生物技术通报 ›› 2021, Vol. 37 ›› Issue (6): 171-180.doi: 10.13560/j.cnki.biotech.bull.1985.2021-0224
康凌云1(), 陈建胜2, 甘瀚凌2, 韩露露1, 冯海霞3, 刁其玉1, 邢凯2, 崔凯1()
收稿日期:
2021-02-26
出版日期:
2021-06-26
发布日期:
2021-07-08
作者简介:
康凌云,男,硕士研究生,研究方向:反刍动物营养;E-mail: 基金资助:
KANG Ling-yun1(), CHEN Jian-sheng2, GAN Han-ling2, HAN Lu-lu1, FENG Hai-xia3, DIAO Qi-yu1, XING Kai2, CUI Kai1()
Received:
2021-02-26
Published:
2021-06-26
Online:
2021-07-08
摘要:
本试验旨在通过RNA-seq技术在转录组水平分析早期蛋白质限制与后期补偿对羔羊抗氧化性能的影响。试验选取15日龄断母乳湖羊公羔32只,随机分为两组,一组饲喂正常蛋白水平的代乳粉(CP为25%)和开食料(CP为21%),记为对照组(normal protein level,NPL);另一组饲喂蛋白水平分别为19%的代乳粉和15%的开食料,记为试验组(low protein level,LPL)。人工饲喂相应的代乳粉至60日龄,开食料自由采食。61-90 d所有试验羊均自由采食正常蛋白水平(CP为21%)的开食料。分别在羔羊60和90日龄,每组随机选取2只羔羊进行屠宰,采用RNA-seq技术鉴定蛋白质限制与补偿条件下肝脏组织差异表达基因(DEGs),通过生物信息学分析,筛选与抗氧化功能密切相关的通路,利用qRT-PCR的方法验证抗氧化酶系基因表达水平。低蛋白水平日粮引起羔羊肝脏组织差异表达基因有302个,其中23个差异表达基因参与机体抗氧化调节过程,且表达水平呈显著下调。GO富集分析发现差异表达基因参与氧化还原酶活性(GO:0016491)、谷胱甘肽转移酶活性(GO:0004364)和氧化还原过程(GO:0055114)。KEGG分析发现,抗氧化相关基因主要富集到P450介导的外源性物质代谢和谷胱甘肽代谢通路;细胞因子受体作用通路相关基因表达水平显著提高。恢复蛋白水平30 d后,抗氧化相关基因表达水平与对照组无差异。日粮蛋白质水平与机体抗氧化功能密切相关。蛋白质限制导致肝脏基因表达发生改变,降低了抗氧化相关基因的表达水平,DEGs可通过外源性物质代谢、谷胱甘肽代谢、细胞因子受体作用通路等信号通路影响肝脏抗氧化和免疫功能。
康凌云, 陈建胜, 甘瀚凌, 韩露露, 冯海霞, 刁其玉, 邢凯, 崔凯. 基于转录组学技术分析蛋白质限制与补偿对羔羊肝脏抗氧化性能的影响[J]. 生物技术通报, 2021, 37(6): 171-180.
KANG Ling-yun, CHEN Jian-sheng, GAN Han-ling, HAN Lu-lu, FENG Hai-xia, DIAO Qi-yu, XING Kai, CUI Kai. Effects of Dietary Protein Deficiency Followed by Realimentation on the Antioxidation of Lamb Based on Transcriptomics Analysis[J]. Biotechnology Bulletin, 2021, 37(6): 171-180.
