Welcome to Acta Agronomica Sinica,

Acta Agronomica Sinica ›› 2018, Vol. 44 ›› Issue (9): 1334-1346.doi: 10.3724/SP.J.1006.2018.01334

• RESEARCH PAPERS • Previous Articles     Next Articles

Identification and Bioinformatics Analysis of the PIN Family Gene in Brassica napus

Kun GAO1,2(),Ying-Peng HUA1,2,Hai-Xing SONG1,2,Chun-Yun GUAN3,Zhen-Hua ZHANG1,2,Ting ZHOU1,2,*()   

  1. 1 College of Resource and Environment, Hunan Agricultural University, Changsha 410128, Hunan, China
    2 Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha 410128, Hunan, China
    3 Hunan Branch, National Oil Crops Improvement Center, Changsha 410128, Hunan, China
  • Received:2018-01-30 Accepted:2018-06-12 Online:2018-09-10 Published:2018-09-12
  • Contact: Ting ZHOU E-mail:gaokun0874@foxmail.com;zhoutingplant@foxmail.com
  • Supported by:
    This study was supported by the National Key R&D Program of China(2017YFD0200103);National Natural Science Foundation of China(31101596);National Natural Science Foundation of China(31372130);Research Starting Foundation for New Teachers of Hunan Agricultural University(30555|550100100021);Youth Foundation of Hunan Agricultural University(17QN40);China Agriculture Research System


The PIN family is a type of important carrier elements that regulate the polar transportation of auxin. The PIN genes encode auxin efflux carriers with multiple transmembrane domains that mediate auxin transport in plants. However, there is a lack of systematic research in the genome of complexity Brassica napus. In this study, the BnPIN genes were screened from the Brassica Database using bioinformatics, and study on molecular characteristics of BnPIN proteins, such as copy number variations, transmembrane domains, conserved motifs, chromosomal locations, phylogenetic relationships, secondary and three-dimensional structures, and high-throughput transcriptome sequencing was used to analyze the transcriptional level under low nitrate stress. The results showed that most of the BnPIN proteins which is belonged to the stable protein consisting of basic amino acids. The BnPIN family proteins contained secondary structures similar to those of Arabidopsis PINs accompanied by conserved N-terminal domains. The phylogenetic analysis showed that BnPIN genes were similar to the corresponding homologs of Brassica oleracea and Brassica rapa. High-throughput transcriptome analysis showed that the BnPIN1s, BnPIN2s, and BnPIN3s genes were mainly expressed in roots of Brassica napus under long-term (72 h) low nitrate (NO3 -) stress. The BnPIN6s and BnPIN8s genes were mainly expressed in the shoot and limited NO3 - repressed the BnPIN6s expression. This study is valuable for the research that the roles of the BnPIN family in the regulation of auxin transport. Our results also provide reference for the integrated genomic and transcriptomic studies of gene family in plant species with complex genomes.

Key words: Brassica napus, auxin, PIN, gene family, bioinformatics

Fig. 1

Copy number variation of PIN family genes in Brassica napus, Arabidopsis thaliana, Brassica rapa, and Brassica oleraceaThe number at the top of the histogram is the number of genes copied for that species."

Fig. 2

Domains architecture of BnPINsTransmembrane regions are in blue and low complexities are in pink."

Fig. 3

Amino acid sequence alignment and conserved domain analysis of PIN family in Brassica napusThe yellow area is a highly conserved amino acid site."

Fig. 4

Chromosome mapping of the 23 BnPINs"

Fig. 5

Distribution of conserved motifs in the BnPINsThe different colors on the right correspond to the positions of different conserved motifs on the series, respectively."

Fig. 6

Evolutionary relationships of BnPINs taxaDifferent clades are in different colors, I and II above clades indicate the two subgroups of PIN family."

Fig. 7

Secondary structure analysis of BnPIN5b proteinGOR4 and PSIPRED are two tools for the secondary structure analysis."

Fig. 8

Prediction of three-dimensional structure of BnPIN2a proteinThe three-dimensional structure predicts that the crystal is a transporter."

Fig. 9

Transcriptome analysis of PIN family genes in Brassica napus under low nitrate concentration conditionsS: shoot; R: root; 0, 3, and 72 (h) represent the time course of nitrogen deficiency. The results represent the average of three biological replicates."

Fig. 10

Co-expression network analysis and expression of PIN family genes in Brassica napus under low nitrate concentration conditionA: co-expression network analysis; B: expression of PIN family genes; cycle nodes represent genes, and the size of the nodes represents the power of the interrelation among the nodes by degree value, edges between two nodes represent interactions between genes; S: shoot; R: root; 0, 3, and 72 (h) represents the time course of nitrogen deficiency. The results represent the average of three biological replicates."

