Identification and analysis of members of the FBA gene family in alfalfa

doi:10.11686/cyxb2023373

Abstract

Abstract:

Fructose-1，6-bisphosphate aldolase （FBA） is a key enzyme in glycolysis， gluconeogenesis， and the Calvin cycle， and plays an important role in the regulation of plant growth and development and abiotic stresses. In this study， the alfalfa （Medicago sativa） FBA gene family was identified at the genome-wide level using bioinformatics methods and analysed for physicochemical properties， phylogenetic relationships， chromosomal localization， gene structural features， promoter cis-acting elements and gene expression patterns. The results showed that there were 11 MsFBA genes in alfalfa， distributed on chromosomes 1， 4， 5， 7， 8 and contig633end. Analysis of physicochemical properties showed that MsFBAs encoded for between 111 and 437 amino acids； all of these proteins were predicted to be hydrophilic. Phylogenetic relationship analysis showed that MsFBA family proteins were classified into two subfamilies， and MsFBAs were highly conserved among different species. The results of collinear correlations between alfalfa， Arabidopsis thaliana and Medicago truncatulaFBAs showed higher homology between alfalfa and M. truncatula. The results of promoter cis-acting element prediction showed that many phytohormone-responsive elements and abiotic stress-responsive elements existed in the promoter region of MsFBAs. Analysis of the expression pattern of MsFBAs in different tissues and abiotic stresses showed that the expression of MsFBAs in aboveground tissues was significantly higher than that in belowground tissues， which was tissue-specific； the expression of MsFBAs was induced by low temperature， abscisic acid， drought， and salt stress， which indicated that MsFBAs have an important role in the regulation of abiotic stresses. This study provides initial data to support ongoing research on the function of FBA genes in alfalfa.

Key words: alfalfa, FBA gene family, bioinformatics, growth and development, abiotic stress

Xiao-tong WANG, Xiao-hong LI, Xu-xia MA, Wen-qi CAI, Xue-li FENG, Shu-xia LI. Identification and analysis of members of the FBA gene family in alfalfa[J]. Acta Prataculturae Sinica, 2024, 33(9): 81-93.

