生物技术通报 ›› 2023, Vol. 39 ›› Issue (4): 136-147.doi: 10.13560/j.cnki.biotech.bull.1985.2022-0533
赖瑞联(), 冯新, 高敏霞, 路喻丹, 刘晓驰, 吴如健, 陈义挺()
收稿日期:
2022-04-29
出版日期:
2023-04-26
发布日期:
2023-05-16
通讯作者:
陈义挺,男,研究员,研究方向:果树生物技术与遗传资源;E-mail: chyiting@163.com作者简介:
赖瑞联,男,助理研究员,研究方向:果树生物技术与遗传资源;E-mail: lairl0618@163.com
基金资助:
LAI Rui-lian(), FENG Xin, GAO Min-xia, LU Yu-dan, LIU Xiao-chi, WU Ru-jian, CHEN Yi-ting()
Received:
2022-04-29
Published:
2023-04-26
Online:
2023-05-16
摘要:
过氧化氢酶(Catalase,CAT)是植物主要的抗氧化酶之一。为揭示猕猴桃CAT(AcCAT)基因家族序列特征和潜在功能,对其进行了全基因组鉴定和表达分析。对AcCAT基因家族进行全基因组鉴定和生物信息学分析,并研究其在不同器官以及果实贮藏过程中的表达变化。从猕猴桃基因组中鉴定出9个AcCAT基因并根据其在染色体上的位置分别命名为AcCAT1-AcCAT9,不同成员之间蛋白理化性质、基因结构、保守基序、启动子作用元件等存在较高相似性。AcCAT基因不均匀地分布在猕猴桃的4条染色体上,其中的5个AcCAT基因形成2个串联基因簇,6个AcCAT基因发生片段复制。基于psRNAtarget分析,AcCAT基因可能主要受miR166家族调控。系统进化分析结果显示,来源于猕猴桃、茶树、棉花和水稻的23个CAT蛋白分为3个类群,其归类并未完全按物种划分。在不同猕猴桃器官中,AcCAT3主要在根中表达,AcCAT1和AcCAT4主要在花中表达,AcCAT2、AcCAT5、AcCAT6、AcCAT8和AcCAT9主要在叶中表达,AcCAT7则同时在根和花中高水平表达;在猕猴桃果实贮藏过程中,AcCAT5和AcCAT6表达水平逐渐降低,AcCAT1和AcCAT2主要在贮藏前期表达,而AcCAT3、AcCAT4和AcCAT8主要在贮藏后期表达。此外,miR166家族成员在果实贮藏过程中的表达量逐步升高。AcCAT基因在进化过程中存在保守性,其在猕猴桃生长发育和果实贮藏软化过程中发挥调控作用。
赖瑞联, 冯新, 高敏霞, 路喻丹, 刘晓驰, 吴如健, 陈义挺. 猕猴桃过氧化氢酶基因家族全基因组鉴定与表达分析[J]. 生物技术通报, 2023, 39(4): 136-147.
LAI Rui-lian, FENG Xin, GAO Min-xia, LU Yu-dan, LIU Xiao-chi, WU Ru-jian, CHEN Yi-ting. Genome-wide Identification of Catalase Family Genes and Expression Analysis in Kiwifruit[J]. Biotechnology Bulletin, 2023, 39(4): 136-147.