[1] 刘士平, 王璐, 王继荣, 薛艳红, 寿惠霞 . 高等植物的PIN基因家族. 植物生理学通讯, 2009,45:833-841
Liu S P, Wang L, Wang J R, Xue Y H, Shou H X . PIN gene family in higher plants.. Plant Physiol Commun, 2009,45:833-841 (in Chinese)
[2] Petrášek J, Friml J . Auxin transport routes in plant development. Development, 2009,136:2675-2688
[3] Paponov I A, Teale W D, Trebar M, Blilou I, Palme K . The PIN auxin efflux facilitators: evolutionary and functional perspectives. Trends Plant Sci, 2005,10:170-177
doi: 10.1016/j.tplants.2005.02.009 pmid: 15817418
[4] Abas L, Benjamins R, Malenica N, Paciorek T, Wiśniewska J, Anzola J M, Sieberer T, Friml J, Luschnig C . Intracellular trafficking and proteolysis of the Arabidopsis auxin efflux facilitator PIN2 are involved in root gravitropism. Nat Cell Biol, 2006,8:249-256
[5] Schnabel E L, Frugoli J . The PIN and LAX families of auxin transport genes in Medicago truncatula. Mol Genet Genomics, 2004,272:420-432
[6] Krecek P, Skupa P, Libus J, Naramoto S, Tejos R, Friml J, Zažímalová E. The PIN-FORMED ( PIN) protein family of auxin transporters. Genome Biol, 2009,10:249-254
[7] Gälweiler L, Guan C, Müller A, Wisman E, Mendgen K, Yephremov A, Palme K . Regulation of polar auxin transport by AtPIN1 in Arabidopsis vascular tissue. Science, 1998,282:2226-2230
doi: 10.1126/science.282.5397.2226 pmid: 9856939
[8] Blilou I, Xu J, Wildwater M, Willemsen V, Paponov I, Friml J, Heidstra R, Aida M, Palme K, Scheres B . The PIN auxin efflux facilitator network controls growth and patterning in Arabidopsis roots. Nature, 2005,433:39-44
doi: 10.1038/nature03184 pmid: 15635403
[9] Ding Z , Galván-Ampudia C S, Demarsy E, Łangowski L, Kleine-Vehn J, Fan Y, Morita M T, Tasaka M, Fankhauser C, Offringa R. Light-mediated polarization of the PIN3 auxin transporter for the phototropic response in Arabidopsis. Nat Cell Biol, 2011,13:447-452
[10] Friml J, Benková E, Blilou I, Wisniewska J, Hamann T, Ljung K, Woody S, Sandberg G, Scheres B, Jürgens G . AtPIN4 mediates sink-driven auxin gradients and root patterning in Arabidopsis. Cell, 2002,108:661-673
doi: 10.1016/S0092-8674(02)00656-6 pmid: 11893337
[11] Mravec J, Skupa P, Bailly A, Hoyerová K, Krecek P, Bielach A, Petrásek J, Zhang J, Gaykova V, Stierhof Y D, Dobrev P, Schwarzerová K, Rolcík J, Seifertová D, Luschnig C, Benková E, Zazimalová E, Geisler M, Friml J . Subcellular homeostasis of phytohormone auxin is mediated by the ER-localized PIN5 transporter. Nature, 2009,459:1133-1140
doi: 10.1038/nature08066 pmid: 19506555
[12] Benková E, Michniewicz M, Sauer M, Teichmann T, Seifertová D, Jürgens G, Friml J . Local, efflux-dependent auxin gradients as a common module for plant organ formation. Cell, 2003,115:591-602
doi: 10.1016/S0092-8674(03)00924-3 pmid: 14651850
[13] Kleine-Vehn J, Ding Z, Jones A R, Tasaka M, Morita M T, Friml J . Gravity-induced PIN transcytosis for polarization of auxin fluxes in gravity-sensing root cells. Proc Natl Acad Sci USA, 2010,107:22344-22349
doi: 10.1073/pnas.1013145107 pmid: 21135243
[14] Ding Z, Wang B, Moreno I, Dupláková N, Simon S, Carraro N, Reemmer J, Pěnčík A, Chen X, Tejos R, Skupa P, Pollmann S, Mravec J, Petrášek J, Zažímalová E, Honys D, Rolčík J, Murphy A, Orellana A, Geisler M, Friml J . ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis. Nat Commun, 2012,3:941
[15] Chen R, Hilson P, Sedbrook J, Rosen E, Caspar T, Masson P H . The Arabidopsis thaliana AG-RAVITROPIC1 gene encodes a component of the polar-auxin-transport efflux carrier. Proc Natl Acad Sci USA, 1998,95:15112-15117
