生物技术通报 ›› 2021, Vol. 37 ›› Issue (4): 18-27.doi: 10.13560/j.cnki.biotech.bull.1985.2020-1128
高玲(), 王斐, 谢双全, 陈喜凤, 沈海涛, 李鸿彬()
收稿日期:
2020-09-05
出版日期:
2021-04-26
发布日期:
2021-05-13
作者简介:
高玲,女,硕士研究生,研究方向:生物化学与分子生物学;E-mail:基金资助:
GAO Ling(), WANG Fei, XIE Shuang-quan, CHEN Xi-feng, SHEN Hai-tao, LI Hong-bin()
Received:
2020-09-05
Published:
2021-04-26
Online:
2021-05-13
摘要:
钙依赖磷酸酶B类似蛋白(Calcineurin B-like proteins,CBL)是植物特有的一类Ca2+传感蛋白,在植物逆境应答及发育过程中发挥重要作用。为挖掘乌拉尔甘草CBL家族成员特征并预测CBL功能,利用生物信息学方法从乌拉尔甘草基因组中鉴定出10个CBL基因,命名为GuCBL1-GuCBL10,分别定位在10个不同的支架上。氨基酸序列比对发现,CBL家族成员在C-末端都含有4个与钙离子结合的EF-motif,部分CBL成员N端含有肉豆蔻酰化位点及棕榈酰化位点,预测可能与CBL蛋白的亚细胞定位有关。进化树分析显示,乌拉尔甘草CBL基因家族可分为4个亚家族,且各亚族中都包含拟南芥和大豆的CBL基因家族成员,说明它们具有高同源性。在乌拉尔甘草CBL基因的上游序列中,存在一些应答多种激素和逆境的顺式元件,预测CBL基因家族可能具有不同的生物学功能。组织表达分析表明,GuCBL在乌拉尔甘草根、茎和叶片中均有表达,在根中的表达量最高。荧光定量分析显示,在盐、氧化、干旱、高温和低温胁迫下,CBL家族基因受到不同程度的诱导,说明乌拉尔甘草CBL家族基因的表达与逆境胁迫响应之间的密切联系。该研究结果为深入理解CBL基因响应非生物胁迫的调控机制和解析其参与次生代谢物质累积的功能奠定基础。
高玲, 王斐, 谢双全, 陈喜凤, 沈海涛, 李鸿彬. 乌拉尔甘草CBL基因家族的鉴定与表达分析[J]. 生物技术通报, 2021, 37(4): 18-27.
GAO Ling, WANG Fei, XIE Shuang-quan, CHEN Xi-feng, SHEN Hai-tao, LI Hong-bin. Genome-wide Identification and Expression Analysis of CBL Gene Family in Glycyrrhiza uralensis[J]. Biotechnology Bulletin, 2021, 37(4): 18-27.
引物名称Primer name | 引物序列Primer sequence(5'-3') | 引物功能 Primer function |
---|---|---|
GuCBL1-F | CGAGCTTGACGTTGGGAGAG | GuCBL的RT-PCR检测 qRT-PCR detection of GuCBL |
GuCBL1-R | CTGGCGAGGGCGACAATATC | |
GuCBL2-F | TTTGTTTGCTGATCGGGTGT | |
GuCBL2-R | ATTCCGCAAGCGTAGCAACT | |
GuCBL3-F | CCGATTCGTCAAAGCAACCT | |
GuCBL3-R | AGGATCCCATTGTGCTTTGTG | |
GuCBL4-F | GAGAGGCGGTTTGCGTATTG | |
GuCBL4-R | GCCTTTTTACGGTTCCTGGC | |
GuCBL5-F | TGTCAGTGAGGTTGAGGCATT | |
GuCBL5-R | CGCATTTGGGTGGAAGACAT | |
GuCBL6-F | GCAGTGCAGTTATTGACGATGG | |
GuCBL6-R | TGATGCACTGGGATGGAAGAC | |
GuCBL7-F | GCTGTGTGCGGTGTTCATTC | |
GuCBL7-R | GCGCAACGCCTCAATTTCAT | |
GuCBL8-F | ATGAGGATCCCACCGTTCTTG | |
GuCBL8-R | ACCCCATTGCGCTTGACATC | |
GuCBL9-F | TCCTTGCTTCTGAAACACCCT | |
GuCBL9-R | TGGCCATTGCGATTGACATC | |
GuCBL10-F | CAGCAACAGCACAGGCATTT | |
GuCBL10-R | CAGCAAGGCGAGCGAAATC | |
GuActin-F | CCTCAACCCAAAGGTCAACAG | 内参基因 Internal reference gene |
GuActin-R | GACCAGCGAGATCCAAACGAA | |
GuCBL4-1 | GAAATTGAAGCATTATATGATCTGT | 全长基因克隆 Full-length gene cloning |
GuCBL4-2 | GGAGCCTATGGAAAAACGCCAGCAA | |
GuCBL7-1 | ACTTCGTAGCTAGCACTCCG | |
GuCBL7-2 | GACTGCATGATGGCGGAAAA | |