蛋白名称 Protein name | 氨基酸 Amino acids | 分子量 Molecular weight/kD | 等电点 Theoretical pI | 不稳定系数 Instability index | 脂肪系数 Aliphatic index | 亲水性系数 Grand average of hydropathicity |
---|---|---|---|---|---|---|
AcCAT1 | 450 | 52.16 | 6.85 | 39.98 | 69.93 | -0.585 |
AcCAT2 | 757 | 87.31 | 7.24 | 48.49 | 72.60 | -0.631 |
AcCAT3 | 1 285 | 148.21 | 5.89 | 42.86 | 79.04 | -0.420 |
AcCAT4 | 459 | 53.40 | 7.82 | 38.03 | 76.06 | -0.497 |
AcCAT5 | 501 | 58.01 | 6.39 | 44.37 | 71.40 | -0.537 |
AcCAT6 | 526 | 60.67 | 6.53 | 41.73 | 70.06 | -0.535 |
AcCAT7 | 302 | 35.33 | 6.09 | 44.08 | 73.61 | -0.542 |
AcCAT8 | 490 | 57.08 | 6.88 | 38.26 | 69.63 | -0.536 |
AcCAT9 | 91 | 10.34 | 5.90 | 37.97 | 63.19 | -0.676 |
表1 猕猴桃AcCAT蛋白的理化性质
Table 1 Physicochemical properties of AcCAT proteins in A. chinensis
蛋白名称 Protein name | 氨基酸 Amino acids | 分子量 Molecular weight/kD | 等电点 Theoretical pI | 不稳定系数 Instability index | 脂肪系数 Aliphatic index | 亲水性系数 Grand average of hydropathicity |
---|---|---|---|---|---|---|
AcCAT1 | 450 | 52.16 | 6.85 | 39.98 | 69.93 | -0.585 |
AcCAT2 | 757 | 87.31 | 7.24 | 48.49 | 72.60 | -0.631 |
AcCAT3 | 1 285 | 148.21 | 5.89 | 42.86 | 79.04 | -0.420 |
AcCAT4 | 459 | 53.40 | 7.82 | 38.03 | 76.06 | -0.497 |
AcCAT5 | 501 | 58.01 | 6.39 | 44.37 | 71.40 | -0.537 |
AcCAT6 | 526 | 60.67 | 6.53 | 41.73 | 70.06 | -0.535 |
AcCAT7 | 302 | 35.33 | 6.09 | 44.08 | 73.61 | -0.542 |
AcCAT8 | 490 | 57.08 | 6.88 | 38.26 | 69.63 | -0.536 |
AcCAT9 | 91 | 10.34 | 5.90 | 37.97 | 63.19 | -0.676 |
图4 猕猴桃AcCAT基因在染色体上的分布 ①为染色体基因密度,②为GC含量,③为GC偏移,④为未知碱基分布
Fig. 4 Distribution of AcCAT genes on the chromosomes of A. chinensis ①indicates chromosome gene density, ② indicates GC ratio, ③ indicates GC skew, and ④ indicates Nratio
miRNA | 靶基因Target | 期望值Expectation | 序列比对Alignment | 抑制方式Inhibition |
---|---|---|---|---|
ach-miR166k-3p | AcCAT5 | 2.0 | miRNA 21 UCCCUAACUUCGGACCAGGCU 1 : : : : : : : : : : : : : : : :. : : Target 1338 AUGGAUUGAAGCCUUGUCUGA 1358 | 剪切 Cleavage |
ach-miR166k-3p | AcCAT6 | 2.0 | miRNA 21 UCCCUAACUUCGGACCAGGCU 1 : : : : : : : : : : : : : : : :. : : Target 1449 AUGGAUUGAAGCCUUGUCUGA 1469 | 剪切 Cleavage |
ach-miR166a-3p | AcCAT6 | 3.0 | miRNA 21 CCCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : :. : : Target 1449 AUGGAUUGAAGCCUUGUCUGA 1469 | 剪切 Cleavage |
ach-miR166a-3p | AcCAT5 | 3.0 | miRNA 21 CCCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : :. : : Target 1338 AUGGAUUGAAGCCUUGUCUGA 1358 | 剪切 Cleavage |
ach-miR166b | AcCAT6 | 3.0 | miRNA 21 AUCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : :. : : Target 1449 AUGGAUUGAAGCCUUGUCUGA 1469 | 剪切 Cleavage |
ach-miR166b | AcCAT5 | 3.0 | miRNA 21 AUCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : :. : : Target 1338 AUGGAUUGAAGCCUUGUCUGA 1358 | 剪切 Cleavage |
ach-miR166g-3p | AcCAT5 | 3.0 | miRNA 21 CUCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : :. : : Target 1338 AUGGAUUGAAGCCUUGUCUGA 1358 | 剪切 Cleavage |
