赫氏颗石藻(Emiliania huxleyi)响应病毒感染的microRNA转录组分析
收稿日期: 2021-04-30
修回日期: 2021-07-14
网络出版日期: 2021-07-29
基金资助
国家自然科学基金面上项目编号(42076086);国家自然科学基金面上项目编号(31771972);福建省自然科学基金编号资助(2019J01696);福建省自然科学基金编号资助(2020J01676)
Analysis of microRNA expression profile in Emiliania huxleyi in response to virus infection
Received date: 2021-04-30
Revised date: 2021-07-14
Online published: 2021-07-29
Supported by
Supported by National Natural Science Foundation of China Nos(42076086);Supported by National Natural Science Foundation of China Nos(31771972);Fujian Province Natural Science Foundation of China Nos(2019J01696);Fujian Province Natural Science Foundation of China Nos(2020J01676)
海洋颗石藻病毒-宿主互作是影响海洋碳、硫生物地化循环及全球气候变化的重要环节。作为大的双链DNA病毒,颗石藻病毒进化出一种“病毒细胞代谢”模式,通过重编程宿主代谢途径以满足其代谢需求,但对这一代谢模式的调控机制尚缺乏足够的认识。MicroRNA (miRNA)作为一种基因表达调控的重要因子,能够通过调控代谢过程中的靶基因表达,从而调节相关代谢通路。本研究采用small RNA测序技术分析病毒感染颗石藻差异表达的miRNA及其靶基因功能,鉴定出26条成熟miRNA (包括2条病毒来源的miRNA),均来自23条新的miRNA前体序列,其中5条miRNA显著差异表达,包括4条上调,1条下调。实时荧光定量PCR (quantitative real-time PCR, qRT-PCR)验证结果与miRNA-seq结果基本一致。功能富集分析显示,5个差异表达的miRNA可能参与调节糖代谢、脂代谢和氨基酸等代谢。此外,差异表达miRNA的表达水平与脂质代谢相关靶基因如ACC-1、SPT、ACOX、ACAT、CERS、ACADS等的表达水平呈负相关,说明这些miRNA可能在病毒感染过程中对宿主的脂质代谢发挥重要的调控作用。
关键词： 赫氏颗石藻; 颗石藻病毒; small RNA测序; microRNA; 脂代谢
张恩权, 蔡伟聪, 李桂玲, 李健, 刘静雯 . 赫氏颗石藻(Emiliania huxleyi)响应病毒感染的microRNA转录组分析[J]. 遗传, 2021 , 43(11) : 1088 -1100 . DOI: 10.16288/j.yczz.21-164
The interactions between Emiliania huxleyi and E. huxleyi virus (EhV) regulate marine carbon and sulfur biogeochemical cycle and play a prominent role in global climate change. As a large DNA virus, EhVs have developed a novel “virocell metabolism” model to meet their higher metabolic needs. However, the regulatory mechanism of this metabolic model is still largely unclear. MicroRNAs (miRNAs) can regulate biological pathways through targeting hub genes in the metabolic processes. Here, we performed high-throughput small RNA sequencing to analyse miRNA expression in EhV99B1 infected E. huxleyi BOF92. A total of 26 miRNAs (including 2 virus-derived miRNAs) were identified, including four up-regulated and one down-regulated miRNAs. These results were further validated through quantitative real-time PCR. Functional enrichment analysis showed that five differentially-expressed miRNAs might be involved in the regulation of carbohydrate metabolism, lipid metabolism and amino acid metabolism. Moreover, the expression levels of differentially-expressed miRNAs were negatively correlated with that of several lipid metabolism-related genes, such as ACC-1, SPT, ACOX, ACAT, CERS and ACADS, indicating that these miRNAs might play an important regulatory role in virus-mediated lipid metabolism.
