Bulletin of Botanical Research ›› 2024, Vol. 44 ›› Issue (5): 774-782.doi: 10.7525/j.issn.1673-5102.2024.05.014
• Molecular biology • Previous Articles Next Articles
Xinyi YU, Huiyue JI, Pingping LU, Jiayu ZHOU, Hai LIAO()
Received:
2024-02-18
Online:
2024-09-20
Published:
2024-09-23
Contact:
Hai LIAO
E-mail:ddliaohai@home.swjtu.edu.cn
CLC Number:
Xinyi YU, Huiyue JI, Pingping LU, Jiayu ZHOU, Hai LIAO. The Bioinformatic Analysis on the Plant Isopentenyl Pyrophosphate Isomerase[J]. Bulletin of Botanical Research, 2024, 44(5): 774-782.
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URL: https://bbr.nefu.edu.cn/EN/10.7525/j.issn.1673-5102.2024.05.014
Table 2
Quantitative PCR primers used
基因 Gene | 引物 Primer | 序列(5′→3′) Sequence(5′→3′) |
---|---|---|
AT5G16440 | AtIPP1-F | AGAAGGCTGATGCTGGAGATGAAG |
AtIPP1-R | CCCTTTTCAACATGATCCCACCAC | |
AT3G02780 | AtIPP2-F | TCGCTTGAATCTCCTTCGCTGTATG |
AtIPP2-R | TTAGGGTTAGGGTTAGGGCTTCTCC | |
NC_003074.8 | At18s-F | CAGTCGGGGGCATTCGTATTT |
At18s-R | CAGCCTTGCGACCATACTCC | |
Os05g0413400 | OsIPP1-F | CCACAGAGCGTTCAGTGTTTTT |
OsIPP1-R | GTTCATGTTCGCCCCATTTTCC | |
Os07g0546000 | OsIPP2-F | CGAGAAAGGCACCCTCAACGA |
OsIPP2-R | CCAAGCTCCAAACCCAGAAAC | |
NM_001418593.1 | OsACT-F | AGGAAGGCTGGAAGAGGACC |
OsACT-R | CGGGAAATTGTGAGGGACAT |
Table 3
Physicochemical properties of IPP protein
蛋白质 Protein | 氨基酸长度 Number of amino acids/aa | 相对分子质量 Relative molecular mass | 等电点 Isoelectric point | 相对疏水性 Gravy |
---|---|---|---|---|
D7KZL1 | 283 | 32 469.32 | 6.10 | -0.267 |
D7M847 | 289 | 33 103.88 | 5.72 | -0.256 |
A0A1I9LM15 | 237 | 27 550.78 | 5.71 | -0.281 |
A0A5S9X8V2 | 284 | 32 607.49 | 6.10 | -0.264 |
A0A5S9Y4N3 | 291 | 33 213.95 | 5.69 | -0.298 |
A0A0Q3G4K6 | 296 | 33 266.11 | 5.86 | -0.241 |
I1GTN8 | 236 | 27 253.05 | 4.82 | -0.374 |
A0A0A0LHK1 | 286 | 32 466.14 | 5.84 | -0.165 |
A0A0A0M046 | 235 | 27 025.92 | 5.00 | -0.307 |
A0A165WP97 | 234 | 27 066.85 | 5.06 | -0.366 |
A0A2C9UNS0 | 303 | 34 303.98 | 5.82 | -0.300 |
A0A2C9USD6 | 302 | 34 024.76 | 5.62 | -0.251 |
A0A0N7KKS3 | 301 | 34 220.17 | 6.07 | -0.255 |
A0A0P0X7B7 | 238 | 27 341.20 | 4.90 | -0.330 |
A0A2T7EDT1 | 298 | 33 051.92 | 5.94 | -0.175 |
A0A2T7EX19 | 234 | 26 812.49 | 5.06 | -0.412 |
A0A2T7EX32 | 237 | 27 259.10 | 5.01 | -0.384 |
V7D3U4 | 301 | 34 171.89 | 5.75 | -0.300 |
A0A2K1WQ15 | 309 | 34 896.81 | 5.78 | -0.293 |
K3Z8E5 | 297 | 32 873.71 | 5.94 | -0.136 |
K3ZWJ9 | 237 | 27 269.04 | 4.93 | -0.433 |
K4A2A8 | 233 | 26 535.25 | 5.19 | -0.368 |
A0A4U6VF90 | 297 | 32 907.73 | 5.94 | -0.140 |
A0A4V6DBX0 | 237 | 27 269.04 | 4.93 | -0.433 |
M1AB35 | 302 | 34 658.83 | 6.17 | -0.322 |
M1C547 | 235 | 27 168.10 | 5.06 | -0.289 |
A0A1Z5R2L3 | 296 | 32 862.54 | 6.01 | -0.228 |
C5XAU4 | 237 | 27 271.11 | 4.86 | -0.357 |
A0A438BYS2 | 191 | 22 326.46 | 5.86 | -0.572 |
A0A3L6DPN5 | 296 | 33 028.79 | 5.94 | -0.199 |
A0A3L6E2U3 | 237 | 27 242.02 | 4.84 | -0.356 |
Table 4
Chromosome localization of IPP gene in each species
