Published:2021-12-05
Contact: Xinhui XING

ARTP诱变钝顶螺旋藻突变体比较组学研究

苏楠¹(),吴亦楠¹(),陈韵亿¹,金丽华²,张翀¹,Aikawa Shimpei³,Hasunuma Tomohisa³,Kondo Akihiko³,邢新会^1,^4,⁵()

^1.清华大学化学工程系生物化工研究所，工业生物催化教育部重点实验室，合成与系统生物学中心，北京 100084
^2.北京电子科技职业技术学院生物技术系，北京 100029
^3.神户大学工程研究生院，化学科学与工程系，日本神户 657-8501
^4.清华大学深圳国际研究生院生物医药与健康工程研究院，广东深圳 518055
^5.深圳湾实验室医药健康技术与工程研究所，广东深圳 518055

通讯作者: 邢新会
作者简介:苏楠（1983—），男，博士，sunan12345@126.com|吴亦楠（1992—），男，博士，wuyinan1992@qq.com
基金资助:
国家重点研发计划项目(2016YFD0102106);国家自然科学基金委国家重大科研仪器设备研制专项(21627812)

Abstract

Abstract:

As an important biological resource on the earth, microalgae provides a large number of primary metabolites for the hydrosphere, and is an important chassis microorganism for the research and application of synthetic biology and biological manufacturing. Spirulina platensis is one of the cyanobacteria that has advantages of high polysaccharide content, high nutritional value, mature culture technology and wide application. The mutagenesis breeding and comparative omics studies can provide important basis for the development of microalgae cell-factory system modification. With atmospheric and room temperature plasmas (ARTP) mutagenesis method, we obtained three S. platensis mutants. By continuous light culture in this study, we characterized the mutants' important physiological characteristics. It was found that the mutants have much higher flocculation intensity than wild strain and differences in important metabolites content. Furthermore, through the mutants' metabolomic analysis and whole genome sequencing, we preliminarily analyzed the mechanism related to mutant phenotype.

Key words: Spirulina platensis, flocculation, ARTP mutagenesis, metabolomics, comparative genomics analysis, bioenergy, biological engineering, biotechnology

摘要：

微藻作为地球上重要的生物资源，为水圈提供了大量的初级代谢产物，是合成生物学和生物制造研究和应用的重要底盘微生物。其中，钝顶螺旋藻(Spirulina platensis)具有多糖含量高、营养价值高、培养工艺成熟、应用范围广等特点，其诱变育种及比较组学研究可为微藻细胞工厂系统改造技术发展提供重要依据。本课题组前期通过常压室温等离子体(atmospheric and room temperature plasmas，ARTP)诱变方法获得了三株钝顶螺旋藻突变体。本研究在连续光照培养条件下，对三株突变体的重要生理特征进行了表征，发现突变株具有高絮凝表型，且重要化合物含量也与野生型具有一定的差异。进一步，本研究通过对其主要代谢产物的代谢组学分析和全基因组测序，对突变表型产生的机理进行了初步解析。

关键词: 钝顶螺旋藻, 絮凝, ARTP诱变, 代谢组学, 基因组比较组学, 生物能源, 生物工程, 生物技术

CLC Number:

Q 819

Nan SU, Yinan WU, Yinyee TAN, Lihua JIN, Chong ZHANG, Aikawa SHIMPEI, Hasunuma TOMOHISA, Kondo AKIHIKO, Xinhui XING. Comparative omics study of Spirulinaplatensis mutants based on ARTP mutagenesis breeding system[J]. CIESC Journal, 2021, 72(12): 6298-6310.

苏楠, 吴亦楠, 陈韵亿, 金丽华, 张翀, Aikawa Shimpei, Hasunuma Tomohisa, Kondo Akihiko, 邢新会. ARTP诱变钝顶螺旋藻突变体比较组学研究[J]. 化工学报, 2021, 72(12): 6298-6310.

