油菜脯氨酸代谢基因家族的生物信息学分析与核心成员鉴定

doi:10.3724/SP.J.1006.2022.14131

作物学报 ›› 2022, Vol. 48 ›› Issue (8): 1977-1995.doi: 10.3724/SP.J.1006.2022.14131

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

油菜脯氨酸代谢基因家族的生物信息学分析与核心成员鉴定

张天宇(), 王越, 刘影, 周婷, 岳彩鹏, 黄进勇, 华营鹏^*()

郑州大学农学院, 河南郑州 450001

收稿日期:2021-07-25 接受日期:2021-10-19 出版日期:2022-08-12 网络出版日期:2021-11-02
通讯作者: 华营鹏
作者简介:E-mail: zhangtianyu010@163.com
基金资助:
国家自然科学基金项目(31801923);河南省科技攻关项目(22170004);郑州大学重点学科专项(xkzdjc201905);郑州大学青年学科专项(XKZDQN202002);国家超算郑州中心创新生态科技专项(201400210600)

Bioinformatics analysis and core member identification of proline metabolism gene family in Brassica napus L.

ZHANG Tian-Yu(), WANG Yue, LIU Ying, ZHOU Ting, YUE Cai-Peng, HUANG Jin-Yong, HUA Ying-Peng^*()

School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China

Received:2021-07-25 Accepted:2021-10-19 Published:2022-08-12 Published online:2021-11-02
Contact: HUA Ying-Peng
Supported by:
National Natural Science Foundation of China(31801923);Key Science and Technology Project of Henan Province(22170004);Key Discipline Project of Zhengzhou University(xkzdjc201905);Special Project for Youth Discipline of Zhengzhou University(XKZDQN202002);Innovation Ecosystem Construction Science and Technology Special Project of National Supercomputing Zhengzhou Center(201400210600)

摘要/Abstract

摘要：

脯氨酸积累是植物在生物和非生物胁迫下的一种重要的代谢适应性机制。吡咯啉-5-羧酸合成酶(P5CS)、吡咯啉-5-羧酸还原酶(P5CR)酶、脯氨酸脱氢酶(PDH)、吡咯啉-5-羧酸脱氢酶(P5CDH)是依赖谷氨酸的脯氨酸生物合成途径中的关键酶。油菜是世界上重要的油料作物, 在油菜生长发育过程中, 其时常遭受各类生物和非生物胁迫。然而迄今为止, 在异源四倍体油菜中缺乏关于这些脯氨酸代谢基因家族的系统分析报道。本研究利用甘蓝型油菜‘中双11'基因组注释信息, 分别鉴定到上述10个BnaP5CSs、6个BnaP5CRs、8个BnaPDHs以及3个BnaP5CDHs基因。这些基因家族在系统发育上分为不同的进化分支, 同一亚组中的成员具有相似的理化特性、基因/蛋白质结构和保守的基序。进化压力分析表明, 这些基因均遭受了强烈的纯化选择。启动子区的顺式作用元件分析揭示了油菜上述4类基因家族之间均存在共同的和特异的转录调控机制。本研究分别对‘中双11'油菜幼苗进行盐胁迫、低钾、低磷以及铵毒胁迫处理, 分别取地上部及根部进行转录组测定与分析。结果显示, 脯氨酸合成相关基因的表达水平在上述4种胁迫下普遍上调, 而调控脯氨酸降解基因的表达水平则在盐胁迫和低磷胁迫情况下调; 基因共表达分析显示BnaC4.P5CS1a、BnaA5.P5CS1等基因可能在脯氨酸介导的油菜逆境响应网络中发挥核心作用。本研究通过脯氨酸代谢基因家族的生物信息学鉴定以及多种非生物逆境下的转录特征分析, 将为深入研究脯氨酸介导的逆境抗性提供理论依据, 也将为脯氨酸介导油菜非生物胁迫抗性的遗传改良提供优异的基因资源。

关键词: 甘蓝型油菜, 脯氨酸代谢, 基因家族, 转录组, 养分胁迫

Abstract:

Proline accumulation is an important metabolic adaptative mechanism of plants under biotic and abiotic stress. P5CS, P5CR, PDH, and P5CDH are key enzymes in the glutamate-dependent proline biosynthesis pathway. Rapeseed, an important oil crop in the world, is often subjected to various biotic and abiotic stresses during its growth and development. However, no systematic analysis of these proline metabolic gene families has been reported in Brassica napus so far. In this study, 10 BnaP5CSs, 6 BnaP5CRs, 8 BnaPDHs, and 3 BnaP5CDHs were identified by using the genomic annotation information of ‘Zhongshuang 11'. Phylogenetically, these gene families were divided into different evolutionary branches, and members of the same subgroups had similar physical and chemical properties, gene / protein structure, and conserved motifs. Evolutionary pressure analysis showed that these genes were subjected to strong purification selection. Cis-acting element analysis revealed that there were common and specific transcriptional regulatory mechanisms among the four kinds of gene families. In this study, rapeseed seedlings were respectively treated with salt stress, low potassium (K), low phosphate (P), and ammonium toxicity, and both shoots and roots were respectively sampled for transcriptomic analysis. The results indicated that the relative expression levels of genes related to proline synthesis were generally up-regulated under the above-mentioned four stresses, whereas the relative expression levels of genes regulating proline degradation were down-regulated under salt and low P stresses. Gene co-expression network analysis demonstrated that BnaC4.P5CS1a and BnaA5.P5CS1 might play central roles in the proline-mediated stress responsive networks in rapeseed. Through bioinformatics identification of proline metabolism gene family and analysis of transcription characteristics under various abiotic stresses, this study will provide a theoretical basis for further study of proline-mediated stress resistance, and will also provide excellent gene resources for genetic improvement of abiotic stress resistance mediated by proline metabolism in Brassica napus.

Key words: Brassica napus, proline metabolism, gene family, transcriptome, nutrient stress

张天宇, 王越, 刘影, 周婷, 岳彩鹏, 黄进勇, 华营鹏. 油菜脯氨酸代谢基因家族的生物信息学分析与核心成员鉴定[J]. 作物学报, 2022, 48(8): 1977-1995.

ZHANG Tian-Yu, WANG Yue, LIU Ying, ZHOU Ting, YUE Cai-Peng, HUANG Jin-Yong, HUA Ying-Peng. Bioinformatics analysis and core member identification of proline metabolism gene family in Brassica napus L.[J]. Acta Agronomica Sinica, 2022, 48(8): 1977-1995.

图/表 16

表1

表2

脯氨酸代谢相关的4类基因家族在拟南芥和甘蓝型油菜中分子特征"