GuCBL10-1 | AGCAACAGCACAGGCATTTCC | |
GuCBL10-2 | CAGCCTCCGATTTGAAAACAAAACT |
表1 所使用的引物
Table 1 Primers used in this study
引物名称Primer name | 引物序列Primer sequence(5'-3') | 引物功能 Primer function |
---|---|---|
GuCBL1-F | CGAGCTTGACGTTGGGAGAG | GuCBL的RT-PCR检测 qRT-PCR detection of GuCBL |
GuCBL1-R | CTGGCGAGGGCGACAATATC | |
GuCBL2-F | TTTGTTTGCTGATCGGGTGT | |
GuCBL2-R | ATTCCGCAAGCGTAGCAACT | |
GuCBL3-F | CCGATTCGTCAAAGCAACCT | |
GuCBL3-R | AGGATCCCATTGTGCTTTGTG | |
GuCBL4-F | GAGAGGCGGTTTGCGTATTG | |
GuCBL4-R | GCCTTTTTACGGTTCCTGGC | |
GuCBL5-F | TGTCAGTGAGGTTGAGGCATT | |
GuCBL5-R | CGCATTTGGGTGGAAGACAT | |
GuCBL6-F | GCAGTGCAGTTATTGACGATGG | |
GuCBL6-R | TGATGCACTGGGATGGAAGAC | |
GuCBL7-F | GCTGTGTGCGGTGTTCATTC | |
GuCBL7-R | GCGCAACGCCTCAATTTCAT | |
GuCBL8-F | ATGAGGATCCCACCGTTCTTG | |
GuCBL8-R | ACCCCATTGCGCTTGACATC | |
GuCBL9-F | TCCTTGCTTCTGAAACACCCT | |
GuCBL9-R | TGGCCATTGCGATTGACATC | |
GuCBL10-F | CAGCAACAGCACAGGCATTT | |
GuCBL10-R | CAGCAAGGCGAGCGAAATC | |
GuActin-F | CCTCAACCCAAAGGTCAACAG | 内参基因 Internal reference gene |
GuActin-R | GACCAGCGAGATCCAAACGAA | |
GuCBL4-1 | GAAATTGAAGCATTATATGATCTGT | 全长基因克隆 Full-length gene cloning |
GuCBL4-2 | GGAGCCTATGGAAAAACGCCAGCAA | |
GuCBL7-1 | ACTTCGTAGCTAGCACTCCG | |
GuCBL7-2 | GACTGCATGATGGCGGAAAA | |
GuCBL10-1 | AGCAACAGCACAGGCATTTCC | |
GuCBL10-2 | CAGCCTCCGATTTGAAAACAAAACT |
基因名称 Gene name | 染色体位置 Chromosome location | 开放阅读框长度 Open reading frame sequence length/bp | 氨基酸数目Amino acid number/aa | 分子量Molecular weight/kD | 等电点Isoelectric point | N-端氨基酸 N-terminal amino acid | 棕榈酰化位点 Palmitoylation site | 豆蔻酰化位点 Myristoylation site | 亚细胞定位 Subcellular localization |
---|---|---|---|---|---|---|---|---|---|
GuCBL1 | Scaffold00021(+):357697-361866 | 828 | 275 | 31.68 | 4.99 | MMIDMDFS | √ | × | 质膜 Plasma membrane |
GuCBL2 | Scaffold00027(+):170105-174365 | 699 | 232 | 26.76 | 4.77 | MVKRDIML | √ | × | 质膜 Plasma membrane |
GuCBL3 | Scaffold00030(-):499662-505101 | 750 | 249 | 28.71 | 4.93 | MPDSDSLF | √ | × | 质膜 Plasma membrane |
GuCBL4 | Scaffold00036(-):366361-373219 | 1 008 | 331 | 37.63 | 9.31 | WLIFQKLK | √ | × | 质膜 Plasma membrane |
GuCBL5 | Scaffold00067(+):227402-231449 | 642 | 213 | 24.36 | 4.67 | MGCFNSKA | √ | √ | 质膜 Plasma membrane |
GuCBL6 | Scaffold00088(-):140793-143426 | 681 | 226 | 25.72 | 4.57 | MVQFLDEL | √ | × | 质膜 Plasma membrane |