Figures/Tables 10

References 35

1	Zhao W， Liu H F， Zhang L， et al. Genome-wide identification and characterization of FBA gene family in polyploid crop Brassica napus. International Journal of Molecular Sciences， 2019， 20（22）： 5749.
2	Nakahara K， Yamamoto H， Miyake C， et al. Purification and characterization of class-Ⅰ and class-Ⅱ fructose-1，6-bisphosphate aldolases from the cyanobacterium Synechocystis sp. PCC 6803. Plant and Cell Physiology， 2003， 44（3）： 326-333.
3	Carrera D Á， George G M， Fischer-Stettler M， et al. Distinct plastid fructose bisphosphate aldolases function in photosynthetic and non-photosynthetic metabolism in Arabidopsis. Journal of Experimental Botany， 2021， 72（10）： 3739-3755.
4	Lu W， Tang X L， Huo Y Q， et al. Identification and characterization of fructose 1，6-bisphosphate aldolase genes in Arabidopsis reveal a gene family with diverse responses to abiotic stresses. Gene， 2012， 503（1）： 65-74.
5	Song J B， Wang Y X， Li H B， et al. The F-box family genes as key elements in response to salt， heavy mental， and drought stresses in Medicago truncatula. Functional & Integrative Genomics， 2015， 15（4）： 495-507.
6	Zhao Y， Jiao F C， Tang H， et al. Genome-wide characterization， evolution， and expression profiling of FBA gene family in response to light treatments and abiotic stress in Nicotiana tabacum. Plant Signaling & Behavior， 2021， 16（10）： 1938442.
7	Cai B B， Li Q， Xu Y C， et al. Genome-wide analysis of the fructose 1，6-bisphosphate aldolase （FBA） gene family and functional characterization of FBA7 in tomato. Plant Physiology and Biochemistry， 2016， 108（7）： 251-265.
8	Qiu Z M， Bai M Y， Kuang H Q， et al. Cytosolic fructose-1，6-bisphosphate aldolases modulate primary metabolism and phytohormone homeostasis in soybean. Agronomy， 2023， 13（5）： 1383.
9	Gao L T， Jia S Z， Cao L， et al. An F-box protein from wheat， TaFBA-2A， negatively regulates JA biosynthesis and confers improved salt tolerance and increased JA responsiveness to transgenic rice plants. Plant Physiology and Biochemistry， 2022， 182（4）： 227-239.
10	Feng C H， Niu M X， Liu X， et al. Genome-wide analysis of the FBA subfamily of the poplar F-box gene family and its role under drought stress. International Journal of Molecular Sciences， 2023， 24（5）： 4823.
11	Long R C， Yang Q C， Kang J M， et al. Cloning and characterization of a fructose-1，6-bisphosphate aldolase gene in Medicago sativa L. Acta Botanica Boreali-Occidentalia Sinica， 2010， 30（6）： 1075-1082.
	龙瑞才，杨青川，康俊梅，等. 紫花苜蓿果糖-1，6-二磷酸醛缩酶基因全长克隆及分析. 西北植物学报， 2010， 30（6）： 1075-1082.
12	Li Y Q， Jiao S Y， Zhang J N， et al. Effect of alfalfa on improving soil in constructed reclamation land. Chinese Journal of Grassland， 2016， 38（3）： 78-83.
	李永强，焦树英，张佳楠，等. 紫花苜蓿对建筑复垦土壤的改良效果. 中国草地学报， 2016， 38（3）： 78-83.
13	Yuan Y Y， Yu J Q， Kong L Z L， et al. Genome-wide investigation of the PLD gene family in alfalfa （Medicago sativa L.）： identification， analysis and expression. BMC Genomics， 2022， 23（1）： 243.
14	Zhao M R， Shen Y H， Li Y C， et al. Research progress in the genetic engineering of alfalfa stress resistance. Acta Agrestia Sinaca， 2014， 22（2）： 243-248.
	赵美荣，申玉华，李永春，等. 紫花苜蓿抗逆基因工程研究进展. 草地学报， 2014， 22（2）： 243-248.
15	Shen C， Du H L， Chen Z， et al. The chromosome-level genome sequence of the autotetraploid alfalfa and resequencing of core germplasms provide genomic resources for alfalfa research. Molecular Plant， 2020， 13（9）： 1250-1261.
16	Blum M， Chang H Y， Chuguransky S， et al. The interPro protein families and domains database： 20 years on. Nucleic Acids Research， 2021， 49（D1）： D344-D354.
17	Artimo P， Jonnalagedda M， Arnold K， et al. ExPASy： SIB bioinformatics resource portal. Nucleic Acids Research， 2012， 40（W1）： W597-W603.
18	Krogh A， Larsson B， von Heijne G， et al. Predicting transmembrane protein topology with a hidden markov model： application to complete genomes. Journal of Molecular Biology， 2001， 305（3）： 567-580.
19	Geourjon C， Deléage G. SOPMA： significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Bioinformatics， 1995， 11（6）： 681-684.
20	Waterhouse A， Bertoni M， Bienert S， et al. SWISS-MODEL： homology modelling of protein structures and complexes. Nucleic Acids Research， 2018， 46（W1）： W296-W303.
21	Kumar S， Tamura K， Nei M. MEGA： Molecular evolutionary genetics analysis software for microcomputers. Bioinformatics， 1994， 10（2）： 189-191.
22	Yuan J， Amend A， Borkowski J， et al. MULTICLUSTAL： a systematic method for surveying Clustal W alignment parameters. Bioinformatics， 1999， 15（10）： 862-863.
23	Saitou N， Nei M. The neighbor-joining method： a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution， 1987， 4（4）： 406-425.
24	Bailey T L， Boden M， Buske F A， et al. MEME Suite： tools for motif discovery and searching. Nucleic Acids Research， 2009， 37（suppl_2）： W202-W208.
25	Chen C J， Chen H， Zhang Y， et al. TBtools： An integrative toolkit developed for interactive analyses of big biological data. Molecular Plant， 2020， 13（8）： 1194-1202.
26	Lescot M， Déhais P， Thijs G， et al. PlantCARE， a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Research， 2002， 30（1）： 325-327.
27	Zhou Q， Luo D， Chai X T， et al. Multiple regulatory networks are activated during cold stress in Medicago sativa L. International Journal of Molecular Sciences， 2018， 19（10）： 3169.
28	Luo D， Wu Y G， Liu J， et al. Comparative transcriptomic and physiological analyses of Medicago sativa L. indicates that multiple regulatory networks are activated during continuous ABA treatment. International Journal of Molecular Sciences， 2019， 20（1）： 47.
29	Luo D， Zhou Q， Wu Y G， et al. Full-length transcript sequencing and comparative transcriptomic analysis to evaluate the contribution of osmotic and ionic stress components towards salinity tolerance in the roots of cultivated alfalfa （Medicago sativa L.）. BMC Plant Biology， 2019， 19（1）： 32.
30	O’Rourke J A， Fu F L， Bucciarelli B， et al. The Medicago sativa gene index 1.2： a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies. BMC Genomics， 2015， 16（1）： 502.
31	Lu W. Genome-wide analysis of the fructose bisphosphate aldolases in Arabidopsis. Tai’an： Shandong Agricultural University， 2011.
	路玮. 拟南芥果糖1， 6-二磷酸醛缩酶家族分析. 泰安：山东农业大学， 2011.
32	Kopecká R， Kameniarová M， Černý M， et al. Abiotic stress in crop production. International Journal of Molecular Sciences， 2023， 24（7）： 6603.
33	Wood N T. Synthetic promoters illuminate roles of cis-acting elements in plant defence. Trends in Plant Science， 2002， 7（7）： 288.
34	Mu J Q， Fu Y J， Liu B C， et al. SiFBA5， a cold-responsive factor from Saussurea involucrata promotes cold resilience and biomass increase in transgenic tomato plants under cold stress. BMC Plant Biology， 2021， 21（1）： 75.
35	Shehzad M， Ditta A， Cai X Y， et al. Genome wide characterization， evolution and expression analysis of FBA gene family under salt stress in Gossypium species. Biologia， 2019， 74（11）： 1539-1552.

