Identification and Tissue Specific Expression Analysis of AKR Gene Family in Grape

doi:10.13560/j.cnki.biotech.bull.1985.2021-0068

Abstract

Abstract:

Aldo-Keto Reductase（AKR）is a kind of NADP-dependent oxidoreductase. Through the identification and analysis of grape AKR genes,the aim is to reveal the molecular biological function and genetic regulation mechanism of AKR genes. Based on the latest assembly reference genome data of grape in 2020,bioinformatics was used to analyze the physicochemical properties,gene structure,Motif analysis,cis-acting elements,subcellular localization,secondary structure prediction,and tissue-specific expression analysis of grape AKR genes. Finally,fluorescence quantitative analysis was used to analyze the change of grape AKR gene expressions under salt stress. Thirteen members of AKR gene family were identified at the genome-wide level and divided into 2 subfamilies. Genetic structure analysis demonstrated that the number and location of exons among different members varied. Motif analysis showed that the conserved domains of AKR protein were highly similar. The cis-acting element analysis showed that the upstream promoter elements of this gene not only had core elements and enhancement elements,but also had various hormone and stress response elements,organ specific elements and light regulatory elements. The prediction of secondary structure and subcellular localization indicated that the gene family was mainly expressed in the nucleus,and was dominated by α-helix and irregular coil. Analysis via gene chip expression profile showed that the expression levels of AKR family members were significantly different and had tissue specificity. Fluorescence quantitative results showed that the expression levels of VvAKR02,VvAKR05,VvAKR07,VvAKR11,VvAKR12 and VvAKR13 were up-regulated under salt stress. In conclusion,13 AKR family genes were identified from grape and their expression levels under salt stress were analyzed,which may provide a theoretical and experimental basis for mining salt-tolerant genes in AKR family of grape.

Key words: grape, the AKR gene family, bioinformatics, gene chip expression profile, salt stress

MA Ya-nan, LU Xu, WEI Yun-chun, LI Kang, WEI Ruo-nan, LI Sheng, MA Shao-ying. Identification and Tissue Specific Expression Analysis of AKR Gene Family in Grape[J]. Biotechnology Bulletin, 2021, 37(8): 141-151.

Figures/Tables 9

References 33

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基因Gene	上游引物Forward primer（5'-3'）	下游引物Reverse primer（5'-3'）
VvAKR01	AGGAGGCAGCAGTGTCAAAATGG	CCAGCCACCGCATCATCATCTC
VvAKR02	ACCATTGAAAGCCTCAGCCAGTG	GGCGTTGTCAGAGGGTTATCGTC
VvAKR03	TTGTGCTGAGGAAGCTGGGTAAAC	GCCGCAGAGTGGGAACAAGAAG
VvAKR04	AGCGGTGATTTGAATGCCTTTTGC	GGCGGTCAATACGGTGGAGATG
VvAKR05	AGCGGGTTCATCTCCACTTGATTG	GGAAGGCATGGAAGAGTGTCAGAG
VvAKR06	TCTGCTCTGTCTTGTGCGAAACC	GAACCAACCCCATACCCTAAAGCC
VvAKR07	TGCTGCCAAAGTGGGTTCATCTC	GTCAGAAGCTCGGTCTCACCAAA
VvAKR08	AAAGCTTTGGTGCACCGACG	TCCCAGGCTTCAAGCTCACC
VvAKR09	TAGCCGCCTTAAGAGCCTGTCC	ACGCTGTCTTCACCGGCAATCG
VvAKR10	GACACTGTGACCGCTCTGAATACC	CTCTCGGCGTACTCTCCTCTTGG
VvAKR11	CTTGGATGACAGCAGGAGGAACAC	AGCACATGGAGAGCAATGGAAGC
VvAKR12	AGTGCTTCCATTGCTCTCCATGTG	CTTATCCATTGGCCGGTCCGTATG
VvAKR13	CTGCCTGCTCTTGCCAGATGTG	CCGTGTTCCTCCTGCTGTCAATC
UBI	GCTCGCTGTTTTTGCAGTTCTAC	AACATAGGTGAGGCCGCACTT

基因Gene	上游引物Forward primer（5'-3'）	下游引物Reverse primer（5'-3'）
VvAKR01	AGGAGGCAGCAGTGTCAAAATGG	CCAGCCACCGCATCATCATCTC
VvAKR02	ACCATTGAAAGCCTCAGCCAGTG	GGCGTTGTCAGAGGGTTATCGTC
VvAKR03	TTGTGCTGAGGAAGCTGGGTAAAC	GCCGCAGAGTGGGAACAAGAAG
VvAKR04	AGCGGTGATTTGAATGCCTTTTGC	GGCGGTCAATACGGTGGAGATG
VvAKR05	AGCGGGTTCATCTCCACTTGATTG	GGAAGGCATGGAAGAGTGTCAGAG
VvAKR06	TCTGCTCTGTCTTGTGCGAAACC	GAACCAACCCCATACCCTAAAGCC
VvAKR07	TGCTGCCAAAGTGGGTTCATCTC	GTCAGAAGCTCGGTCTCACCAAA
VvAKR08	AAAGCTTTGGTGCACCGACG	TCCCAGGCTTCAAGCTCACC
VvAKR09	TAGCCGCCTTAAGAGCCTGTCC	ACGCTGTCTTCACCGGCAATCG
VvAKR10	GACACTGTGACCGCTCTGAATACC	CTCTCGGCGTACTCTCCTCTTGG
VvAKR11	CTTGGATGACAGCAGGAGGAACAC	AGCACATGGAGAGCAATGGAAGC
VvAKR12	AGTGCTTCCATTGCTCTCCATGTG	CTTATCCATTGGCCGGTCCGTATG
VvAKR13	CTGCCTGCTCTTGCCAGATGTG	CCGTGTTCCTCCTGCTGTCAATC
UBI	GCTCGCTGTTTTTGCAGTTCTAC	AACATAGGTGAGGCCGCACTT

基因Gene	登录号 Gene accession No.	染色体定位 Chromosomal location	全长Full length/bp	CDS/bp	氨基酸 Amino acid	分子量 Molecular weight/bp	等电点 pI	不稳定系数 Instability index	脂肪系数Aliphatic index	平均亲水性Hydropathicity
VvAKR01	GSVIVT01009396001	chr18:7983438..7986889	3452	969	322	36192.49	5.9	38.98	89.66	-0.238
VvAKR02	GSVIVT01010238001	chr1:18082562..18106134	23573	1002	333	36674.09	7.07	34.21	90.75	-0.213
VvAKR03	GSVIVT01011576001	chr1:6306239..6307845	1607	867	288	32083.49	9.01	42.94	96.88	-0.086
VvAKR04	GSVIVT01011577001	chr1:6298552..6305704	7153	912	303	34017.51	6.54	47.47	89.8	-0.164
VvAKR05	GSVIVT01011579001	chr1:6289243..6290820	1578	951	316	35455.01	5.85	51.55	95.73	-0.206
VvAKR06	GSVIVT01011582001	chr1:6274423..6285766	11344	1293	430	48655.51	7.1	43.48	94.12	-0.184
VvAKR07	GSVIVT01011583001	chr1:6264420..6272529	8110	909	302	34322.71	6.34	27.01	92.02	-0.274
VvAKR08	GSVIVT01011585001	chr1:6241008..6248273	7266	1092	363	40730.95	5.98	49.92	95.92	-0.228
VvAKR09	GSVIVT01030263001	chr8:9745143..9747339	2197	969	322	35975.24	6.17	45.07	83.57	-0.319
VvAKR10	GSVIVT01034098001	chr8:15157629..15161115	3487	948	315	35068.99	5.83	50.57	89.46	-0.243
VvAKR11	GSVIVT01034099001	chr8:15153012..15157096	4085	828	275	30440	6.45	46.14	87.56	-0.204
VvAKR12	GSVIVT01034101001	chr8:15144714..15149849	5136	903	300	33663.65	6.76	42.71	88.37	-0.317

基因Gene	登录号 Gene accession No.	染色体定位 Chromosomal location	全长Full length/bp	CDS/bp	氨基酸 Amino acid	分子量 Molecular weight/bp	等电点 pI	不稳定系数 Instability index	脂肪系数Aliphatic index	平均亲水性Hydropathicity
VvAKR01	GSVIVT01009396001	chr18:7983438..7986889	3452	969	322	36192.49	5.9	38.98	89.66	-0.238
VvAKR02	GSVIVT01010238001	chr1:18082562..18106134	23573	1002	333	36674.09	7.07	34.21	90.75	-0.213
VvAKR03	GSVIVT01011576001	chr1:6306239..6307845	1607	867	288	32083.49	9.01	42.94	96.88	-0.086
VvAKR04	GSVIVT01011577001	chr1:6298552..6305704	7153	912	303	34017.51	6.54	47.47	89.8	-0.164
VvAKR05	GSVIVT01011579001	chr1:6289243..6290820	1578	951	316	35455.01	5.85	51.55	95.73	-0.206
VvAKR06	GSVIVT01011582001	chr1:6274423..6285766	11344	1293	430	48655.51	7.1	43.48	94.12	-0.184
VvAKR07	GSVIVT01011583001	chr1:6264420..6272529	8110	909	302	34322.71	6.34	27.01	92.02	-0.274
VvAKR08	GSVIVT01011585001	chr1:6241008..6248273	7266	1092	363	40730.95	5.98	49.92	95.92	-0.228
VvAKR09	GSVIVT01030263001	chr8:9745143..9747339	2197	969	322	35975.24	6.17	45.07	83.57	-0.319
VvAKR10	GSVIVT01034098001	chr8:15157629..15161115	3487	948	315	35068.99	5.83	50.57	89.46	-0.243
VvAKR11	GSVIVT01034099001	chr8:15153012..15157096	4085	828	275	30440	6.45	46.14	87.56	-0.204
VvAKR12	GSVIVT01034101001	chr8:15144714..15149849	5136	903	300	33663.65	6.76	42.71	88.37	-0.317

基因 Gene	分子式 Formula	α-螺旋 Alpha helix/%	β-转角 Beta turn/%	扩展链结构 Hydropathicity/%	不规则卷曲 Random coil/%	亚细胞定位 Subcellular localization
VvAKR01	C₁₆₂₁H₂₅₃₃N₄₃₇O₄₇₃S₁₅	42.55	4.04	14.29	39.13	Nucleus,cytosol,cytoskeleton and chloroplast
VvAKR02	C₁₆₃₀H₂₅₈₄N₄₅₂O₄₈₀S₁₅	37.84	6.01	15.32	40.84	Nucleus,cytosol,cytoskeleton and chloroplast
VvAKR03	C₁₄₃₇H₂₃₁₄N₃₈₈O₄₀₉S₁₆	41.32	4.51	18.06	36.11	Nucleus,membrane,cytosol,chloroplast and mitochondrion,peroxisome
VvAKR04	C₁₅₃₃H₂₄₁₈N₄₀₂O₄₃₇S₁₇	42.57	4.62	13.86	38.94	Nucleus,cytosol,cytoskeleton and chloroplast
VvAKR05	C₁₅₈₄H₂₅₃₄N₄₂₄O₄₆₆S₁₅	43.04	3.80	15.51	37.66	Extracellular,cytosol,chloroplast,mitochondrion and endoplasmic reticulum
VvAKR06	C₂₂₀₇H₃₄₈₁N₅₇₁O₆₂₇S₁₉	34.42	3.95	17.44	44.19	Nucleus,membrane,cytosol,cytoskeleton,chloroplast and mitochondrion
VvAKR07	C₁₅₆₀H₂₄₄₅N₄₀₁O₄₄₅S₁₂	41.39	5.30	13.58	39.74	Nucleus,extracellular,cytosol and cytoskeleton
VvAKR08	C₁₈₂₉H₂₉₀₀N₄₉₀O₅₃₃S₁₄	42.15	4.41	13.50	39.94	Nucleus,membrane,cytosol and cytoskeleton
VvAKR09	C₁₆₀₁H₂₅₁₈N₄₄₂O₄₆₉S₁₆	40.37	8.39	14.60	36.65	Nucleus,membrane,cytosol,cytoskeleton and chloroplast
VvAKR10	C₁₅₈₂H₂₄₅₁N₄₁₉O₄₆₃S₁₀	42.54	6.67	13.97	36.83	Nucleus,cytosol and chloroplast
VvAKR11	C₁₃₇₈H₂₁₄₇N₃₆₃O₃₉₅S₁₀	43.27	5.09	14.18	37.45	Nucleus,cytosol,cytoskeleton,endoplasmic reticulum and vacuole
VvAKR12	C₁₅₁₈H₂₃₇₅N₄₁₁O₄₃₅S₁₀	43.00	6.67	12.00	38.33	Nucleus,membrane,cytosol,cytoskeleton and vacuole
VvAKR013	C₁₈₇₂H₂₉₁₆N₄₉₂O₅₃₁S₁₁	48.91	6.25	11.41	33.42	Nucleus,cytosol and chloroplast