Figures/Tables 16

References 31

1	Miyamoto K. Renewable Biological Systems for Alternative Sustainable Energy Production[M]. Netherlands: Elsevier Ltd., 1997.
2	Jagadevan S, Banerjee A, Banerjee C, et al. Recent developments in synthetic biology and metabolic engineering in microalgae towards biofuel production[J]. Biotechnology for Biofuels, 2018, 11: 185.
3	Casazza A A, Spennati E, Converti A, et al. Production of carbon-based biofuels by pyrolysis of exhausted Arthrospira platensis biomass after protein or lipid recovery[J]. Fuel Processing Technology, 2020, 201: 106336.
4	Khan M I, Shin J H, Kim J D. The promising future of microalgae: current status, challenges, and optimization of a sustainable and renewable industry for biofuels, feed, and other products[J]. Microbial Cell Factories, 2018, 17(1): 36.
5	Liestianty D, Rodianawati I, Arfah R A, et al. Nutritional analysis of Spirulina sp. to promote as superfood candidate[J]. IOP Conference Series: Materials Science and Engineering, 2019, 509: 012031.
6	Nasirian F, Dadkhah M, Moradi-Kor N, et al. Effects of Spirulina platensis microalgae on antioxidant and anti-inflammatory factors in diabetic rats[J]. Diabetes, Metabolic Syndrome and Obesity: Targets and Therapy, 2018, 11: 375-380.
7	Aydi S S, Aydi S, Ben Abdallah Kolsi R, et al. CO₂ enrichment: enhancing antioxidant, antibacterial and anticancer activities in Arthrospira platensis[J]. Food Bioscience, 2020, 35: 100575.
8	Saranraj P, Sivasakthi S. Spirulina platensis-food for future: a review[J]. Asian J. Pharm. Sci. Technol., 2014, 4(1): 26-33.
9	Mukhopadhyay C D. Engineering spirulina for enhanced medicinal application[M]//Algal Biorefinery: An Integrated Approach. Cham: Springer International Publishing, 2015: 235-252.
10	Saini D K, Chakdar H, Pabbi S, et al. Enhancing production of microalgal biopigments through metabolic and genetic engineering[J]. Critical Reviews in Food Science and Nutrition, 2020, 60(3): 391-405.
11	Ragusa I, Nardone G N, Zanatta S, et al. Spirulina for skin care: a bright blue future[J]. Cosmetics, 2021, 8(1): 7.
12	Rempel A, de Souza Sossella F, Margarites A C, et al. Bioethanol from Spirulina platensis biomass and the use of residuals to produce biomethane: an energy efficient approach[J]. Bioresource Technology, 2019, 288: 121588.
13	Kawata Y, Yano S, Kojima H, et al. Transformation of Spirulina platensis strain C1 (Arthrospira sp. PCC9438) with Tn5 transposase-transposon DNA-cation liposome complex[J]. Marine Biotechnology, 2004, 6(4): 355-363.
14	Dehghani J, Adibkia K, Movafeghi A, et al. Stable transformation of Spirulina (Arthrospira) platensis: a promising microalga for production of edible vaccines[J]. Applied Microbiology and Biotechnology, 2018, 102(21): 9267-9278.
15	Jeamton W, Dulsawat S, Tanticharoen M, et al. Overcoming intrinsic restriction enzyme barriers enhances transformation efficiency in Arthrospira platensis C1[J]. Plant and Cell Physiology, 2017, 58(4): 822-830.
16	Cheevadhanarak S, Paithoonrangsarid K, Prommeenate P, et al. Draft genome sequence of Arthrospira platensis C1 (PCC9438)[J]. Standards in Genomic Sciences, 2012, 6(1): 43-53.
17	殷春涛, 胡鸿钧, 李夜光, 等. 中温螺旋藻新品系的选育研究[J]. 武汉植物学研究, 1997, 15(3): 250-254.
	Yin C T, Hu H J, Li Y G, et al. Studies on middle temperature strains selection of Spirulina platensis[J]. Journal of Wuhan Botanical Research, 1997, 15(3): 250-254.
18	李建宏, 郑卫, 倪霞, 等. 两株钝顶螺旋藻紫外诱变株的特征[J]. 水生生物学报, 2001, 25(5): 486-490.
	Li J H, Zheng W, Ni X, et al. Characteristics of two Spirulina platensis mutants induced by ultraviolet[J]. Acta Hydrobiologica Sinica, 2001, 25(5): 486-490.
19	Fang M, Jin L, Zhang C, et al. Rapid mutation of Spirulina platensis by a new mutagenesis system of atmospheric and room temperature plasmas (ARTP) and generation of a mutant library with diverse phenotypes[J]. PLoS One, 2013, 8(10): e77046.
20	Shirnalli G G, Kaushik M S, Kumar A, et al. Isolation and characterization of high protein and phycocyanin producing mutants of Arthrospira platensis[J]. Journal of Basic Microbiology, 2018, 58(2): 162-171.
21	Cheng J, Lu H X, He X, et al. Mutation of Spirulina sp. by nuclear irradiation to improve growth rate under 15% carbon dioxide in flue gas[J]. Bioresource Technology, 2017, 238: 650-656.
22	Zhu Y X, Cheng J, Zhang Z, et al. Mutation of Arthrospira platensis by gamma irradiation to promote phenol tolerance and CO₂ fixation for coal-chemical flue gas reduction[J]. Journal of CO₂ Utilization, 2020, 38: 252-261.
23	An J, Gao F L, Ma Q Y, et al. Screening for enhanced astaxanthin accumulation among Spirulina platensis mutants generated by atmospheric and room temperature plasmas[J]. Algal Research, 2017, 25: 464-472.
24	Fujisawa T, Narikawa R, Okamoto S, et al. Genomic structure of an economically important cyanobacterium, Arthrospira (Spirulina) platensis NIES-39[J]. DNA Research, 2010, 17(2): 85-103.
25	Cheng J, Lu H X, Li K, et al. Enhancing growth-relevant metabolic pathways of Arthrospira platensis (CYA-1) with gamma irradiation from ⁶⁰Co[J]. RSC Advances, 2018, 8(30): 16824-16833.
26	Kurdrid P, Senachak J, Sirijuntarut M, et al. Comparative analysis of the Spirulina platensis subcellular proteome in response to low- and high-temperature stresses: uncovering cross-talk of signaling components[J]. Proteome Sci., 2011, 9: 39.
27	Depraetere O, Deschoenmaeker F, Badri H, et al. Trade-off between growth and carbohydrate accumulation in nutrient-limited Arthrospira sp. PCC 8005 studied by integrating transcriptomic and proteomic approaches[J]. PLoS One, 2015, 10(7): e0132461.
28	Kumaresan V, Nizam F, Ravichandran G, et al. Transcriptome changes of blue-green algae, Arthrospira sp. in response to sulfate stress[J]. Algal Research, 2017, 23: 96-103.
29	Ismaiel M M S, Piercey-Normore M D, Rampitsch C. Proteomic analyses of the cyanobacterium Arthrospira (Spirulina) platensis under iron and salinity stress[J]. Environmental and Experimental Botany, 2018, 147: 63-74.
30	Tan Y, Fang M Y, Jin L H, et al. Culture characteristics of the atmospheric and room temperature plasma-mutated Spirulina platensis mutants in CO₂ aeration culture system for biomass production[J]. Journal of Bioscience and Bioengineering, 2015, 120(4): 438-443.
31	Vonshak A. Spirulina platensis (Arthrospira): Physiology, Cell Biology and Biotechnology[M]. London: CRC Press, 1997.