基因登录号 Gene ID	基因名 Gene name	染色体号 Chromosome number	氨基酸长度 Amino acid length （aa）	分子质量 Molecular weight （MW， Da）	等电点 pI	总平均亲水性 GRAVY	不稳定系数 Instability index （Ⅱ）	跨膜结构域数目 Number of transmembrane helices	亚细胞定位 Subcellular localization
MsG0180003404.01.T01	MsFBA1	Chr1	333	35812.29	8.35	-0.083	33.89	0	细胞质Cytoplasm
MsG0180005906.01.T01	MsFBA2	Chr1	387	42396.99	7.68	-0.315	41.72	0	叶绿体Chloroplast
MsG0480021327.01.T01	MsFBA3	Chr4	400	43179.18	6.86	-0.131	36.27	0	叶绿体Chloroplast
MsG0480021331.01.T01	MsFBA4	Chr4	398	43036.90	6.39	-0.139	36.93	0	叶绿体Chloroplast
MsG0580028117.01.T01	MsFBA5	Chr5	437	46728.29	5.54	-0.115	28.23	0	细胞质Cytoplasm
MsG0580028118.01.T01	MsFBA6	Chr5	364	39003.51	6.05	-0.071	29.82	0	细胞质Cytoplasm
MsG0780041081.01.T01	MsFBA7	Chr7	358	38635.98	6.56	-0.236	31.16	0	细胞质Cytoplasm
MsG0780041082.01.T01	MsFBA8	Chr7	358	38560.96	6.63	-0.221	32.19	0	细胞质Cytoplasm
MsG0880047090.01.T01	MsFBA9	Chr8	111	11971.70	9.52	-0.132	48.21	0	细胞质Cytoplasm
MsG0880047091.01.T01	MsFBA10	Chr8	211	23009.69	8.60	-0.006	32.72	1	胞外Extracellular
MsG0080049045.01.T01	MsFBA11	contig633end	358	38332.81	7.00	-0.153	32.62	0	细胞质Cytoplasm

基因登录号 Gene ID	基因名 Gene name	染色体号 Chromosome number	氨基酸长度 Amino acid length （aa）	分子质量 Molecular weight （MW， Da）	等电点 pI	总平均亲水性 GRAVY	不稳定系数 Instability index （Ⅱ）	跨膜结构域数目 Number of transmembrane helices	亚细胞定位 Subcellular localization
MsG0180003404.01.T01	MsFBA1	Chr1	333	35812.29	8.35	-0.083	33.89	0	细胞质Cytoplasm
MsG0180005906.01.T01	MsFBA2	Chr1	387	42396.99	7.68	-0.315	41.72	0	叶绿体Chloroplast
MsG0480021327.01.T01	MsFBA3	Chr4	400	43179.18	6.86	-0.131	36.27	0	叶绿体Chloroplast
MsG0480021331.01.T01	MsFBA4	Chr4	398	43036.90	6.39	-0.139	36.93	0	叶绿体Chloroplast
MsG0580028117.01.T01	MsFBA5	Chr5	437	46728.29	5.54	-0.115	28.23	0	细胞质Cytoplasm
MsG0580028118.01.T01	MsFBA6	Chr5	364	39003.51	6.05	-0.071	29.82	0	细胞质Cytoplasm
MsG0780041081.01.T01	MsFBA7	Chr7	358	38635.98	6.56	-0.236	31.16	0	细胞质Cytoplasm
MsG0780041082.01.T01	MsFBA8	Chr7	358	38560.96	6.63	-0.221	32.19	0	细胞质Cytoplasm
MsG0880047090.01.T01	MsFBA9	Chr8	111	11971.70	9.52	-0.132	48.21	0	细胞质Cytoplasm
MsG0880047091.01.T01	MsFBA10	Chr8	211	23009.69	8.60	-0.006	32.72	1	胞外Extracellular
MsG0080049045.01.T01	MsFBA11	contig633end	358	38332.81	7.00	-0.153	32.62	0	细胞质Cytoplasm

基因登录号 Gene ID	基因名 Gene name	蛋白质 Protein	α-螺旋 Alpha helix	β-转角 Beta turn	延伸链 Extended strand	无规则卷曲 Random coil
MsG0180003404.01.T01	MsFBA1	MsFBA1	52.25	6.61	13.51	27.63
MsG0180005906.01.T01	MsFBA2	MsFBA2	50.13	6.98	12.40	30.49
MsG0480021327.01.T01	MsFBA3	MsFBA3	47.50	6.75	13.00	32.75
MsG0480021331.01.T01	MsFBA4	MsFBA4	50.25	5.53	12.56	31.66
MsG0580028117.01.T01	MsFBA5	MsFBA5	49.89	6.18	14.65	29.29
MsG0580028118.01.T01	MsFBA6	MsFBA6	51.92	6.59	12.64	28.85
MsG0780041081.01.T01	MsFBA7	MsFBA7	50.84	7.54	14.80	26.82
MsG0780041082.01.T01	MsFBA8	MsFBA8	47.77	8.66	14.11	29.47
MsG0880047090.01.T01	MsFBA9	MsFBA9	56.76	1.80	10.81	30.63
MsG0880047091.01.T01	MsFBA10	MsFBA10	52.61	7.58	13.74	26.07
MsG0080049045.01.T01	MsFBA11	MsFBA11	51.68	6.70	13.69	27.93

基因登录号 Gene ID	基因名 Gene name	蛋白质 Protein	α-螺旋 Alpha helix	β-转角 Beta turn	延伸链 Extended strand	无规则卷曲 Random coil
MsG0180003404.01.T01	MsFBA1	MsFBA1	52.25	6.61	13.51	27.63
MsG0180005906.01.T01	MsFBA2	MsFBA2	50.13	6.98	12.40	30.49
MsG0480021327.01.T01	MsFBA3	MsFBA3	47.50	6.75	13.00	32.75
MsG0480021331.01.T01	MsFBA4	MsFBA4	50.25	5.53	12.56	31.66
MsG0580028117.01.T01	MsFBA5	MsFBA5	49.89	6.18	14.65	29.29
MsG0580028118.01.T01	MsFBA6	MsFBA6	51.92	6.59	12.64	28.85
MsG0780041081.01.T01	MsFBA7	MsFBA7	50.84	7.54	14.80	26.82
MsG0780041082.01.T01	MsFBA8	MsFBA8	47.77	8.66	14.11	29.47
MsG0880047090.01.T01	MsFBA9	MsFBA9	56.76	1.80	10.81	30.63
MsG0880047091.01.T01	MsFBA10	MsFBA10	52.61	7.58	13.74	26.07
MsG0080049045.01.T01	MsFBA11	MsFBA11	51.68	6.70	13.69	27.93

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