项目Item | 饲粮Diet | ||||
---|---|---|---|---|---|
开食料Starter | 代乳粉Milk replacer | ||||
NPL组 | LPL组 | NPL组 | LPL组 | ||
成分Ingredients/% | |||||
玉米Corn | 49.10 | 65.90 | - | - | |
豆粕Soybean | 28.90 | 12.10 | - | - | |
麸皮Bran | 8.00 | 8.00 | - | - | |
苜蓿Alfalfa | 10.00 | 10.00 | - | - | |
预混料Premix | 4.00 | 4.00 | - | - | |
总计Total | 100.00 | 100.00 | - | - | |
营养水平Nutrient level/% | |||||
干物质DM | 89.65 | 90.36 | 97.73 | 97.94 | |
粗蛋白CP | 21.08 | 15.02 | 25.08 | 19.23 | |
代谢能DE(MJ·kg-1) | 13.06 | 13.06 | 18.38 | 18.32 | |
粗脂肪EE | 1.70 | 1.70 | 11.18 | 12.98 | |
粗灰分Ash | 7.40 | 6.50 | 5.29 | 4.85 | |
中性洗涤纤维NDF | 15.46 | 14.79 | - | - | |
酸性洗涤纤维ADF | 7.84 | 7.47 | - | - | |
钙Ca | 0.96 | 0.98 | 1.13 | 1.09 | |
磷P | 0.57 | 0.51 | 0.51 | 0.48 |
表1 NPL组和LPL组开食料的成分及代乳粉和开食料营养水平(风干基础)
Table 1 Ingredients and nutrient composition of the milk replacer and starter(dry matter basis)
项目Item | 饲粮Diet | ||||
---|---|---|---|---|---|
开食料Starter | 代乳粉Milk replacer | ||||
NPL组 | LPL组 | NPL组 | LPL组 | ||
成分Ingredients/% | |||||
玉米Corn | 49.10 | 65.90 | - | - | |
豆粕Soybean | 28.90 | 12.10 | - | - | |
麸皮Bran | 8.00 | 8.00 | - | - | |
苜蓿Alfalfa | 10.00 | 10.00 | - | - | |
预混料Premix | 4.00 | 4.00 | - | - | |
总计Total | 100.00 | 100.00 | - | - | |
营养水平Nutrient level/% | |||||
干物质DM | 89.65 | 90.36 | 97.73 | 97.94 | |
粗蛋白CP | 21.08 | 15.02 | 25.08 | 19.23 | |
代谢能DE(MJ·kg-1) | 13.06 | 13.06 | 18.38 | 18.32 | |
粗脂肪EE | 1.70 | 1.70 | 11.18 | 12.98 | |
粗灰分Ash | 7.40 | 6.50 | 5.29 | 4.85 | |
中性洗涤纤维NDF | 15.46 | 14.79 | - | - | |
酸性洗涤纤维ADF | 7.84 | 7.47 | - | - | |
钙Ca | 0.96 | 0.98 | 1.13 | 1.09 | |
磷P | 0.57 | 0.51 | 0.51 | 0.48 |
分组 Group | 样品名 Sample | 原始序列 Raw reads | 过滤后序列 Clean reads | 过滤后碱基数量Clean bases | Q20比例Q20 ratio /% | Q30 比例Q30/% | GC含量 GC content /% |
---|---|---|---|---|---|---|---|
NPL60 | NP1 | 59304426 | 57538562 | 8.63G | 96.40 | 91.31 | 49.26 |
NP2 | 52921108 | 50561072 | 7.58G | 95.47 | 89.64 | 47.87 | |
LPL60 | LP1 | 55080900 | 53703926 | 8.06G | 96.61 | 91.75 | 50.04 |
LP2 | 41189720 | 40057846 | 6.01G | 96.33 | 91.07 | 48.88 | |
NPL90 | NP3 | 62798110 | 60592144 | 9.09G | 96.13 | 90.98 | 48.40 |
NP4 | 42917164 | 41617614 | 6.24G | 96.41 | 91.44 | 48.88 | |
LPL90 | LP3 | 54828428 | 53056652 | 7.96G | 96.65 | 91.91 | 49.26 |
LP4 | 60109450 | 58311854 | 8.75G | 96.23 | 91.03 | 49.35 |
表2 所有样品的测序数据评估表
Table 2 Data information of all samples collected by RNA-seq