聚类分析	3-A10	3-B2	4-B3
生物学过程相关 (BP)	910	913	910
细胞组分相关 (CC)	103	101	101
分子功能相关 (MF)	668	672	667

聚类分析	3-A10	3-B2	4-B3
生物学过程相关 (BP)	910	913	910
细胞组分相关 (CC)	103	101	101
分子功能相关 (MF)	668	672	667

序列差异性	对照	3-A10	3-B2	4-B3
单碱基突变数量	241873	243818	241020	244320
过滤野生型基因后的数量	—	4063	2532	4536
同义单碱基突变	—	1040	681	1229
错义单碱基突变	—	1591	1059	1823
进化率	—	1.53	1.55	1.48
序列插入突变数量	345	353	330	362
过滤野生型基因后的数量	—	134	101	123
错义插入突变	—	82	56	81

序列差异性	对照	3-A10	3-B2	4-B3
单碱基突变数量	241873	243818	241020	244320
过滤野生型基因后的数量	—	4063	2532	4536
同义单碱基突变	—	1040	681	1229
错义单碱基突变	—	1591	1059	1823
进化率	—	1.53	1.55	1.48
序列插入突变数量	345	353	330	362
过滤野生型基因后的数量	—	134	101	123
错义插入突变	—	82	56	81