[16] 李俊华, 种康 . 植物生长素极性运输调控机理的研究进展. 植物学通报, 2006,23:466-477
Li J H, Chong K . Current research advances on polar auxin transport in plant. Chin Bull Bot, 2006,23:466-477 (in Chinese with English abstract)
[17] 刘进平 . 生长素运输机制研究进展. 中国农学通报, 2007,23(5):432-433
Liu J P . Research advances on auxin transport mechanism. Chin Agric Sci Bull, 2007,23(5):432-433 (in Chinese with English abstract)
[18] 李运合, 孙光明, 吴蓓 . 植物生长素的极性运输载体研究进展. 西北植物学报, 2009,29:1714-1722
Li Y H, Sun G M, Wu B . Advances on carriers of plant polar auxin transport. Acta Bot Boreali-Occident Sin, 2009,29:1714-1722 (in Chinese with English abstract)
[19] 朱德进, 张辉, 黄卉, 宁运旺, 张永春 . 不同施肥处理对不同地力水平油菜产量和经济效益的影响. 江苏农业科学, 2013,41(10):73-76
Zhu D J, Zhang H, Huang H, Ning Y W, Zhang Y C . Different fertilization treatments on rape yield at different soil fertility levels and the impact of economic benefits. Jiangsu Agric Sci, 2013,41(10):73-76 (in Chinese with English abstract)
[20] Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun J H, Bancroft I, Cheng F . The genome of the mesopolyploid crop species Brassica rapa. Nat Genet, 2011,43:1035-1039
[21] Bayer P E, Hurgobin B, Golicz A, Chan C K, Yuan Y, Lee H T, Renton M, Meng J, Li R, Long Y, Zou J, Bancroft I, Chalhoub B, King G J, Batley J, Edwards D . Assembly and comparison of two closely related Brassica napus genomes. Plant Biotechnol J, 2017,10:1-9
[22] Rathke G W, Christen O, Diepenbrock W . Effects of nitrogen source and rate on productivity and quality of winter oilseed rape (Brassica napus L.) grown in different crop rotations. Field Crops Res, 2005,94:103-113
[23] de Jong M, George G, Ongaro V, Williamson L, Willetts B, Ljung K, Leyser O . Auxin and strigolactone signaling are required for modulation of Arabidopsis shoot branching by nitrogen supply. Plant Physiol, 2014,166:384-395
[24] Liu J X, An X, Cheng L, Chen F J, Bao J, Yuan L X, Zhang F S, Mi G H . Auxin transport in maize roots in response to localized nitrate supply. Ann Bot, 2010,106:1019-1026
doi: 10.1093/aob/mcq202 pmid: 29906712025
[25] Finn R D, Bateman A, Clements J, Coggill P, Eberhardt R Y, Eddy S R, Heger A, Hetherington K, Holm L, Mistry J , Sonnhammer E L L, Tate J, Punta M. Pfam: the protein families database. Nucl Acids Res, 2013,27:1-9
[26] Letunic I, Doerks T, Bork P . SMART: recent updates, new developments and status in 2015. Nucl Acids Res, 2015,43:D257-D260
doi: 10.1093/nar/gku949 pmid: 25300481
[27] Gasteiger E, Hoogland C, Gattiker A, Hoogland C, Ivanyi I, Appel R D, Bairoch A . ExPASy: the proteomics server for in-depth. Nucl Acids Res, 2003,31:3784-3788
[28] Hofmann K, Stoffel W . TM base-A database of membrane spanning protein segments. Biol Chem Hoppe Seyler, 1993,374:1-6
doi: 10.1056/NEJM199001043220121
[29] Bailey T L, Elkan C . Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intel Syst Mol Biol, 1994,2:28-36
pmid: 7584402
[30] Larkin M A, Blackshields G, Brown N P, Chenna R ,McGettigan P A, McWilliam H, Valentin F, Wallace I M, Wilm A, Lopez R, Thompson J D, Gibson T J, Higgins D G. , Clustal W and Clustal X version 2.0. Bioinformatics, 2007,23:2947-2948
[31] Kumar S, Nei M, Dudley J, Tamura K . MEGA: a biologist centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform, 2008,9:299-306
doi: 10.1093/bib/bbn017 pmid: 2562624
[32] Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones S J, Marra M A . Circos an information aesthetic for comparative genomics. Genome Res, 2009,19:1639-1645
