Identification and Bioinformatics Analysis of Gene in the Magnesium Transporter Family in Cassava

doi:10.13560/j.cnki.biotech.bull.1985.2024-0521

Abstract

Abstract:

【Objective】Magnesium transporters（MGTs）are vital for magnesium transportation，thus analyzing the basic information, the physiological and chemical characteristics of the MeMGT gene family in cassava serves as a foundational step for understanding the functions of these genes.【Method】In this study, we identified and named 13 putative MeMGTs genes in cassava（Manihot esculenta Crantz）based on the cassava genome database through homologous sequence alignments, designated as MeMGT2;1-MeMGT10;2. We conducted chromosomal localization, conserved motif analysis, and phylogenetic analysis of the MeMGT family genes. Additionally, we predicted the biochemical properties, structure, and function of the corresponding proteins. 【Result】Chromosomal analysis revealed that the 13 MeMGTs genes were distributed across 8 chromosomes, each containing 4 to 13 exons. Tissue-specific expression patterns indicated differential expressions of MeMGTs genes across various developmental stages. MeMGT4;2 was mainly expressed in cassava fibrous root and storage root, which might potentially play a role in storage root development, and MeMGT7 was mainly expressed in cassava leave, vein and stem with function possibly involved in long-distance Mg²⁺ transport. Cis-acting element analysis revealed the presence of numerous photoresponsive and hormone-responsive elements in the promoter regions of MeMGTs genes, suggesting regulation by multiple factors. Phylogenetic analysis of the MGT gene family categorized these genes into five distinct clusters between cassava and selected model species. Protein sequence analysis identified MeMGTs member proteins as hydrophilic proteins with two conserved transmembrane domains and a Gly-Met-Asn（GMN）tripeptide motif, devoid of signal peptides. Phosphorylation analysis indicated the presence of phosphorylation sites, including serine, threonine, and tyrosine sites, which may contribute to the functionality of MeMGTs member proteins.【Conclusion】MeMGTs genes are regulated by various elements including light, hormone, drought and cold responses, might play a crucial role in the growth, development and adversity stress of cassava.

Key words: cassava, magnesium transporter, MeMGT gene family, gene identification, bioinformatics

TAN Bo-wen, ZHANG Yi, ZHANG Peng, WANG Zhen-yu, MA Qiu-xiang. Identification and Bioinformatics Analysis of Gene in the Magnesium Transporter Family in Cassava[J]. Biotechnology Bulletin, 2024, 40(9): 20-32.

Figures/Tables 13

References 53

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基因Gene	氨基酸数Amino-acid number	蛋白质分子量Molecular weight/Da	等电点Isoelectric point	不稳定系数Instability index	脂肪指数Aliphaic index	亚细胞定位Subcellular localization
MeMGT2;1	441	5 116.63	5.24	61.16	99.71	Plasma membrane
MeMGT2;2	443	50 084.46	5.17	60.79	99.68	Plasma membrane
MeMGT3;1	419	46 929.10	5.31	41.71	105.89	Plasma membrane
MeMGT3;2	420	47 276.18	5.15	39.36	100.98	Plasma membrane
MeMGT4;1	495	55 072.03	4.85	41.36	91.23	Cytoplasmic
MeMGT4;2	496	55 057.13	4.94	42.90	89.46	Cytoplasmic
MeMGT6	449	50 165.42	5.59	48.10	100.56	Chloroplast
MeMGT7	391	44 564.62	4.87	34.30	102.23	Golgi apparatus
MeMGT9;1	400	44 715.05	5.07	40.07	99.27	Plasma membrane
MeMGT9;2	402	44 505.71	4.92	41.99	100.00	Chloroplast
MeMGT9;3	423	47 245.86	5.06	51.35	97.09	Cytoplasmic
MeMGT10;1	444	49 771.50	5.82	54.37	106.01	Plasma membrane
MeMGT10;2	447	50 089.05	5.75	54.74	107.25	Plasma membrane

