甘蓝型油菜BnMYB80基因的生物信息学分析

doi:10.11983/CBB16006

摘要/Abstract

摘要： 在高等植物花药发育和花粉形成中, MYB转录因子起着非常重要的作用, 其中MYB80是参与绒毡层发育及引起雄性不育的重要转录因子。该研究以拟南芥(Arabidopsis thaliana) AtMYB80为参考序列, 通过BLAST比对分析, 在白菜(Brassica rapa)、甘蓝(B. oleracea)和甘蓝型油菜(B. napus)中分别获得MYB80基因的2、2和6个同源序列, 运用生物信息学方法对其核苷酸序列及编码的氨基酸序列进行组成成分、亚细胞定位、磷酸化位点、疏水性/亲水性、蛋白质二级、三级结构和功能域分析。结果表明, MYB80转录因子亚细胞定位于细胞核, 具有多个不同的磷酸化位点, 肽链表现为亲水性; 二级、三级结构预测显示, MYB80蛋白以α-螺旋和无规则卷曲为主要结构元件; 保守结构域分析表明, 其N端具有2个串联的SANT功能域, 属于R2R3型MYB转录因子。多重序列比对和进化树分析结果表明, 甘蓝型油菜与白菜、甘蓝的序列相似性大于92%, 且MYB80转录因子的功能结构域具有较高的同源性和较强的序列保守性。该研究结果对深入解析甘蓝型油菜MYB80的生物学功能及育性调控的分子机理具有重要意义, 为甘蓝型油菜杂种优势利用提供了依据。

关键词: 生物信息学, 甘蓝型油菜, MYB80, 花粉发育, 绒毡层

Abstract: MYB transcription factors play a key role in anther development and pollen formation in higher plants, and MYB80 is an important transcription factor involved in the development of tapetum and initiation of male sterility. In this study, we performed BLASTN and TBLASTX searches of the Arabidopsis thaliana MYB80 (AtMYB80) amino acid sequences against the published database and identified 2, 2 and 6 homologous sequences of MYB80 gene in Brassica rapa, B. oleracea and B. napus, respectively. The composition of nucleic acid sequence and amino acid sequences, subcellular localization, phosphorylation sites, hydrophilicity and hydrophobicity, secondary and tertiary structure of protein, conserved domains of the MYB80 were predicted and analyzed by bioinformatics tools and resources from the Internet. The results showed that the MYB80 transcription factors are located in the nucleus by analyzing subcellular localization, with a number of different phosphorylation sites, and the peptide chains are hydrophilia. The predicted secondary structure and tertiary structure showed that the main structural elements of the MYB80 protein were α helix and random coil. Conserved domain analysis indicated that the MYB80 transcription factor belongs to the MYB-R2R3 type transcription factor, with 2 tandem SANT domains in the N-terminal sequence. The multiple sequence ratio and phylogenetic tree were constructed with MYB80 proteins from different plants; similarity among B. napus and B. rapa, and B. oleracea was more than 92%, and the conserved functional domains had high homology and strong sequence conservation. These results are helpful for resolving the biological functions of MYB80 and the molecular mechanism of sterility regulation and lay a foundation for the heterosis utilization in B. napus.

Key words: bioinformatics, Brassica napus, MYB80, pollen development, tapetum

贾乐东, 李施蒙, 许代香, 曲存民, 李加纳, 王瑞. 甘蓝型油菜BnMYB80基因的生物信息学分析. 植物学报, 2016, 51(5): 620-630.

Jia Ledong, Li Shimeng, Xu Daixiang, Qu Cunmin, Li Jiana, Wang Rui. Bioinformatics Analysis of BnMYB80 Genes in Brassica napus . Chinese Bulletin of Botany, 2016, 51(5): 620-630.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB16006

https://www.chinbullbotany.com/CN/Y2016/V51/I5/620

图/表 7

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Gene name	Gene ID	Chromosome	Length (aa)	MW (kDa)	pI	Instability	Aliphatic index	Gravy
BrMYB80A02	103851848	A02	320	36.1054	6.95	35.89	65.88	-0.808
BrMYB80A10	103845046	A10	320	35.8452	7.24	33.15	69.81	-0.721
BolMYB80C02	106327859	C02	324	36.5430	7.75	37.04	66.57	-0.790
BolMYB80C09	106317148	C09	320	35.9113	7.22	31.94	68.56	-0.740
BnMYB80A02	106389601	A02	322	36.3678	6.95	35.55	65.47	-0.792
BnMYB80A10	674915774	A10	320	35.8232	7.24	34.62	68.59	-0.712
BnMYB80C02	106379735	C02	320	35.9113	7.22	31.94	68.56	-0.740
BnMYB80C03	106385056	C03	320	35.9113	7.22	31.94	68.56	-0.740
BnMYB80C05	106400365	C05	319	35.7842	6.90	33.76	68.50	-0.738
BnMYB80Cnn	106389601	Cnn	324	36.5490	6.93	35.65	66.57	-0.771