物种 Species | 基因 Gene | 染色体定位 Gene localization |
---|---|---|
琴叶拟南芥 Arabidopsis lyrata | ARALYDRAFT_477520 | 3 |
ARALYDRAFT_488496 | 6 | |
拟南芥 Arabidopsis thaliana | AT3G02780 | 3 |
AT5G16440 | 5 | |
菜豆 Phaseolus vulgaris | PHAVU_L002800g | 未确定 |
毛果杨 Populus trichocarpa | POPTR_019G053700 | 19 |
黄瓜 Cucumis sativus | Csa_2G074290 | 2 |
Csa_1G656460 | 1 | |
胡萝卜 Daucus carota var. sativa | DCAR_015080 | 4 |
木薯 Manihot esculenta | MANES_13G005300 | 13 |
MANES_12G005500 | 12 | |
马铃薯 Solanum tuberosum | PGSC0003DMG400007268 | 4 |
PGSC0003DMG400023359 | 5 | |
葡萄 Vitis vinifera | Vitvi04g01175 | 4 |
二穗短柄草 Brachypodium distachyon | BRADI_2g25360v3 | 2 |
BRADI_1g25350v3 | 1 | |
稻 Oryza sativa | Os05g0413400 | 5 |
Os07g0546000 | 7 | |
粱 Setaria italica | SETIT_022815mg | 3 |
SETIT_030981mg | 2 | |
SETIT_033005mg | 2 | |
狗尾草 Setaria viridis | SEVIR_3G247700v2 | 3 |
SEVIR_2G354200v2 | 2 | |
高粱 Sorghum bicolor | SORBI_3009G137700 | 9 |
SORBI_3002G330500 | 2 | |
霍尔稷草 Panicum hallii var. hallii | GQ55_3G269900 | 3 |
GQ55_2G389900 | 2 | |
GQ55_2G390000 | 2 | |
玉蜀黍 Zea mays | Zm00001eb349410 | 8 |
Zm00001eb323510 | 7 |
Table 5
Cis-acting elements in Arabidopsis and Oryza sativaIPP gene promoters
顺式作用元件 Cis-acting elements | AT3G02780 | AT5G16440 | Os05t0413400 | Os07t0546000 |
---|---|---|---|---|
脱落酸响应元件 ABRE | 3 | 1 | 4 | 7 |
抗氧化响应元件 ARE | 2 | 3 | 2 | 3 |
防御和应激响应元件 Defense and stress responsive | 0 | 1 | 0 | 0 |
干旱响应元件 Drought induced-responsive | 2 | 1 | 0 | 1 |
雌激素响应元件 ERE | 2 | 0 | 2 | 0 |
光响应元件 Light responsive | 10 | 8 | 15 | 12 |
低温响应元件 LTR | 1 | 0 | 1 | 1 |
茉莉酸甲酯响应元件 MeJA-responsive | 0 | 2 | 6 | 4 |
分生组织表达 Meristem expression | 1 | 1 | 0 | 0 |
氧化应激响应元件 As-1 | 0 | 1 | 0 | 0 |
水杨酸响应元件 Salicylic acid-responsive | 2 | 1 | 0 | 0 |
盐应激响应元件 Salt stress-responsive | 5 | 10 | 0 | 0 |
压力响应元件 Stress-responsive | 6 | 7 | 5 | 3 |
伤口响应元件 Wounding responsive | 1 | 1 | 4 | 0 |
玉米醇溶蛋白代谢响应元件 Zein metabolism regulation | 1 | 0 | 0 | 0 |
Fig.2
Interaction network and analysis of IPP between Oryza sativa and Arabidopsis thalianaA and B are the IPP protein interaction networks of Oryza sativa and Arabidopsis;C and D are the GO analysis of IPP interacting proteins of O. sativa and Arabidopsis IPP;E and F are KEGG analysis of IPP interacting proteins of O. sativa and Arabidopsis.
Fig.3
The expressional pattern of A. thaliana and O. sativaIPP genes in different organs and under different stress conditionsA and F represent the relative expression of A. thaliana and O. sativa IPP genes in different organs; B, C, D and E represent the expression changes of AT5G16440, AT3G02780, Os05g0413400 and Os07g0546000 genes under short-term stress, respectively; G, H, I and J represent the relative expression levels of AT5G16440, AT3G02780, Os05g0413400 and Os07g0546000 genes after one week of stress, respectively. * indicates significant difference, and ** indicates extremely significant difference.
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