基因Gene	氨基酸数Amino-acid number	蛋白质分子量Molecular weight/Da	等电点Isoelectric point	不稳定系数Instability index	脂肪指数Aliphaic index	亚细胞定位Subcellular localization
MeMGT2;1	441	5 116.63	5.24	61.16	99.71	Plasma membrane
MeMGT2;2	443	50 084.46	5.17	60.79	99.68	Plasma membrane
MeMGT3;1	419	46 929.10	5.31	41.71	105.89	Plasma membrane
MeMGT3;2	420	47 276.18	5.15	39.36	100.98	Plasma membrane
MeMGT4;1	495	55 072.03	4.85	41.36	91.23	Cytoplasmic
MeMGT4;2	496	55 057.13	4.94	42.90	89.46	Cytoplasmic
MeMGT6	449	50 165.42	5.59	48.10	100.56	Chloroplast
MeMGT7	391	44 564.62	4.87	34.30	102.23	Golgi apparatus
MeMGT9;1	400	44 715.05	5.07	40.07	99.27	Plasma membrane
MeMGT9;2	402	44 505.71	4.92	41.99	100.00	Chloroplast
MeMGT9;3	423	47 245.86	5.06	51.35	97.09	Cytoplasmic
MeMGT10;1	444	49 771.50	5.82	54.37	106.01	Plasma membrane
MeMGT10;2	447	50 089.05	5.75	54.74	107.25	Plasma membrane

基因Gene	基因ID Gene ID	MeMGTs基因家族蛋白质二级结构预测Prediction of secondary structure of MeMGTs gene family proteins/%
基因Gene	基因ID Gene ID	α-螺旋α-helix	延伸链Extended strand	β-转角β-turn	无规则卷曲Random coil
MeMGT2;1	Manes.11G068600	53.74	6.80	2.04	37.41
MeMGT2;2	Manes.04G101500	51.02	7.45	2.93	38.60
MeMGT3;1	Manes.05G110400	54.89	7.16	2.63	35.32
MeMGT3;2	Manes.01G027400	54.05	7.62	2.38	35.95
MeMGT4;1	Manes.07G053800	52.93	5.45	2.22	39.39
MeMGT4;2	Manes.10G084800	55.44	4.64	1.21	38.71
MeMGT6	Manes.07G020300	50.78	6.68	2.23	40.31
MeMGT7	Manes.05G085100	57.80	8.44	3.32	30.43
MeMGT9;1	Manes.03G169600	60.00	7.50	2.50	30.00
MeMGT9;2	Manes.15G036500	59.20	6.97	3.23	30.60
MeMGT9;3	Manes.15G036400	56.50	9.22	4.26	30.02
MeMGT10;1	Manes.11G155200	47.52	8.33	2.93	41.22
MeMGT10;2	Manes.04G011000	51.01	7.38	2.46	39.15

基因Gene	基因ID Gene ID	MeMGTs基因家族蛋白质二级结构预测Prediction of secondary structure of MeMGTs gene family proteins/%
基因Gene	基因ID Gene ID	α-螺旋α-helix	延伸链Extended strand	β-转角β-turn	无规则卷曲Random coil
MeMGT2;1	Manes.11G068600	53.74	6.80	2.04	37.41
MeMGT2;2	Manes.04G101500	51.02	7.45	2.93	38.60
MeMGT3;1	Manes.05G110400	54.89	7.16	2.63	35.32
MeMGT3;2	Manes.01G027400	54.05	7.62	2.38	35.95
MeMGT4;1	Manes.07G053800	52.93	5.45	2.22	39.39
MeMGT4;2	Manes.10G084800	55.44	4.64	1.21	38.71
MeMGT6	Manes.07G020300	50.78	6.68	2.23	40.31
MeMGT7	Manes.05G085100	57.80	8.44	3.32	30.43
MeMGT9;1	Manes.03G169600	60.00	7.50	2.50	30.00
MeMGT9;2	Manes.15G036500	59.20	6.97	3.23	30.60
MeMGT9;3	Manes.15G036400	56.50	9.22	4.26	30.02
MeMGT10;1	Manes.11G155200	47.52	8.33	2.93	41.22
MeMGT10;2	Manes.04G011000	51.01	7.38	2.46	39.15

基因Gene	基因ID Gene ID	MeMGTs基因家族蛋白质磷酸化位点数量Number of phosphorylation sites of MeMGTs gene family proteins
基因Gene	基因ID Gene ID	丝氨酸Ser	苏氨酸Thr	酪氨酸Tyr
MeMGT2;1	Manes.11G068600	33	9	4
MeMGT2;2	Manes.04G101500	33	11	3
MeMGT3;1	Manes.05G110400	18	15	4
MeMGT3;2	Manes.01G027400	22	14	4
MeMGT4;1	Manes.07G053800	16	20	3
MeMGT4;2	Manes.10G084800	25	25	3
MeMGT6	Manes.07G020300	22	13	3
MeMGT7	Manes.05G085100	22	17	6
MeMGT9;1	Manes.03G169600	19	13	3
MeMGT9;2	Manes.15G036500	19	12	5
MeMGT9;3	Manes.15G036400	22	12	2
MeMGT10;1	Manes.11G155200	27	10	3
MeMGT10;2	Manes.04G011000	31	7	4