代谢途径	突变体			代谢途径	突变体			代谢途径	突变体
代谢途径	3-A10	3-B2	4-B3	代谢途径	3-A10	3-B2	4-B3	代谢途径	3-A10	3-B2	4-B3
糖酵解	9	9	9	苯丙氨酸代谢	2	2	2	乙醛酸、二羧酸代谢	4	4	4
三羧酸循环	2	2	2	色氨酸代谢	1	1	1	丙酸代谢	1	1	1
磷酸戊糖途径	7	6	7	苯丙氨酸、酪氨酸、色氨酸合成	10	10	10	苯乙烯降解	1	1	1
果糖、甘露糖代谢	5	5	5	苯丙氨酸、酪氨酸、色氨酸合成	10	10	10	叶酸合成	8	8	8
半乳糖代谢	4	4	4	新生毒素生物合成	1	1	1	甲烷代谢	6	6	6
脂肪酸合成	3	3	3	β-丙氨酸代谢	2	2	2	碳固定及光合作用	8	8	8
氧化磷酸化	5	5	5	牛磺酸代谢	1	1	1	原核生物碳固定途径	6	5	5
光合作用	2	2	2	有机含硒化合物代谢	2	2	2	硫胺素代谢	3	3	3
嘌呤代谢	17	17	17	氨基甲酸代谢	2	2	2	核黄素代谢	7	7	7
丙氨酸、天冬氨酸、谷氨酸代谢	5	5	4	D-谷氨酰胺、D-谷氨酸代谢	1	1	1	维生素B₆代谢	1	1	1
丙氨酸、天冬氨酸、谷氨酸代谢	5	5	4	D-谷氨酰胺、D-谷氨酸代谢	1	1	1	烟酸盐、烟酰胺代谢	3	3	3
四环素合成	1	1	1	D-丙氨酸代谢	1	1	1	泛酸盐及辅酶a生物合成	8	8	8
黄曲霉毒素合成	1	1	1	谷胱甘肽代谢	7	7	7	泛酸盐及辅酶a生物合成	8	8	8
甘氨酸、丝氨酸、苏氨酸代谢	4	4	4	淀粉、蔗糖代谢	7	7	7	生物素代谢	1	1	1
甘氨酸、丝氨酸、苏氨酸代谢	4	4	4	氨基糖、核苷酸糖代谢	6	6	6	叶酸生物合成	3	3	3
半胱氨酸、蛋氨酸代谢	6	5	6	链霉素生物合成	5	5	5	阿特拉津降解	1	1	1
缬氨酸、亮氨酸、异亮氨酸生物合成	2	2	2	聚酮糖单元生物合成	2	2	2	卟啉、叶绿素代谢	15	15	15
缬氨酸、亮氨酸、异亮氨酸生物合成	2	2	2	丁松香和新霉素生物合成	2	2	2	萜类化合物生物合成	3	3	3
赖氨酸生物合成	2	2	2	丁松香和新霉素生物合成	2	2	2	萜类化合物生物合成	3	3	3
精氨酸、脯氨酸代谢	8	8	8	脂多糖生物合成	1	1	0	氮代谢	7	7	7
组氨酸代谢	4	4	4	肽聚糖生物合成	3	3	3	糖代谢	6	6	6
氨基苯甲酸降解	2		2	甘油酯代谢	2	2	2	苯丙素生物合成	1	1	1
药物代谢相关酶类	2	2	2	磷酸肌醇代谢	2	2	2	氨酰基-tRNA生物合成	6	6	6
磷脂酰肌醇信号系统	1	1	1	甘油磷脂代谢	4	4	4	氨酰基-tRNA生物合成	6	6	6
丙酮酸代谢	7	7	7	鞘脂类代谢	2	2	2	细胞色素P450代谢	1	1	1
鞘糖脂生物合成	1	1	1	鞘糖脂生物合成乳糖	1	1	1

Comparative omics study of Spirulinaplatensis mutants based on ARTP mutagenesis breeding system

ARTP诱变钝顶螺旋藻突变体比较组学研究

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