| [1] | Tong SY, Gao KS, Hutchins DA. Adaptive evolution in the coccolithophoreGephyrocapsa oceanica following 1,000 generations of selection under elevated CO2. Glob Chang Biol, 2018, 24(7):3055-3064. |
| [2] | Sun J. Organic carbon pump and carbonate counter pump of living coccolithophorid. Adv Earth Sci, 2007, 22(12):1231-1239. |
| [2] | 孙军. 今生颗石藻的有机碳泵和碳酸盐反向泵. 地球科学进展, 2007, 22(12):1231-1239. |
| [3] | Zhang J, Li JR, Yang L, Yue NN. Coccolithophores and their characteristics. Marin Sci, 2018, 42(2):150-158. |
| [3] | 张健, 李佳芮, 杨璐, 岳娜娜. 球石藻及其生态功能. 海洋科学, 2018, 42(2):150-158. |
| [4] | Daniels CJ, Poulton AJ, Balch WM, Marañón E, Adey T, Bowler BC, Cermeño P, Charalampopoulou A, Crawford DW, Drapeau D, Feng YY, Fernández A, Fernández E, Fragoso GM, González N, Graziano LM, Heslop R, Holligan PM, Hopkins J, Huete-Ortega M, Hutchins DA, Lam PJ, Lipsen MS, López-Sandoval DC, Loucaides S, Marchetti A, Mayers KMJ, Rees AP, Sobrino C, Tynan E, Tyrrell, T. A global compilation of coccolithophore calcification rates. Earth Syst Sci Data, 2018, 10(4):1859-1876. |
| [5] | Ruiz E, Oosterhof M, Sandaa RA, Larsen A, Pagarete A. Emerging interaction patterns in the Emiliania huxleyi- EhV system. Viruses, 2017, 9(3):61. |
| [6] | Highfield A, Evans C, Walne A, Miller PI, Schroeder DC. How many coccolithovirus genotypes does it take to terminate an Emiliania huxleyi bloom? Virology, 2014, 466-467:138-145. |
| [7] | Rosenwasser S, Mausz MA, Schatz D, Sheyn U, Malitsky S, Aharoni A, Weinstock E, Tzfadia O, Ben-Dor S, Feldmesser E, Pohnert G, Vardi A. Rewiring host lipid metabolism by large viruses determines the fate of Emiliania huxleyi, a bloom-forming alga in the ocean. Plant Cell, 2014, 26(6):2689-2707. |
| [8] | Rosenwasser S, Ziv C, Creveld SG, Vardi A. Virocell metabolism: metabolic innovations during host-virus interactions in the ocean. Trends Microbiol, 2016, 24(10):821-832 |
| [9] | Ziv C, Malitsky S, Othman A, Ben-Dor S, Wei Y, Zheng SN, Aharoni A, Hornemann T, Vardi A. Viral serine palmitoyltransferase induces metabolic switch in sphingolipid biosynthesis and is required for infection of a marine alga. Proc Natl Acad Sci USA, 2016, 113(13):E1907-E1916. |
| [10] | Evans C, Pond DW, Wilson WH. Changes in Emiliania huxleyi fatty acid profiles during infection with EhV86: physiological and ecological implications. Aquat Microb Ecol, 2009, 55(3):219-228. |
| [11] | Zeng J, Liu SSY, Cai WC, Jiang HR, Lu X, Li GL, Li J, Liu JW. Emerging lipidome patterns associated with marine Emiliania huxleyi-virus model system. Sci Total Environ, 2019, 688:521-528. |
| [12] | Schatz D, Rosenwasser S, Malitsky S, Wolf SG, Feldmesser E, Vardi A. Communication via extracellular vesicles enhances viral infection of a cosmopolitan alga. Nat Microbiol, 2017, 2(11):1485-1492. |
| [13] | Sheyn U, Rosenwasser S, Ben-Dor S, Porat Z, Vardi A. Modulation of host ROS metabolism is essential for viral infection of a bloom-forming coccolithophore in the ocean. ISME J, 2016, 10(7):1742-1754. |
