Identification of Potato G6PDH Gene Family and Its Expression Analysis in Damaged Tubers

doi:10.13560/j.cnki.biotech.bull.1985.2024-0243

Abstract

Abstract:

【Objective】Glucose-6-phosphate dehydrogenase（G6PDH）plays an important role in plant response to abiotic stress. Identification of the G6PDH gene family in potato and analysis of its expression pattern in damaged tubers would provide a reference for the subsequent in-depth study of the role of potato G6PDH genes in damage stress. 【Method】We used bioinformatics methods to identify the G6PDH gene family members of the potato w, and to analyze the chromosomal distribution, protein physicochemical properties, secondary structure, evolutionary relationships, gene structure, conserved motifs, and promoter cis-acting elements of proteins encoded by members of the gene family, as well as the expression pattern in different organs and damaged tubers of potato.【Result】A total of 4 G6PDH family members in potato genome were identified and distributed on 4 chromosomes, named StG6PDH1-StG6PDH4. Based on the subcellular localization and phylogenetic analysis, StG6PDH1, StG6PDH3 and StG6PDH4 were located in the chloroplasts and belonged to the plastidic type, StG6PDH2 was located in the cytoplasm and belonged to the cytoplasmic type. The number of amino acids of potato G6PDH proteins ranged from 511 to 596 aa, molecular weights from 58.48 to 66.65 kD, isoelectric points from 5.83 to 8.57, and instabilities coefficient from 39.79 to 47.53. The secondary structure of protein showed the highest percentage of α-helices and irregular coils and the least of β-turns. In addition, the promoters of StG6PDHs contained a large number of phytohormone, light, and stress response elements. The four StG6PDHs were expressed in the roots, stems, leaves and tubers of potato, and the expression in the leaves was higher than in other organs. The members of StG6PDHs were involved in the responses of potato tubers to injury stress. The expressions of StG6PDH1, StG6PDH2 and StG6PDH3 were upregulated within 36 h after tubers injured, and StG6PDH4 was down-regulated in injured potato tubers. 【Conclusion】A total of four potato StG6PDHs gene family members are identified, unevenly distributed on four chromosomes, of which one is cytoplasmic and three are plastidic. The promoter region of StG6PDHs includes light, hormone, and stress response elements. The expression of StG6PDHs in wounded tubers is differential, and the members synergistically regulate the responses of potato tubers to damage stress.

Key words: potato, G6PDH gene family, bioinformatics analysis, damage stress, expression analysis

SONG Bing-fang, LIU Ning, CHENG Xin-yan, XU Xiao-bin, TIAN Wen-mao, GAO Yue, BI Yang, WANG Yi. Identification of Potato G6PDH Gene Family and Its Expression Analysis in Damaged Tubers[J]. Biotechnology Bulletin, 2024, 40(9): 104-112.

Figures/Tables 9

Table 1 Primers’ sequences for RT-qPCR

基因名称 Gene name	基因ID Gene ID	引物序列 Primer sequence（5'-3'）
StG6PDH1	Soltu.DM.01G040700	F: GCTTTCACCAGTATCGCTATCA
StG6PDH1	Soltu.DM.01G040700	R: CGGACAACAACGGTAGGTAAT
StG6PDH2	Soltu.DM.02G033900	F: CAAGAAACCTGGGCTTGAAATG
StG6PDH2	Soltu.DM.02G033900	R: CGTTCATAAGCCTCTGGAATGA
StG6PDH3	Soltu.DM.05G012290	F: ATACCAGGAGTGCGGAAATAAG
StG6PDH3	Soltu.DM.05G012290	R: CGTCAGGTTGAACACGGATAA
StG6PDH4	Soltu.DM.07G015360	F: GCTGACCAGATCCCTAAAGAAG
StG6PDH4	Soltu.DM.07G015360	R: GACAAGATTCGAGAACCGAAGA
StEF1α	Soltu.DM.06G005580	F: ATTGATGCCCCTGGTCACAG
StEF1α	Soltu.DM.06G005580	R: CATGTTCACGGGTCTGACCA

Fig. 1 Chromosome location of G6PDH gene family in potato

Table 2 Prediction of subcellular localization of G6PDH protein in potato

基因名称 Gene name	基因ID Gene ID	染色体位置 Chromosome location	亚细胞定位 Subcellular location
StG6PDH1	Soltu.DM.01G040700	chr.01	叶绿体Chloroplast
StG6PDH2	Soltu.DM.02G033900	chr.02	细胞质Cytoplasmic
StG6PDH3	Soltu.DM.05G012290	chr.05	叶绿体Chloroplast
StG6PDH4	Soltu.DM.07G015360	chr.07	叶绿体Chloroplast

Table 3 Protein physicochemical properties and secondary structures of potato G6PDH gene family

基因名称 Gene name	理化性质Physicochemical property				二级结构Secondary structure
基因名称 Gene name	氨基酸长度 Amino acid length/aa	相对分子量 Mw/kD	等电点 pI	不稳定系数Instability index	α-螺旋 α-helix/%	β-转角 β-turn/%	无规则卷曲 Random coil/%	延伸链 Extended strand/%
StG6PDH1	596	66.65	5.83	47.31	36.91	5.87	40.27	16.95
StG6PDH2	511	58.48	5.97	47.53	40.51	5.28	39.33	16.87
StG6PDH3	582	66.21	8.57	39.79	38.14	6.53	39.87	17.53
StG6PDH4	577	65.72	6.88	39.84	37.78	6.59	39.17	16.46

Fig. 2 Phylogenetic tree of G6PDH proteins in Solanum tuberosum, Arabidopsis thaliana, Solanum lycopersicum, Zea mays and Oryza sativa

Fig. 3 Evolutionary relationships（A）, gene structure（B）and conserved motifs（C）of the potato G6PDH gene family

Fig. 4 Cis-acting elements of potato G6PDH gene family Light responsiveness: GATA-motif, GT1, Box-4, MRE, G-Box, AT1-motif. Low-temperature responsiveness: LTR. Anaerobic induction: ARE. Gibberellin responsiveness: GARE, TATC-box. Auxin responsiveness: AuxRE-core, TGA-element. Abscisic acid responsiveness: ABRE. Me-JA responsiveness: CGTCA-motif. Salicylic acid responsiveness: TCA-element. Drought-induced response element: MBS. Zein metabolism regulation: O2-site. Defense and stress responsiveness: TC-rich. Other: Box III, AT-rich

Fig. 5 Relative expressions of G6PDH in different organs of potato Different lowercase letters in the same gene indicate significant difference（P<0.05）

Fig. 6 Relative expression of StG6PDH1s in damaged potato tubers * indicates a significant difference between the control group and the treatment group（P<0.05）

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