[33] Combet C, Blanchet C, Geourjon C, Deléage G . Network protein sequence analysis. Trends Biochem Sci, 2000,25:147-150
[34] Jones D T . Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol, 1999,292:195-202
doi: 10.1006/jmbi.1999.3091 pmid: 10493868
[35] Buchan D W A, Minneci F, Nugent T C O, Bryson K, Jones D T . Scalable web services for the PSIPRED protein analysis workbench. Nucl Acids Res, 2013,41:W340-W348
[36] Mezulis S Sternberg M J E, Kelley L A. , Phyre Storm: a web server for fast structural searches against the PDB. J Mol Biol, 2016,428:702-708
doi: 10.1016/j.jmb.2015.10.017 pmid: 26517951
[37] Hoagland D R, Arnon D I . The water culture method for growing plants without soil. Calif Agric Exp Stn Circ, 1950,347:32
doi: 10.1016/S0140-6736(00)73482-9
[38] Morin D, Bainbridge M, Fejes A, Hirst M, Krzywinski M, Pugh T J , McDonald H, Varhol R, Jones S J M, Marra M A. Profiling the He La S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques, 2008,45:81-94
[39] Eisen M B, Spellman P T, Brown P O, Botstein D . Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA, 1998,95:14863-14868
[40] Kohl M, Wiese S, Warscheid B . Cytoscape: software for visualization and analysis of biological networks. Methods Mol Biol, 2011,696:291-303
[41] 王占军, 金伦, 徐忠东, 欧祖兰 . 麻风树LEC1基因的生物信息学分析. 生物学杂志, 2014,31(4):68-72
Wang Z J, Jin L, Xu Z D, Ou Z L . Bioinformatics analysis of gene LEC1 from Jatropha curcas. J Biol, 2014,31(4):68-72 (in Chinese with English abstract)
[42] Cazzonelli1 C I, Vanstraelen M, Simon S, Yin K, Carron-Arthur A, Nisar N, Tarle G, Cuttriss A J, Searle I R, Benkova E, Mathesius U, Masle J, Friml J, Pogson B J . Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. PLoS One, 2013,8:1-14
[43] 倪迪安, 许智宏 . 生长素的生物合成、代谢、受体和极性运输. 植物生理学通讯, 2001,37:346-352
Ni D A, Xu Z H . Auxin biosynthesis, metabolism, receptor and polar transport. Plant Physiol Commun, 2001,37:346-352 (in Chinese)
[44] Li K, Kamiya T, Fujiwara T . Differential roles of PIN1 and PIN2 in root meristem maintenance under low-B conditions in Arabidopsis thaliana. Plant Cell Physiol, 2015,56:1205-1214
[45] Niu Y F, Jin G L, Li X, Tang C X, Zhang Y S, Liang Y C, Yu J Q . Phosphorus and magnesium interactively modulate the elongation and directional growth of primary roots in Arabidopsis thaliana( L.) Heynh. J Exp Bot, 2015,66:3-14
[46] Wu D, Shen H, Yokawa K, Baluška F . Alleviation of aluminium-induced cell rigidity by overexpression of OsPIN2 in rice roots. J Exp Bot, 2014,65:5305-5315
[47] 陈赢男 . 生长素转运蛋白对水稻株型、根系生长和磷素营养的调控作用. 南京农业大学博士学位论文, 江苏南京, 2012
Chen Y N . Regulation of Auxin Transporter on Plant Type, Root Growth and Phosphorus Nutrition in Rice. PhD Dissertation of Nanjing Agricultural University, Nanjing, Jiangsu,China, 2012 (in Chinese with English abstract)
[48] Peer W N, Bandyopadhyay A, Blakeslee J J, Makam S N, Chen R J, Masson P H, Murphy A S . Variation in expression and protein localization of the PIN family of auxin efflux facilitator proteins in flavonoid mutants with altered auxin transport in Arabidopsis thaliana. Plant Cell, 2004,16:1898-1911
[1] CHEN Song-Yu, DING Yi-Juan, SUN Jun-Ming, HUANG Deng-Wen, YANG Nan, DAI Yu-Han, WAN Hua-Fang, QIAN Wei. Genome-wide identification of BnCNGC and the gene expression analysis in Brassica napus challenged with Sclerotinia sclerotiorum and PEG-simulated drought [J]. Acta Agronomica Sinica, 2022, 48(6): 1357-1371.
