Scientia Agricultura Sinica ›› 2019, Vol. 52 ›› Issue (23): 4333-4349.doi: 10.3864/j.issn.0578-1752.2019.23.014

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• SPECIAL FOCUS: MOLECULAR BIOLOGY OF APPLE • Previous Articles     Next Articles

Genome-Wide Identification and Expression Pattern Analysis of NLP (Nin-Like Protein) Transcription Factor Gene Family in Apple

WANG Xun,CHEN XiXia,LI HongLiang,ZHANG FuJun,ZHAO XianYan,HAN YuePeng,WANG XiaoFei(),HAO YuJin()   

  1. College of Horticulture Science and Engineering, Shandong Agricultural University/State Key Laboratory of Crop Biology, Tai’an 271018, Shandong
  • Received:2019-04-28 Accepted:2019-06-26 Online:2019-12-01 Published:2019-12-01
  • Contact: XiaoFei WANG,YuJin HAO E-mail:xfwang2004@163.com;haoyujin@sdau.edu.cn

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Abstract:

【Objective】The study was carried out to explore the whole genome characteristics and expression patterns of NLP transcription factors in apple, and further understand its structural characteristics and mechanism.【Method】Based on the local BLAST database and Pfam database, the members of NLP transcription factor family in the whole genome of apple were identified by using two query strategies with blastp and hmmsearch. Through strict filtration and confirmation, the results were used for further analysis, and analysis mainly divides into three parts, including NLP proteins analysis, analysis of NLP genes and NLP expression analysis in apple. Programs or softwares, such as ProtParam, Clustal Omega, MEGA7, MEME 5.0.2, SOPMA, Phyre 2, WoLF PSORT and STRING, were used for protein analysis, online tools included MG2C, GSDS2.0, PlantCARE, psRNATarget, were used for gene analysis, and the expression of MdNLP gene was quantitatively detected by qRT-PCR.【Result】6 NLP members were identified from apple protein databases, which were classified into three categories by phylogenetic analysis: I, II and III. The protein secondary structure was dominated by random coil, followed by alpha-helix, and the smallest proportion was beta-turn. The prediction of subcellular localization was located in the nucleus, which was consistent with the characteristics of transcription factors. Chromosome localization showed that five genes (except MDP0000584547) were located on four chromosomes. Promoter analysis revealed a large number of cis-acting elements related to hormone and stress response, suggesting that MdNLP genes might be involved in the regulation of hormone and stress signals. In addition, a nitrogen-responsive GCN4 element was also identified, further indicating that such transcription factors were closely related to nitrogen. By quantitative detection, the pattern which NLP family had high expression in stem and leaf of apple was revealed. And the expression analysis results also confirmed that MdNLP genes responded to nitrogen starvation and drought stress, and so on.【Conclusion】Through the apple genome analysis, 6 NLP transcription factors were found; the analysis of structure and conserved domain of protein for 6 gene suggested that there had a very high similarity and conservation between them, at the same time, they were different in a way; the associated protein network of NLP family in Arabidopsis thaliana were used for MdNLPs, MDP0000132856, which had the highest homology with AtNLP7, might also have complicated features and functions.

Key words: apple, NLP transcription factor, nitrogen signal, bioinformatics

Table 1

Real-time fluorescence quantitative PCR primers for relative expression of NLP gene in apple"

基因Gene 上游引物Forward primer (5′-3′) 下游引物Reverse primer (5′-3′)
MdNLP2 CTATGCATCGAGGAAACAGCTTG CAATTCCCTCACCTTCCTCAAGA
MdNLP3 GAAATGGAGAAAGAGGGCTCTGA TTCAGAAGGGCTTGGATACTTCC
MdNLP4 GTCAGTATGCTCTCGATCCTGATA CAGTAAGATGTGTAGGATGTTGGC
MdNLP5 GCTTGCTTCTGTGGAGACATTAC TCCAGTATGAGTGCTCTGTAAGC
MdActin GGACAGCGAGGACATTCAGC CTGACCCATTCCAACCATAACA

Fig. 1

Multi-sequence alignment and typical conserved domains of NLP proteins between Arabidopsis thaliana and apple"

Fig. 2

Phylogenetic evolution of NLP proteins in apple, Arabidopsis thaliana and rice(a) and conserved motifs of NLP proteins in apple (b) In figure 2-a, the red solid dot represents apple NLP protein, the green solid triangle represents Arabidopsis NLP protein, and the blue solid square represents rice NLP protein"

Table 3

The secondary structure of NLP protein in apple"

蛋白质Protein α-螺旋α-helix β-转角β-turn 无规则卷曲Random coil 延长链Extended strand
MdNLP1 28.69% 3.79% 53.11% 14.41%
MdNLP2 33.94% 5.57% 43.14% 17.35%
MdNLP3 23.40% 6.40% 55.89% 14.32%
MdNLP4 27.46% 5.90% 50.23% 16.41%
MdNLP5 26.52% 4.01% 55.50% 13.98%
MdNLP6 28.33% 6.27% 49.90% 15.49%