GuCBL7 | Scaffold00219(-):429-5651 | 861 | 364 | 41.46 | 5.33 | MDFVASTP | √ | × | 质膜 Plasma membrane |
GuCBL8 | Scaffold00461(-):93781-104251 | 651 | 216 | 24.87 | 4.76 | MGCYCSTS | √ | √ | 质膜 Plasma membrane |
GuCBL9 | Scaffold00669(-):36499-39615 | 717 | 238 | 27.41 | 5.38 | MGCRSSKV | √ | √ | 质膜 Plasma membrane |
GuCBL10 | Scaffold01818(+):19453-23753 | 735 | 269 | 31.13 | 5.35 | MLQQQHRH | √ | × | 质膜 Plasma membrane |
表2 乌拉尔甘草CBL基因家族特征分析
Table 2 Characteristic analysis of G. uralensis CBL family genes
基因名称 Gene name | 染色体位置 Chromosome location | 开放阅读框长度 Open reading frame sequence length/bp | 氨基酸数目Amino acid number/aa | 分子量Molecular weight/kD | 等电点Isoelectric point | N-端氨基酸 N-terminal amino acid | 棕榈酰化位点 Palmitoylation site | 豆蔻酰化位点 Myristoylation site | 亚细胞定位 Subcellular localization |
---|---|---|---|---|---|---|---|---|---|
GuCBL1 | Scaffold00021(+):357697-361866 | 828 | 275 | 31.68 | 4.99 | MMIDMDFS | √ | × | 质膜 Plasma membrane |
GuCBL2 | Scaffold00027(+):170105-174365 | 699 | 232 | 26.76 | 4.77 | MVKRDIML | √ | × | 质膜 Plasma membrane |
GuCBL3 | Scaffold00030(-):499662-505101 | 750 | 249 | 28.71 | 4.93 | MPDSDSLF | √ | × | 质膜 Plasma membrane |
GuCBL4 | Scaffold00036(-):366361-373219 | 1 008 | 331 | 37.63 | 9.31 | WLIFQKLK | √ | × | 质膜 Plasma membrane |
GuCBL5 | Scaffold00067(+):227402-231449 | 642 | 213 | 24.36 | 4.67 | MGCFNSKA | √ | √ | 质膜 Plasma membrane |
GuCBL6 | Scaffold00088(-):140793-143426 | 681 | 226 | 25.72 | 4.57 | MVQFLDEL | √ | × | 质膜 Plasma membrane |
GuCBL7 | Scaffold00219(-):429-5651 | 861 | 364 | 41.46 | 5.33 | MDFVASTP | √ | × | 质膜 Plasma membrane |
GuCBL8 | Scaffold00461(-):93781-104251 | 651 | 216 | 24.87 | 4.76 | MGCYCSTS | √ | √ | 质膜 Plasma membrane |
GuCBL9 | Scaffold00669(-):36499-39615 | 717 | 238 | 27.41 | 5.38 | MGCRSSKV | √ | √ | 质膜 Plasma membrane |
GuCBL10 | Scaffold01818(+):19453-23753 | 735 | 269 | 31.13 | 5.35 | MLQQQHRH | √ | × | 质膜 Plasma membrane |
图1 乌拉尔甘草GuCBL在染色体支架上的分布 GuCBL位于10个单独的支架上,黑线条表示片段重复基因对,各染色体支架以不同颜色的圆形显示
Fig. 1 Chromosomal scaffold distribution of GuCBL genes in G. uralensis GuCBL genes are located on 10 individual scaffolds. Pairs of segmentally duplicated genes are indicated by black lines. Chromosomal scaffolds are showed with different colored circles
图2 CBL家族的系统发育关系分析 红色、绿色和蓝色分别表示乌拉尔甘草、拟南芥和大豆的 CBL 蛋白