ach-miR166g-3p | AcCAT6 | 3.0 | miRNA 21 CUCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : :. : : Target 1449 AUGGAUUGAAGCCUUGUCUGA 1469 | 剪切 Cleavage |
ach-miR166m | AcCAT5 | 3.0 | miRNA 21 UCCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : : :. : : Target 1338 AUGGAUUGAAGCCUUGUCUGA 1358 | 剪切 Cleavage |
ach-miR166m | AcCAT6 | 3.0 | miRNA 21 UCCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : : :. : : Target 1449 AUGGAUUGAAGCCUUGUCUGA 1469 | 剪切 Cleavage |
ach-miR166n | AcCAT5 | 3.0 | miRNA 21 UUCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : : :. : : Target 1338 AUGGAUUGAAGCCUUGUCUGA 1358 | 剪切 Cleavage |
ach-miR166n | AcCAT6 | 3.0 | miRNA 21 UUCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : : :. : : Target 1449 AUGGAUUGAAGCCUUGUCUGA 1469 | 剪切 Cleavage |
ach-miR166a | AcCAT6 | 3.0 | miRNA 19 CCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : :. : : Target 1451 GGAUUGAAGCCUUGUCUGA 1469 | 剪切 Cleavage |
ach-miR166a | AcCAT5 | 3.0 | miRNA 19 CCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : :. : : Target 1340 GGAUUGAAGCCUUGUCUGA 1358 | 剪切 Cleavage |
ach-miR166h-3p | AcCAT5 | 3.0 | miRNA 20 CCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : :. : : Target 1339 UGGAUUGAAGCCUUGUCUGA 1358 | 剪切 Cleavage |
ach-miR166h-3p | AcCAT6 | 3.0 | miRNA 20 CCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : :. : : Target 1450 UGGAUUGAAGCCUUGUCUGA 1469 | 剪切 Cleavage |
表2 靶向调控猕猴桃AcCAT基因的miRNA
Table 2 miRNAs targeting regulating AcCAT genes in A. chinensis
miRNA | 靶基因Target | 期望值Expectation | 序列比对Alignment | 抑制方式Inhibition |
---|---|---|---|---|
ach-miR166k-3p | AcCAT5 | 2.0 | miRNA 21 UCCCUAACUUCGGACCAGGCU 1 : : : : : : : : : : : : : : : :. : : Target 1338 AUGGAUUGAAGCCUUGUCUGA 1358 | 剪切 Cleavage |
ach-miR166k-3p | AcCAT6 | 2.0 | miRNA 21 UCCCUAACUUCGGACCAGGCU 1 : : : : : : : : : : : : : : : :. : : Target 1449 AUGGAUUGAAGCCUUGUCUGA 1469 | 剪切 Cleavage |
ach-miR166a-3p | AcCAT6 | 3.0 | miRNA 21 CCCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : :. : : Target 1449 AUGGAUUGAAGCCUUGUCUGA 1469 | 剪切 Cleavage |
ach-miR166a-3p | AcCAT5 | 3.0 | miRNA 21 CCCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : :. : : Target 1338 AUGGAUUGAAGCCUUGUCUGA 1358 | 剪切 Cleavage |
ach-miR166b | AcCAT6 | 3.0 | miRNA 21 AUCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : :. : : Target 1449 AUGGAUUGAAGCCUUGUCUGA 1469 | 剪切 Cleavage |
ach-miR166b | AcCAT5 | 3.0 | miRNA 21 AUCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : :. : : Target 1338 AUGGAUUGAAGCCUUGUCUGA 1358 | 剪切 Cleavage |
ach-miR166g-3p | AcCAT5 | 3.0 | miRNA 21 CUCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : :. : : Target 1338 AUGGAUUGAAGCCUUGUCUGA 1358 | 剪切 Cleavage |
ach-miR166g-3p | AcCAT6 | 3.0 | miRNA 21 CUCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : :. : : Target 1449 AUGGAUUGAAGCCUUGUCUGA 1469 | 剪切 Cleavage |