分组 Group | 样品名 Sample | 原始序列 Raw reads | 过滤后序列 Clean reads | 过滤后碱基数量Clean bases | Q20比例Q20 ratio /% | Q30 比例Q30/% | GC含量 GC content /% |
---|---|---|---|---|---|---|---|
NPL60 | NP1 | 59304426 | 57538562 | 8.63G | 96.40 | 91.31 | 49.26 |
NP2 | 52921108 | 50561072 | 7.58G | 95.47 | 89.64 | 47.87 | |
LPL60 | LP1 | 55080900 | 53703926 | 8.06G | 96.61 | 91.75 | 50.04 |
LP2 | 41189720 | 40057846 | 6.01G | 96.33 | 91.07 | 48.88 | |
NPL90 | NP3 | 62798110 | 60592144 | 9.09G | 96.13 | 90.98 | 48.40 |
NP4 | 42917164 | 41617614 | 6.24G | 96.41 | 91.44 | 48.88 | |
LPL90 | LP3 | 54828428 | 53056652 | 7.96G | 96.65 | 91.91 | 49.26 |
LP4 | 60109450 | 58311854 | 8.75G | 96.23 | 91.03 | 49.35 |
基因ID Gene ID | 基因名称 Gene symbol | 基因描述 Gene description | 差异倍数 Fold change | P |
---|---|---|---|---|
ENSOARG00000000042 | CYP2E1 | Cytochrome P450,family 2,subfamily E,polypeptide 1 | -1.75 | 0.0424 |
ENSOARG00000000591 | LOC101105314 | Cytochrome P450 2C42-like | -6.74 | 0.0180 |
ENSOARG00000004562 | ZADH2 | Zinc binding alcohol dehydrogenase domain containing 2 | -1.77 | 0.0433 |
ENSOARG00000005352 | - | - | -1.91 | 0.0314 |
ENSOARG00000005747 | - | - | -3.17 | 0.0032 |
ENSOARG00000007128 | CYP2A6 | Cytochrome P450 2A6 | -2.59 | 0.0010 |
ENSOARG00000007880 | SOD1 | Superoxide dismutase 1 | -2.69 | 0.0267 |
ENSOARG00000009277 | LOC101107119 | Prostaglandin F synthase 1-like | -2.61 | 0.0009 |
ENSOARG00000011087 | LOC101109111 | Dihydrodiol dehydrogenase 3 | -2.02 | 0.0140 |
ENSOARG00000011663 | -- | - | -3.26 | 0.0001 |
ENSOARG00000011769 | PYROXD2 | Pyridine nucleotide-disulphide oxidoreductase domain 2 | -2.32 | 0.0085 |
ENSOARG00000012581 | TM7SF2 | Transmembrane 7 superfamily member 2 | -2.50 | 0.0013 |
ENSOARG00000012705 | ALDH1A1 | Aldehyde dehydrogenase 1 family member A1 | -2.40 | 0.0113 |
ENSOARG00000013364 | HHIPL2 | HHIP like 2 | -2.72 | 0.0433 |
ENSOARG00000013700 | LOC101114408 | Carbonyl reductase[NADPH]1 | -1.90 | 0.0276 |
ENSOARG00000014759 | GSTA1-1 | Microsomal glutathione-S-transferase 1-1 | -2.15 | 0.0082 |
ENSOARG00000017584 | GSTA1 | Glutathione S-transferase alpha 1 | -3.14 | 0.0022 |
ENSOARG00000019285 | LOC101107831 | Glutathione S-transferase Mu 1-like | -4.75 | 1.73E-05 |
ENSOARG00000019297 | LOC101108092 | Glutathione S-transferase Mu 1 | -3.13 | 0.0010 |
ENSOARG00000020412 | PHGDH | Phosphoglycerate dehydrogenase | -2.19 | 0.0054 |
ENSOARG00000020582 | MGST1 | Microsomal glutathione S-transferase 1 | -1.89 | 0.0254 |
Novel00632 | - | - | -3.51 | 0.0033 |
Novel02088 | - | - | -2.02 | 0.0425 |
表3 参与抗氧化过程的差异表达基因
Table 3 Different expressed genes related to antioxidation process
基因ID Gene ID | 基因名称 Gene symbol | 基因描述 Gene description | 差异倍数 Fold change | P |
---|---|---|---|---|
ENSOARG00000000042 | CYP2E1 | Cytochrome P450,family 2,subfamily E,polypeptide 1 | -1.75 | 0.0424 |
ENSOARG00000000591 | LOC101105314 | Cytochrome P450 2C42-like | -6.74 | 0.0180 |
ENSOARG00000004562 | ZADH2 | Zinc binding alcohol dehydrogenase domain containing 2 | -1.77 | 0.0433 |
ENSOARG00000005352 | - | - | -1.91 | 0.0314 |
ENSOARG00000005747 | - | - | -3.17 | 0.0032 |
ENSOARG00000007128 | CYP2A6 | Cytochrome P450 2A6 | -2.59 | 0.0010 |
ENSOARG00000007880 | SOD1 | Superoxide dismutase 1 | -2.69 | 0.0267 |
ENSOARG00000009277 | LOC101107119 | Prostaglandin F synthase 1-like | -2.61 | 0.0009 |
ENSOARG00000011087 | LOC101109111 | Dihydrodiol dehydrogenase 3 | -2.02 | 0.0140 |
ENSOARG00000011663 | -- | - | -3.26 | 0.0001 |
ENSOARG00000011769 | PYROXD2 | Pyridine nucleotide-disulphide oxidoreductase domain 2 | -2.32 | 0.0085 |
ENSOARG00000012581 | TM7SF2 | Transmembrane 7 superfamily member 2 | -2.50 | 0.0013 |
ENSOARG00000012705 | ALDH1A1 | Aldehyde dehydrogenase 1 family member A1 | -2.40 | 0.0113 |
ENSOARG00000013364 | HHIPL2 | HHIP like 2 | -2.72 | 0.0433 |
ENSOARG00000013700 | LOC101114408 | Carbonyl reductase[NADPH]1 | -1.90 | 0.0276 |
ENSOARG00000014759 | GSTA1-1 | Microsomal glutathione-S-transferase 1-1 | -2.15 | 0.0082 |
ENSOARG00000017584 | GSTA1 | Glutathione S-transferase alpha 1 | -3.14 | 0.0022 |
ENSOARG00000019285 | LOC101107831 | Glutathione S-transferase Mu 1-like | -4.75 | 1.73E-05 |
ENSOARG00000019297 | LOC101108092 | Glutathione S-transferase Mu 1 | -3.13 | 0.0010 |
ENSOARG00000020412 | PHGDH | Phosphoglycerate dehydrogenase | -2.19 | 0.0054 |
ENSOARG00000020582 | MGST1 | Microsomal glutathione S-transferase 1 | -1.89 | 0.0254 |
Novel00632 | - | - | -3.51 | 0.0033 |
Novel02088 | - | - | -2.02 | 0.0425 |
GO条目 GO term | 基因符号 Gene symbol | P |
---|---|---|
氧化还原酶活性 Oxidoreductase activity GO:0016491 | CYP2E1,ZADH2,SOD1,PYROXD2,CYP2A6,TM7SF2,ALDH1A1,HHIPL2,PHGDH, MGST1,NADPH1,Novel00632,Novel02088,LOC101105314,LOC101107119,LOC101109111, ENSOARG00000011663,ENSOARG00000005352,ENSOARG00000005747 | 0.00043 |