基因ID Gene ID	基因名称 Gene name	区块 Block	蛋白质长度 Protein length	编码区长度 CDS length	DNA 全长 DNA length	外显子/ 内含子 Exon/ intron	异义突变Ka	同义突变Ks	Ka/Ks	进化时间Divergent time (Mya)
AT2G39800	AtP5CS1	J	717	2154	5156
BnaA03T0194400ZS	BnaA3.P5CS1	J	715	2148	4299	18/17	0.035	0.361	0.096	12.04
BnaA04T0253600ZS	BnaA4.P5CS1	J	717	2154	4128	19/18	0.032	0.371	0.087	12.36
BnaA05T0063500ZS	BnaA5.P5CS1	J	717	2154	4499	17/16	0.021	0.378	0.056	12.62
BnaC03T0227700ZS	BnaC3.P5CS1	J	715	2148	4255	18/17	0.035	0.349	0.101	11.64
BnaC04T0069800ZS	BnaC4.P5CS1a	J	717	2154	4584	18/17	0.021	0.376	0.055	12.54
BnaC04T0569500ZS	BnaC4.P5CS1b	J	717	2154	4711	19/18	0.030	0.356	0.084	11.87
AT3G55610	AtP5CS2	N	726	2181	5276
BnaA04T0040200ZS	BnaA4.P5CS2	N	719	2160	4705	20/19	0.047	0.325	0.145	10.83
BnaA09T0513600ZS	BnaA9.P5CS2	N	727	2184	4572	20/19	0.035	0.314	0.110	10.46
BnaC04T0313900ZS	BnaC4.P5CS2	N	726	2181	4571	20/19	0.046	0.345	0.133	11.52
BnaC08T0355700ZS	BnaC8.P5CS2	N	727	2184	4513	20/19	0.033	0.305	0.110	10.15
AT5G14800	AtP5CR	R	276	831	2037
BnaA03T0060400ZS	BnaA3.P5CR	R	464	1395	3245	10/9	0.100	0.459	0.217	15.29
BnaA10T0212800ZS	BnaA10.P5CR	R	276	831	1660	7/6	0.062	0.414	0.150	13.81
基因ID Gene ID	基因名称 Gene name	区块 Block	蛋白质长度 Protein length	编码区长度 CDS length	DNA 全长 DNA length	外显子/ 内含子 Exon/ intron	异义突变Ka	同义突变Ks	Ka/Ks	进化时间Divergent time (Mya)
BnaC03T0069400ZS	BnaC3.P5CR	R	276	831	1478	7/6	0.100	0.485	0.206	16.17
BnaC04T0138900ZS	BnaC4.P5CRa	R	255	768	1258	5/4	0.058	0.427	0.136	14.24
BnaC04T0227600ZS	BnaC4.P5CRb	R	212	639	1239	5/4	0.101	0.389	0.259	12.98
BnaC09T0514400ZS	BnaC9.P5CR	R	299	900	1473	6/5	0.067	0.411	0.162	13.69
AT3G30775	AtPDH1	L	499	1500	2921
BnaA02T0358100ZS	BnaA2.PDH1	L	498	1497	2651	4/3	0.053	0.547	0.097	18.22
BnaA06T0368500ZS	BnaA6.PDH1	L	498	1497	2620	3/2	0.053	0.655	0.081	21.84
BnaA09T0046200ZS	BnaA9.PDH1	L	498	1497	2808	4/3	0.066	0.535	0.123	17.84
BnaC02T0481700ZS	BnaC2.PDH1	L	498	1497	2589	4/3	0.052	0.532	0.098	17.72
BnaC07T0324000ZS	BnaC7.PDH1	L	498	1497	2635	3/2	0.052	0.659	0.079	21.96
BnaC09T0031900ZS	BnaC9.PDH1	L	498	1497	3015	4/3	0.068	0.544	0.125	18.13
AT5G38710	AtPDH2	S	476	1431	3144
BnaA04T0103200ZS	BnaA4.PDH2	S	466	1401	2586	3/2	0.049	0.421	0.116	14.03
BnaC04T0377900ZS	BnaC4.PDH2	S	476	1431	2834	4/3	0.055	0.428	0.130	14.25
AT5G62530	AtP5CDH	X	556	1671	4310
BnaA06T0278700ZS	BnaA6.P5CDH	X	557	1674	3571	15/14	0.026	0.426	0.062	14.20
BnaC02T0533200ZS	BnaC2.P5CDH	X	394	1185	2861	10/9	0.240	0.740	0.324	24.67
BnaC03T0552600ZS	BnaC3.P5CDH	X	557	1674	3554	15/14	0.028	0.370	0.076	12.35

表2

表3

脯氨酸代谢相关的4类基因家族在拟南芥和甘蓝型油菜中分子特征"