| [14] | Vardi A, Haramaty L, Van Mooy BAS, Fredricks HF, Kimmance SA, Larsen A, Bidle KD. Host-virus dynamics and subcellular controls of cell fate in a natural coccolithophore population. Proc Natl Acad Sci, 2012, 109(47):19327-19332. |
| [15] | Bidle KD, Haramaty L, Barcelos E Ramos J, Falkowski P. Viral activation and recruitment of metacaspases in the unicellular coccolithophore Emiliania huxleyi. Proc Natl Acad Sci, 2007, 104(14):6049-6054. |
| [16] | Vardi A, Van Mooy BAS, Fredricks HF, Popendorf KJ, Ossolinski JE, Haramaty L, Bidle KD. Viral glycosphingolipids induce lytic infection and cell death in marine phytoplankton. Science, 2009, 326(5954):861-865. |
| [17] | Liu JW, Cai WC, Fang X, Wang XT, Li GL. Virus-induced apoptosis and phosphorylation form of metacaspase in the marine coccolithophoridEmiliania huxleyi. Arch Microbiol, 2018, 200(3):413-422. |
| [18] | Millar AA, Waterhouse PM. Plant and animal microRNAs: similarities and differences. Funct Integr Genomics, 2005, 5(3):129-135. |
| [19] | Aryal B, Singh AK, Rotllan N, Price N, Fernández- Hernando N. MicroRNAs and lipid metabolism. Curr Opin Lipidol, 2017, 28(3):273-280. |
| [20] | Lopez-Gomollon S, Beckers M, Rathjen T, Moxon S, Maumus F, Mohorianu I, Moulton V, Dalmay T, Mock T. Global discovery and characterization of small non-coding RNAs in marine microalgae. BMC Genomics, 2014, 15(1):697. |
| [21] | Norden-Krichmar TM, Allen AE, Gaasterland T, Hildebrand M. Characterization of the small RNA transcriptome of the diatom, Thalassiosira pseudonana. PLoS One, 2011, 6(8):e22870. |
| [22] | Shi XG, Lin X, Li L, Li MZ, Palenik B, Lin SJ. Transcriptomic and microRNAomic profiling reveals multi-faceted mechanisms to cope with phosphate stress in a dinoflagellate. ISME J, 2017, 11(10):2209-2218. |
| [23] | Tian X, Cai WC, Su JJ, Wu SY, Liu JW. Transcriptome analysis of marine microalga Emiliania huxleyi in response to virus infection. Haiyang Xuebao, 2019, 41(12):103-112. |
| [23] | 田雪, 蔡伟聪, 苏金净, 吴书燕, 刘静雯. 病毒感染海洋球石藻Emiliania huxleyi的转录组分析. 海洋学报, 2019, 41(12):103-112. |
| [24] | Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J, 2011, 17(1):10-12. |
| [25] | Hällman J, Avesson L, Reimegård J, Käller M, Söderbom F. Identification and verification of microRNAs by high-throughput sequencing. Methods Mol Biol, 2013, 983:125-138. |
| [26] | Friedländer MR, Mackowiak SD, Li N, Chen W, Rajewsky N. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res, 2012, 40(1):37-52. |
| [27] | Robinson M, Mccarthy D, Smyth G. EdgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 2009, 26(1):139-140. |
| [28] | Zhang XY, Gamarra J, Castro S, Carrasco E, Hernandez A, Mock T, Hadaegh AR, Read BA. Characterization of the small RNA transcriptome of the marine coccolithophorid, Emiliania huxleyi. PLoS One, 2016, 11(4):e0154279. |
| [29] | Read BA, Kegel J, Klute MJ, Kuo A, Lefebvre SC, Maumus F, Mayer C, Miller J, Monier A, Salamov A, Young J, Aguilar M, Claverie JM, Frickenhaus S, Gonzalez K, Herman EK, Lin YC, Napier J, Ogata H, Sarno AF, Shmutz J, Schroeder D, de Vargas C, Verret F, von Dassow P, Valentin K, Van de Peer Y, Wheeler G, Emiliania huxleyi Annotation Consortium, Dacks JB, Delwiche CF, Dyhrman ST, Glöckner G, John U, Richards T, Worden AZ, Zhang X, Grigoriev IV. Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature, 2013, 499(7457):209-213. |