Gene name	Gene ID	Chromosome	Length (aa)	MW (kDa)	pI	Instability	Aliphatic index	Gravy
BrMYB80A02	103851848	A02	320	36.1054	6.95	35.89	65.88	-0.808
BrMYB80A10	103845046	A10	320	35.8452	7.24	33.15	69.81	-0.721
BolMYB80C02	106327859	C02	324	36.5430	7.75	37.04	66.57	-0.790
BolMYB80C09	106317148	C09	320	35.9113	7.22	31.94	68.56	-0.740
BnMYB80A02	106389601	A02	322	36.3678	6.95	35.55	65.47	-0.792
BnMYB80A10	674915774	A10	320	35.8232	7.24	34.62	68.59	-0.712
BnMYB80C02	106379735	C02	320	35.9113	7.22	31.94	68.56	-0.740
BnMYB80C03	106385056	C03	320	35.9113	7.22	31.94	68.56	-0.740
BnMYB80C05	106400365	C05	319	35.7842	6.90	33.76	68.50	-0.738
BnMYB80Cnn	106389601	Cnn	324	36.5490	6.93	35.65	66.57	-0.771

Gene name	CDS (bp)	Exon	MYB80 conserved domain (aa)
Gene name	CDS (bp)	Exon	SANT	SANT	IRO	KNOX1	Cir_N
BrMYB80A02	1772	3	13-63	66-114	-	-	-
BrMYB80A10	1631	3	13-63	66-114	-	-	-
BolMYB80C02	1891	4	13-63	66-114	123-140	130-173	246-282
BolMYB80C09	1573	3	13-63	66-114	123-140	130-173	-
BnMYB80A02	1653	3	13-63	66-114	123-140	130-173	244-280
BnMYB80A10	1471	3	13-63	66-114	123-140	130-173	-
BnMYB80C02	1471	3	13-63	66-114	123-140	130-173	-
BnMYB80C03	1471	3	13-63	66-144	123-140	130-173	-
BnMYB80C05	1461	3	13-63	66-144	123-140	130-173	-
BnMYB80Cnn	1668	3	13-63	66-144	123-140	130-173	246-282

Gene name	CDS (bp)	Exon	MYB80 conserved domain (aa)
Gene name	CDS (bp)	Exon	SANT	SANT	IRO	KNOX1	Cir_N
BrMYB80A02	1772	3	13-63	66-114	-	-	-
BrMYB80A10	1631	3	13-63	66-114	-	-	-
BolMYB80C02	1891	4	13-63	66-114	123-140	130-173	246-282
BolMYB80C09	1573	3	13-63	66-114	123-140	130-173	-
BnMYB80A02	1653	3	13-63	66-114	123-140	130-173	244-280
BnMYB80A10	1471	3	13-63	66-114	123-140	130-173	-
BnMYB80C02	1471	3	13-63	66-114	123-140	130-173	-
BnMYB80C03	1471	3	13-63	66-144	123-140	130-173	-
BnMYB80C05	1461	3	13-63	66-144	123-140	130-173	-
BnMYB80Cnn	1668	3	13-63	66-144	123-140	130-173	246-282

Gene name	α helix (%)	Extend strand (%)	β turn (%)	Random coil (%)
BrMYB80A02	41.25	11.56	10.00	37.19
BrMYB80A10	37.81	14.06	10.00	38.12
BolMYB80C02	44.14	10.19	8.64	37.04
BolMYB80C09	35.94	15.31	10.94	37.81
BnMYB80A02	42.55	11.18	9.63	36.65
BnMYB80A10	37.19	15.00	10.31	37.50
BnMYB80C02	35.94	15.31	10.94	37.81
BnMYB80C03	35.94	15.31	10.94	37.81
BnMYB80C05	36.68	14.73	10.03	38.56
BnMYB80Cnn	44.14	10.49	9.57	35.80