ach-miR166m | AcCAT5 | 3.0 | miRNA 21 UCCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : : :. : : Target 1338 AUGGAUUGAAGCCUUGUCUGA 1358 | 剪切 Cleavage |
ach-miR166m | AcCAT6 | 3.0 | miRNA 21 UCCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : : :. : : Target 1449 AUGGAUUGAAGCCUUGUCUGA 1469 | 剪切 Cleavage |
ach-miR166n | AcCAT5 | 3.0 | miRNA 21 UUCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : : :. : : Target 1338 AUGGAUUGAAGCCUUGUCUGA 1358 | 剪切 Cleavage |
ach-miR166n | AcCAT6 | 3.0 | miRNA 21 UUCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : : :. : : Target 1449 AUGGAUUGAAGCCUUGUCUGA 1469 | 剪切 Cleavage |
ach-miR166a | AcCAT6 | 3.0 | miRNA 19 CCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : :. : : Target 1451 GGAUUGAAGCCUUGUCUGA 1469 | 剪切 Cleavage |
ach-miR166a | AcCAT5 | 3.0 | miRNA 19 CCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : :. : : Target 1340 GGAUUGAAGCCUUGUCUGA 1358 | 剪切 Cleavage |
ach-miR166h-3p | AcCAT5 | 3.0 | miRNA 20 CCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : :. : : Target 1339 UGGAUUGAAGCCUUGUCUGA 1358 | 剪切 Cleavage |
ach-miR166h-3p | AcCAT6 | 3.0 | miRNA 20 CCCUUACUUCGGACCAGGCU 1 : : : : : : : : : : : : : :. : : Target 1450 UGGAUUGAAGCCUUGUCUGA 1469 | 剪切 Cleavage |
图8 猕猴桃AcCAT基因在果实贮藏过程中的表达谱 CK表示贮藏0 d,Four_1W为4℃条件下贮藏1周,Four_2W为4℃条件下贮藏2周,Four_3W为4℃条件下贮藏3周。下同
Fig. 8 Expression profile of AcCAT genes during the storage of kiwifruit CK indicates control check, Four_1W, Four_2W, Four_3W indicates kiwifruit stored in 4℃ for 1, 2 and 3 week, respectively. The same below
miRNA | AcCAT5 | AcCAT6 | ||||
---|---|---|---|---|---|---|
皮尔逊相关性Pearson correlation | 显著性Significance | 皮尔逊相关性Pearson correlation | 显著性Significance | |||
ach-miR166k-3p | -0.291 | 0.709 | -0.495 | 0.505 | ||
ach-miR166a-3p | -0.479 | 0.521 | -0.651 | 0.349 | ||
ach-miR166b | -0.990* | 0.010 | -0.976* | 0.024 | ||
ach-miR166g-3p | -0.996** | 0.004 | -0.975* | 0.025 | ||
ach-miR166m | -0.069 | 0.931 | -0.259 | 0.741 | ||
ach-miR166n | -0.991** | 0.009 | -0.978* | 0.022 | ||
ach-miR166a | -0.989* | 0.011 | -0.976* | 0.024 | ||
ach-miR166h-3p | -0.482 | 0.518 | -0.653 | 0.347 |
表3 基于表达谱的猕猴桃AcCAT基因与miR166家族成员的相关性分析
Table 3 Correlation analysis of AcCAT genes and miR166 family members in A. chinensis based on expression profile
miRNA | AcCAT5 | AcCAT6 | ||||
---|---|---|---|---|---|---|
皮尔逊相关性Pearson correlation | 显著性Significance | 皮尔逊相关性Pearson correlation | 显著性Significance | |||
ach-miR166k-3p | -0.291 | 0.709 | -0.495 | 0.505 | ||
ach-miR166a-3p | -0.479 | 0.521 | -0.651 | 0.349 | ||
ach-miR166b | -0.990* | 0.010 | -0.976* | 0.024 | ||
ach-miR166g-3p | -0.996** | 0.004 | -0.975* | 0.025 | ||
ach-miR166m | -0.069 | 0.931 | -0.259 | 0.741 | ||
ach-miR166n | -0.991** | 0.009 | -0.978* | 0.022 | ||
ach-miR166a | -0.989* | 0.011 | -0.976* | 0.024 | ||
ach-miR166h-3p | -0.482 | 0.518 | -0.653 | 0.347 |
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