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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*()   

  1. 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*()   

  1. 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)

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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

表1

脯氨酸代谢相关的4个基因家族在拟南芥和芸薹属作物中的拷贝数目"

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
P5CS2 1 2 2 4
P5CR P5CR 1 2 4 6
PDH
PDH1 1 3 4 6
PDH2 1 1 1 2
P5CDH P5CDH 1 1 2 3

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

图1

拟南芥、白菜、甘蓝和甘蓝型油菜脯氨酸代谢相关4类基因家族的系统进化分析 进化树不同颜色代表不同的分支, 树枝上的数字代表进化距离。"

图2

甘蓝型油菜4类脯氨酸代谢基因家族成员的基因结构 绿色的部分代表UTR区域, 黄色的部分代表外显子, 黑色的线代表内含子。"

图3

甘蓝型油菜4类脯氨酸代谢基因家族成员保守结构域分析"

图4

甘蓝型油菜脯氨酸代谢基因启动子区顺式作用调控元件的富集分析 气泡的大小代表顺式作用元件数量, 颜色代表其占总顺式作用元件个数的比例。"

图5

甘蓝型油菜4类脯氨酸代谢基因家族染色体定位及A、C亚基因组共线性分析"

图6

4类脯氨酸代谢基因家族在拟南芥、白菜、甘蓝以及甘蓝型油菜之间的共线性分析"

图7

拟南芥中4类脯氨酸代谢基因家族蛋白-蛋白互作网络"

附图1

拟南芥和甘蓝型油菜4类脯氨酸代谢家族蛋白的二级结构"

附图2

拟南芥脯氨酸代谢4类基因家族的细胞特异性表达模式"

图8

盐胁迫下甘蓝型油菜脯氨酸代谢4类家族基因的差异表达谱热图"

图9

盐胁迫下甘蓝型油菜脯氨酸代谢基因的差异表达火山图"

图10

不同养分胁迫下甘蓝型油菜脯氨酸代谢4类家族基因的差异表达谱热图"

图11

不同处理下甘蓝型油菜脯氨酸代谢4类基因家族差异共表达网络分析 圆形的节点代表基因, 节点的大小代表基因在网络的作用, 2个节点间线的粗细表示基因间的互作程度。"

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