[2] YUAN Da-Shuang, DENG Wan-Yu, WANG Zhen, PENG Qian, ZHANG Xiao-Li, YAO Meng-Nan, MIAO Wen-Jie, ZHU Dong-Ming, LI Jia-Na, LIANG Ying. Cloning and functional analysis of BnMAPK2 gene in Brassica napus [J]. Acta Agronomica Sinica, 2022, 48(4): 840-850.
[3] WU Yan-Fei, HU Qin, ZHOU Qi, DU Xue-Zhu, SHENG Feng. Genome-wide identification and expression analysis of Elongator complex family genes in response to abiotic stresses in rice [J]. Acta Agronomica Sinica, 2022, 48(3): 644-655.
[4] HUANG Cheng, LIANG Xiao-Mei, DAI Cheng, WEN Jing, YI Bin, TU Jin-Xing, SHEN Jin-Xiong, FU Ting-Dong, MA Chao-Zhi. Genome wide analysis of BnAPs gene family in Brassica napus [J]. Acta Agronomica Sinica, 2022, 48(3): 597-607.
[5] JIN Rong, JIANG Wei, LIU Ming, ZHAO Peng, ZHANG Qiang-Qiang, LI Tie-Xin, WANG Dan-Feng, FAN Wen-Jing, ZHANG Ai-Jun, TANG Zhong-Hou. Genome-wide characterization and expression analysis of Dof family genes in sweetpotato [J]. Acta Agronomica Sinica, 2022, 48(3): 608-623.
[6] WANG Rui, CHEN Xue, GUO Qing-Qing, ZHOU Rong, CHEN Lei, LI Jia-Na. Development of linkage InDel markers of the white petal gene based on whole-genome re-sequencing data in Brassica napus L. [J]. Acta Agronomica Sinica, 2022, 48(3): 759-769.
[7] DONG Yan-Kun, HUANG Ding-Quan, GAO Zhen, CHEN Xu. Identification, expression profile of soybean PIN-Like (PILS) gene family and its function in symbiotic nitrogen fixation in root nodules [J]. Acta Agronomica Sinica, 2022, 48(2): 353-366.
[8] JIAN Hong-Ju, SHANG Li-Na, JIN Zhong-Hui, DING Yi, LI Yan, WANG Ji-Chun, HU Bai-Geng, Vadim Khassanov, LYU Dian-Qiu. Genome-wide identification and characterization of PIF genes and their response to high temperature stress in potato [J]. Acta Agronomica Sinica, 2022, 48(1): 86-98.
[9] WANG Yan-Hua, LIU Jing-Sen, LI Jia-Na. Integrating GWAS and WGCNA to screen and identify candidate genes for biological yield in Brassica napus L. [J]. Acta Agronomica Sinica, 2021, 47(8): 1491-1510.
[10] WANG Yan-Peng, LING Lei, ZHANG Wen-Rui, WANG Dan, GUO Chang-Hong. Genome-wide identification and expression analysis of B-box gene family in wheat [J]. Acta Agronomica Sinica, 2021, 47(8): 1437-1449.
[11] SONG Tian-Xiao, LIU Yi, RAO Li-Ping, Soviguidi Deka Reine Judesse, ZHU Guo-Peng, YANG Xin-Sun. Identification and expression analysis of cell wall invertase IbCWIN gene family members in sweet potato [J]. Acta Agronomica Sinica, 2021, 47(7): 1297-1308.
[12] LI Wen-Lan, LI Wen-Cai, SUN Qi, YU Yan-Li, ZHAO Meng, LU Shou-Ping, LI Yan-Jiao, MENG Zhao-Dong. A study of expression pattern of auxin response factor family genes in maize (Zea mays L.) [J]. Acta Agronomica Sinica, 2021, 47(6): 1138-1148.
[13] HUANG Ning, HUI Qian-Long, FANG Zhen-Ming, LI Shan-Shan, LING Hui, QUE You-Xiong, YUAN Zhao-Nian. Identification, localization and expression analysis of beta-carotene isomerase gene family in sugarcane [J]. Acta Agronomica Sinica, 2021, 47(5): 882-893.
[14] TANG Xin, LI Yuan-Yuan, LU Jun-Xing, ZHANG Tao. Morphological characteristics and cytological study of anther abortion of temperature-sensitive nuclear male sterile line 160S in Brassica napus [J]. Acta Agronomica Sinica, 2021, 47(5): 983-990.
[15] LI Jie-Hua, DUAN Qun, SHI Ming-Tao, WU Lu-Mei, LIU Han, LIN Yong-Jun, WU Gao-Bing, FAN Chu-Chuan, ZHOU Yong-Ming. Development and identification of transgenic rapeseed with a novel gene for glyphosate resistance [J]. Acta Agronomica Sinica, 2021, 47(5): 789-798.
Full text



No Suggested Reading articles found!