Fig. 3

Homologous modeling prediction of the three-level structure of the conservative domain of NLP protein in apple"

Table 2

NLP family gene, protein characteristic and prediction of subcellular location in apple"

基因
Gene		 登录号
Accession number		 基因长度
Gene length		 编码序列长度
CDS length		 氨基酸数目
Size of aa		 分子量
MW (D)		 等电点
pI		 亚细胞定位
Subcellular localization
MdNLP1 MDP0000788505 3856 2460 819 90889.49 6.25 细胞核 Nucleus
MdNLP2 MDP0000265619 9510 5121 1706 189398.44 7.9 细胞核 Nucleus
MdNLP3 MDP0000246881 9366 4152 1383 153424.77 7.88 细胞核 Nucleus
MdNLP4 MDP0000239938 8796 3990 1329 147220.18 5.5 细胞核 Nucleus
MdNLP5 MDP0000132856 4454 2949 982 107556.64 5.45 细胞核 Nucleus
MdNLP6 MDP0000584547 10212 3159 1052 117304.32 5.96 细胞核 Nucleus

Fig. 4

Protein interaction network of MdNLPs constructed by referring to AtNLPs The name of apple homologous proteins are highlighted in red"

Fig. 5

Chromosome localization (a) and gene structure analysis (b) of NLP gene in apple"

Table 4

Statistics list of GO classification of NLP gene in apple"

GO分类GO classification GO条目GO term 基因数目Gene number 描述Description
分子功能
Molecular Function		 GO:0005524
GO:0017111
GO:0016887
GO:0000166
GO:0008270
GO:0003676		 1
1
1
3
2
2		 ATP结合 ATP binding
核苷三磷酸酶活性 Nucleoside-triphosphatase activity
ATP酶活性 ATPase activity
核苷酸结合 Nucleotide binding
锌离子结合 Zinc ion binding
核酸结合 Nucleic acid binding
生物途径 Biological Process GO:0006810 1 转运 Transport
细胞组分
Cellular Component		 GO:0016020
GO:0016021		 1
1		 膜 Membrane
膜的整体成分 Integral component of membrane

Table 5

Prediction of cis-acting elements of promoter of NLP gene in apple"

基因
Gene		 脱落酸
ABRE		 低氧
ARE		 茉莉酸甲酯
CGTCA		 乙烯
ERE		 赤霉素
GARE		 氮素
GCN4		 干旱
MBS		 防御和胁迫
TC-rich repeats		 水杨酸
TCA		 生长素
TGA		 病原菌
W-box
MdNLP1 0/1 2/0 1/1 1/1 0/1 1/0 1/0 0/1
MdNLP2 2/3 1/0 3/0 0/1 0/1 0/1
MdNLP3 0/2 0/3 0/1 0/1 0/1 0/1 1/0 0/1
MdNLP4 0/2 0/3 1/0 1/1 1/1 1/1 0/1
MdNLP5 1/1 2/0 1/2 0/1 0/1 1/0 0/1 0/1
MdNLP6 4/3 1/0 3/3 1/0 0/1

Table 6

The prediction of miRNA which response nitrogen associated with NLP in apple"

靶基因
Target gene		 miRNA 抑制类型
Inhibition		 靶基因
Target gene		 miRNA 抑制类型
Inhibition		 靶基因
Target gene		 miRNA 抑制类型
Inhibition
MdNLP2 mdm-miR171a 直接降解Cleavage MdNLP5 mdm-miR169e 直接降解Cleavage MdNLP5 mdm-miR395e 直接降解Cleavage
mdm-miR171b 直接降解Cleavage mdm-miR169f 直接降解Cleavage mdm-miR395f 直接降解Cleavage
mdm-miR395a 直接降解Cleavage mdm-miR171c 抑制翻译Translation mdm-miR395g 直接降解Cleavage
mdm-miR395b 直接降解Cleavage mdm-miR171d 抑制翻译Translation mdm-miR395h 直接降解Cleavage
mdm-miR395c 直接降解Cleavage mdm-miR171e 抑制翻译Translation mdm-miR395i 直接降解Cleavage
mdm-miR395d 直接降解Cleavage mdm-miR171g 抑制翻译Translation
mdm-miR395e 直接降解Cleavage mdm-miR171h 抑制翻译Translation
mdm-miR395f 直接降解Cleavage mdm-miR395a 直接降解Cleavage
mdm-miR395g 直接降解Cleavage mdm-miR395b 直接降解Cleavage
mdm-miR395h 直接降解Cleavage mdm-miR395c 直接降解Cleavage
mdm-miR395i 直接降解Cleavage mdm-miR395d 直接降解Cleavage

Fig. 6

Tissue expression analysis of NLP gene in apple"

Fig. 7

Expression analysis of nitrogen starvation response of MdNLP gene"

Fig. 8

Expression analysis of abiotic stress (drought treatment and ABA treatment) of MdNLP gene"

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