Fig. 2 Phylogenetic relationship analysis of the CBL family The CBL proteins of G. uralensis, A. thaliana, and G. max were indicated in red, green, and blue, respectively
图3 乌拉尔甘草CBL家族基因基因结构和保守基序分析 a:GuCBL 基因的外显子/内含子结构分析。绿框和黑线分别代表外显子和内含子,基因组长度在底部标示。b :GuCBL 蛋白的保守基序分析
Fig. 3 Conserved motif and gene structure analyses of CBL family genes in G. uralensis a: Exon/intron structure analysis of GuCBL genes. Green boxes and black lines represent the exons and introns respectively, and the genomic length is indicated at the bottom. b: Conserved motif analysis of GuCBL proteins
图4 乌拉尔甘草 CBL的多序列比对和保守结构域分析 EF-hand、PFPF-motif、豆蔻酰化位点和 PFPF结构域内的丝氨酸残基分别用红色线框标注
Fig. 4 Multiple alignment and conserved motif analysis of CBL in G. uralensis EF-hand, PFPF-motif, myristoylation site, and serine residue of PFPF-motif are showed in red boxes
图5 乌拉尔甘草、大豆和拟南芥CBL基因的共线性分析 蓝色、红色、紫色线条分别表示乌拉尔甘草重复 CBL 基因对、乌拉尔甘草CBL 基因与拟南芥和大豆 CBL 基因之间的共线关系、及大豆和拟南芥之间或内部的 CBL 基因对
Fig. 5 Syntenic analysis of CBL genes in G. uralensis, G. max, and A. thaliana Blue, red, and purple lines represent duplicated CBL pairs in G. uralensis, syntenic relationships of CBL genes between G. uralensis and the other two species of G. max and A. thaliana, and CBL pairs between or inside G. max and A. thaliana
同源基因 Paralogous genes | Ka | Ks | Ka/Ks | 选择压 Selective pressure |
---|---|---|---|---|
GuCBL1-GuCBL7 | 0.2127 | 0.1996 | 1.0656 | Positive selection |
GuCBL3-GuCBL2 | 0.1968 | 0.1674 | 1.1756 | Positive selection |
表3 乌拉尔甘草同源CBL基因的Ka/Ks比值
Table 3 Ka/Ks ratios for homologous CBL genes in G. uralensis
同源基因 Paralogous genes | Ka | Ks | Ka/Ks | 选择压 Selective pressure |
---|---|---|---|---|
GuCBL1-GuCBL7 | 0.2127 | 0.1996 | 1.0656 | Positive selection |
GuCBL3-GuCBL2 | 0.1968 | 0.1674 | 1.1756 | Positive selection |
测试组 Testing group | 测试值Testing value | |||||
---|---|---|---|---|---|---|
Mtb | M1c | M2d | Χ2 | Pe | ||
GuCBL1/GuCBL7 with GmCBL7 | 174 | 16 | 39 | 9.62 | 0.00193 | |
GuCBL3/GuCBL2 with GmCBL6 | 236 | 19 | 5 | 8.27 | 0.00026 |
表4 乌拉尔甘草中同源CBL基因对的田岛相对进化速率分析a
Table 4 Tajima relative rate tests of homologous CBL gene pairs in G. uralensisa
测试组 Testing group | 测试值Testing value | |||||
---|---|---|---|---|---|---|
Mtb | M1c | M2d | Χ2 | Pe | ||
GuCBL1/GuCBL7 with GmCBL7 | 174 | 16 | 39 | 9.62 | 0.00193 | |
GuCBL3/GuCBL2 with GmCBL6 | 236 | 19 | 5 | 8.27 | 0.00026 |
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