| [30] | Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS. MicroRNA targets in drosophila. Genome Biol 2003, 5(1):R1. |
| [31] | Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc, 2009, 4(1):44-57. |
| [32] | Zhang E, Wu S, Cai W, Zeng J, Li J, Li G, Liu J. Validation of superior reference genes for qRT-PCR and western blot analyses in marine Emiliania huxleyi-virus model system. J Appl Microbiol, 2021, 131(1):257-271. |
| [33] | Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT Method. Methods, 2001, 25(4):402-408. |
| [34] | Manavella1 PA, Yang SW, Palatnik J. Keep calm and carry on: miRNA biogenesis under stress. Plant J, 2019, 99(5):832-843. |
| [35] | Bruscella P, Bottini S, Baudesson C, Pawlotsky JM, Feray C, Trabucchi M. Viruses and miRNAs: more friends than foes. Front Microbiol, 2017, 8:724. |
| [36] | Li C, Lu LG, Qi ZT, Zhu YQ, Su F, Zhao P, Dong H. Transcriptome and miRNome analysis provide new insight into host lipid accumulation, innate immunity, and viral persistence in hepatitis C virus infection in vitro. Front Microbiol, 2020, 11:535673. |
| [37] | Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B, Gaasterland T, Meyer J, Tuschl T. The small RNA profile during Drosophila melanogaster development. Dev Cell, 2003, 5(2):337-350. |
| [38] | Li JR, Wu Y, Qi YJ. MicroRNAs in a multicellular green alga Volvox carteri. Sci China Life Sci, 2014, 57(1):36-45. |
| [39] | Tarver JE, Cormier A, Pinzón N, Taylor RS, Carré W, Strittmatter M, Seitz H, Coelho SM, Cock JM. MicroRNAs and the evolution of complex multicellularity: identification of a large, diverse complement of microRNAs in the brown alga Ectocarpus. Nucleic Acids Res, 2015, 43(13):6384-6398. |
| [40] | Zhao T, Li GL, Mi SJ, Li S, Hannon GJ, Wang XJ, Qi YJ. A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii. Genes Dev, 2007, 21(10):1190-1203. |
| [41] | Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 2004, 116(2):281-297. |
| [42] | Ha MJ, Kim VN. Regulation of microRNA biogenesis. Nat Rev Mol Cell Biol, 2014, 15(8):509-524. |
| [43] | Peng JJ, Yan F, Chen HR, Chen JP. Progress of studies on Dicer structure and function. Hereditas (Beijing), 2008, 30(12):1550-1556. |
| [43] | 彭杰军, 燕飞, 陈海如, 陈剑平. Dicer结构和功能研究进展. 遗传, 2008, 30(12):1550-1556. |
| [44] | Huang AY, He LW, Wang GC. Identification and characterization of microRNAs from Phaeodactylum tricornutum by high-throughput sequencing and bioinformatics analysis. BMC Genomics, 2011, 12(1):337. |
| [45] | Wilson WH, Schroeder DC, Allen MJ, Holden M, Parkhill J, Barrell BG, Churcher C, Harnlin N, Mungall K, Norbertczak H, Quail MA, Price C, Rabbinowitsch E, Walker D, Craigon M, Roy D, Ghazal P. Complete genome sequence and lytic phase transcription profile of a coccolithovirus. Science, 2005, 309(5737): 1090LP-1092. |
/
| 〈 |
|
〉 |
www.chinagene.cn
备案号：京ICP备09063187号-4
总访问:,今日访问:,当前在线:
