裂殖壶藻SlMYB118基因的克隆及生物信息学分析

doi:10.14012/j.cnki.fjsc.2023.03.002

摘要/Abstract

摘要：

裂殖壶藻是一种含有丰富DHA的海洋微藻。本课题组前期发现裂殖壶藻的SlMYB118基因与脂肪酸的合成密切相关,是潜在的DHA合成调控的转录因子。本文通过PCR的方法克隆裂殖壶藻的SlMYB118基因的cDNA全长序列,运用生物信息学的方法对其分析。结果预测SlMYB118蛋白质的等电点为8.75,分子量为84.81 kDa,定位于细胞核,且其具有106个潜在的磷酸化位点。SlMYB118基因的结合位点是探索转录调控机制、建立DHA合成相关转录调控网络的关键,本研究为后续确定其结合位点奠定了理论基础。

关键词: 裂殖壶藻, SlMYB118基因, 克隆, 生物信息学分析

Abstract:

Schizochytrium limacinum SR21 is a kind of marine microalgae rich in DHA.The research group that the author joined previously found that SlMYB118 gene of S.limacinum SR21 was closely related to fatty acid synthesis and was a potential transcription factor for DHA synthesis regulation.In this paper,the full-length cDNA sequence of SlMYB118 gene was cloned by PCR and analyzed by bioinformatics method.The results predicted that SlMYB118 protein had an isoelectric point of 8.75,a molecular weight of 84.81 kDa,was localized in the nucleus,and had 106 potential phosphorylation sites.This study laid the theoretical foundation for the subsequent identification of the binding site of SlMYB118 gene,which was a key issue for the transcriptional regulatory mechanism and the establishment of the transcriptional regulatory network related to DHA synthesis.

Key words: Schizochytrium limacinum SR21, the SlMYB118 gene, cloning, bioinformatics analysis

中图分类号:

Q943.2

陈菁, 苏永昌, 孙化淼, 陈由强, 薛婷, 代容春. 裂殖壶藻SlMYB118基因的克隆及生物信息学分析[J]. 渔业研究, 2023, 45(3): 222-232.

CHEN Jing, SU Yongchang, SUN Huamiao, CHEN Youqiang, XUE Ting, DAI Rongchun. Cloning and bioinformatics analysis of SlMYB118gene from Schizochytrium limacinum SR21[J]. Journal of Fisheries Research, 2023, 45(3): 222-232.

图/表 13

参考文献 30

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基因Gene	引物序列(5’→3’) Primer sequence	退火温度/°C Annealing temperature
SlMYB118	F:CGGAATTCATGTTTGTGGAAGATGGG	60
SlMYB118	R:GCGTCGACTCAATCTAAGAGAATGGA	60

基因Gene	引物序列(5’→3’) Primer sequence	退火温度/°C Annealing temperature
SlMYB118	F:CGGAATTCATGTTTGTGGAAGATGGG	60
SlMYB118	R:GCGTCGACTCAATCTAAGAGAATGGA	60

种类Class	软件与网址Software and URLs
理化性质Physicochemical properties	ProtParam tool(https://web.expasy.org/protparam)
疏水性Hydrophobicity	ProtScale(https://web.expasy.org/protscale)
保守结构域Conservative structural domain	NCBI Batch CD-search(https://www.ncbi.nlm.nih.gov/Structure /bwrpsb /bwrpsb.cgi)
跨膜结构Transmembrane structure	DeepTMHMM(https://dtu.biolib.com/DeepTMHMM)
亚细胞定位Subcellular localization	Hum-mPLoc 2.0(www.csbio.sjtu.edu.cn/bioinf/hum-multi-2/)
信号肽Signal peptide	SignalP-5.0(https://services.healthtech.dtu.dk/service.php?SignalP-5.0)
磷酸化位点Phosphorylation sites	NetPhos-3.1(https://services.healthtech.dtu.dk/service.php?NetPhos-3.1)
二级结构Secondary structure	SOPMA(https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page =/NPSA /npsa_sopma.html)
三级结构Three-level structure	SWISS-MODEL(https://swissmodel.expasy.org/interactive)
同源序列查找Homologous sequence search	NCBI的Protein BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi? PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome)
系统进化树System evolution tree	MEGA11

种类Class	软件与网址Software and URLs
理化性质Physicochemical properties	ProtParam tool(https://web.expasy.org/protparam)
疏水性Hydrophobicity	ProtScale(https://web.expasy.org/protscale)
保守结构域Conservative structural domain	NCBI Batch CD-search(https://www.ncbi.nlm.nih.gov/Structure /bwrpsb /bwrpsb.cgi)
跨膜结构Transmembrane structure	DeepTMHMM(https://dtu.biolib.com/DeepTMHMM)
亚细胞定位Subcellular localization	Hum-mPLoc 2.0(www.csbio.sjtu.edu.cn/bioinf/hum-multi-2/)
信号肽Signal peptide	SignalP-5.0(https://services.healthtech.dtu.dk/service.php?SignalP-5.0)
磷酸化位点Phosphorylation sites	NetPhos-3.1(https://services.healthtech.dtu.dk/service.php?NetPhos-3.1)
二级结构Secondary structure	SOPMA(https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page =/NPSA /npsa_sopma.html)
三级结构Three-level structure	SWISS-MODEL(https://swissmodel.expasy.org/interactive)
同源序列查找Homologous sequence search	NCBI的Protein BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi? PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome)
系统进化树System evolution tree	MEGA11

氨基酸 Amino acid	数量/个 Quantity/pcs	百分比/% Percentage	氨基酸 Amino acid	数量/个 Quantity/pcs	百分比/% Percentage
丙氨酸Ala	61	8.0	赖氨酸Lys	20	2.6
精氨酸Arg	56	7.4	蛋氨酸Met	18	2.4
天冬酰胺Asn	40	5.3	苯丙氨酸Phe	13	1.7
天冬氨酸Asp	42	5.5	脯氨酸Pro	60	7.9
半胱氨酸Cys	4	0.5	丝氨酸Ser	98	12.9
谷氨酰胺Gln	65	8.6	苏氨酸Thr	37	4.9
谷氨酸Glu	30	4.0	色氨酸Trp	8	1.1
甘氨酸Gly	35	4.6	酪氨酸Tyr	11	1.4
组氨酸His	67	8.8	缬氨酸Val	25	3.3
异亮氨酸Ile	24	3.2	吡咯懒氨Pyl	0	0.0
亮氨酸Leu	45	5.9	硒半胱氨酸Sec	0	0.0