基因ID Gene ID	基因名称 Gene name	染色体 Chr.	分子量 MW	等电点 pI	不稳定系数 II	总平均亲水性 GRAVY	亚细胞定位 Subcellular localization
AT2G39800	AtP5CS1		77.70	5.89	33.53	-0.072	chlo
BnaA03T0194400ZS	BnaA3.P5CS1	A3	77.32	5.57	37.03	-0.063	chlo
BnaA04T0253600ZS	BnaA4.P5CS1	A4	77.69	5.69	36.95	-0.084	chlo
BnaA05T0063500ZS	BnaA5.P5CS1	A5	77.82	5.96	35.06	-0.088	chlo
BnaC03T0227700ZS	BnaC3.P5CS1	C3	77.42	5.63	37.15	-0.072	chlo
BnaC04T0069800ZS	BnaC4.P5CS1a	C4	77.74	5.89	34.79	-0.079	chlo
BnaC04T0569500ZS	BnaC4.P5CS1b	C4	77.57	5.47	35.30	-0.074	chlo
AT3G55610	AtP5CS2		78.87	6.35	33.85	-0.092	chlo
BnaA04T0040200ZS	BnaA4.P5CS2	A4	77.76	6.37	33.02	-0.075	chlo
BnaA09T0513600ZS	BnaA9.P5CS2	A9	78.73	6.85	33.40	-0.096	chlo
BnaC04T0313900ZS	BnaC4.P5CS2	C4	78.44	6.13	32.54	-0.066	chlo
BnaC08T0355700ZS	BnaC8.P5CS2	C8	78.71	6.70	34.07	-0.095	chlo
AT5G14800	AtP5CR		28.62	7.81	36.21	0.231	cyto
BnaA03T0060400ZS	BnaA3.P5CR	A3	50.34	6.87	37.45	0.103	cyto
BnaA10T0212800ZS	BnaA10.P5CR	A10	28.71	7.91	34.71	0.155	cyto
BnaC03T0069400ZS	BnaC3.P5CR	C3	28.81	6.00	34.58	0.117	cyto
BnaC04T0138900ZS	BnaC4.P5CRa	C4	27.08	5.43	32.77	0.060	cyto
BnaC04T0227600ZS	BnaC4.P5CRb	C4	22.10	5.26	32.32	0.003	cyto
BnaC09T0514400ZS	BnaC9.P5CR	C9	31.51	8.80	39.13	0.129	cyto
AT3G30775	AtPDH1		54.96	6.41	46.83	-0.184	mito
BnaA02T0358100ZS	BnaA2.PDH1	A2	55.20	6.53	44.27	-0.236	mito
BnaA06T0368500ZS	BnaA6.PDH1	A6	55.04	6.77	44.62	-0.213	mito
BnaA09T0046200ZS	BnaA9.PDH1	A9	54.95	7.29	46.66	-0.183	mito
BnaC02T0481700ZS	BnaC2.PDH1	C2	55.08	6.44	45.90	-0.228	mito
基因ID Gene ID	基因名称 Gene name	染色体 Chr.	分子量 MW	等电点 pI	不稳定系数 II	总平均亲水性 GRAVY	亚细胞定位 Subcellular localization
BnaC07T0324000ZS	BnaC7.PDH1	C7	55.11	6.77	44.46	-0.205	mito
BnaC09T0031900ZS	BnaC9.PDH1	C9	54.95	7.29	46.47	-0.183	mito
AT5G38710	AtPDH2		53.07	7.16	47.60	-0.185	mito
BnaA04T0103200ZS	BnaA4.PDH2	A4	51.76	6.87	51.64	-0.150	mito
BnaC04T0377900ZS	BnaC4.PDH2	C4	53.13	8.50	49.41	-0.122	mito
AT5G62530	AtP5CDH		61.77	6.26	34.70	-0.172	mito
BnaA06T0278700ZS	BnaA6.P5CDH	A6	61.81	6.45	36.19	-0.136	mito
BnaC02T0533200ZS	BnaC2.P5CDH	C2	45.21	9.31	39.76	-0.159	mito
BnaC03T0552600ZS	BnaC3.P5CDH	C3	61.86	6.58	36.41	-0.145	mito

表3

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图3

图4

图5

图6

图7

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附图2

图8

图9

图10

图11

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基因家族 Gene family	基因名称 Gene name	拟南芥 Arabidopsis thaliana (125 Mb)	白菜 Brassica rapa (465 Mb)	甘蓝 Brassica oleracea (485 Mb)	油菜 Brassica napus (1130 Mb)
P5CS	P5CS1	1	2	3	6
P5CS	P5CS2	1	2	2	4
P5CR	P5CR	1	2	4	6
PDH	PDH1	1	3	4	6
PDH	PDH2	1	1	1	2
P5CDH	P5CDH	1	1	2	3

油菜脯氨酸代谢基因家族的生物信息学分析与核心成员鉴定

Bioinformatics analysis and core member identification of proline metabolism gene family in Brassica napus L.

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