谷胱甘肽转移酶活性 Glutathione transferase activity GO:0004364 | MGST1,GSTM1,GSTA1 GSTA1-1 LOC101107831 | 0.00043 |
氧化还原过程 Oxidation-reduction process GO:0055114 | TM7SF2,ALDH1A1,HHIPL2,NADPH1,PHGDH,MGST1,Novel00632,CYP2E1, ZADH2,GSPT1,SOD1,PYROXD2,LOC101105314,LOC101107119,LOC101109111, ENSOARG00000005352,ENSOARG00000005747,ENSOARG00000011663 | 0.003962 |
表4 抗氧化相关基因及GO条目
Table 4 GO terms and genes related to antioxidation process
GO条目 GO term | 基因符号 Gene symbol | P |
---|---|---|
氧化还原酶活性 Oxidoreductase activity GO:0016491 | CYP2E1,ZADH2,SOD1,PYROXD2,CYP2A6,TM7SF2,ALDH1A1,HHIPL2,PHGDH, MGST1,NADPH1,Novel00632,Novel02088,LOC101105314,LOC101107119,LOC101109111, ENSOARG00000011663,ENSOARG00000005352,ENSOARG00000005747 | 0.00043 |
谷胱甘肽转移酶活性 Glutathione transferase activity GO:0004364 | MGST1,GSTM1,GSTA1 GSTA1-1 LOC101107831 | 0.00043 |
氧化还原过程 Oxidation-reduction process GO:0055114 | TM7SF2,ALDH1A1,HHIPL2,NADPH1,PHGDH,MGST1,Novel00632,CYP2E1, ZADH2,GSPT1,SOD1,PYROXD2,LOC101105314,LOC101107119,LOC101109111, ENSOARG00000005352,ENSOARG00000005747,ENSOARG00000011663 | 0.003962 |
KEGG通路 KEGG pathway | 差异表达基因 DEGs | P |
---|---|---|
DEGs显著富集通路(LPL60 vs. NPL60) Significant enrichment pathway based on the DEGs(LPL60 vs. NPL60) | ||
化学物致癌作用 Chemical carcinogenesis | CYP2E1,GSTA1,CCBL1,MGST1,Novel01136,ENSOARG00000007128, ENSOARG00000013700,ENSOARG00000014759,ENSOARG00000019285, ENSOARG00000019297 | 5.07E-09 |
细胞色素P450对外源物质代谢 Metabolism of xenobiotics by cytochrome P450 | MGST1,GSTA1,CYP2E1,Novel01136,ENSOARG00000007128, ENSOARG00000013700,ENSOARG00000014759,ENSOARG00000019285, ENSOARG00000019297 | 1.47E-08 |
细胞色素P450对药物代谢 Drug metabolism-cytochrome P450 | MGST1,GSTA1,CYP2E1,Novel01136,ENSOARG00000014759, ENSOARG00000019285,ENSOARG00000019297 | 3.65E-06 |
谷胱甘肽代谢 Glutathione metabolism | MGST1,GSTA1,ENSOARG00000014759,ENSOARG00000019285, ENSOARG00000019297 | 4.61E-04 |
类固醇激素生物合成 Steroid hormone biosynthesis | CYP2E1. Novel01136,ENSOARG00000009277,ENSOARG00000011087, ENSOARG00000011663 | 9.85E-04 |
花生四烯酸代谢 Arachidonic acid metabolism | CYP2E1,ENSOARG00000009277,ENSOARG00000011087,ENSOARG00000011663, ENSOARG00000013700 | 0.0016 |
甘氨酸、丝氨酸和苏氨酸代谢 Glycine,serine,and threonine metabolism | GLYCTK,ALAS1,PSPH,PHGDH | 0.0017 |
代谢通路 Metabolic pathways | CYP2E1,NADSYN1,PEMT,GLYCTK,ALAS1,CCBL1,PSPH,DCTPP1,TM7SF2, ALDH1A1,PHGDH,Novel01136,ENSOARG00000005352,ENSOARG00000007808, ENSOARG00000009277,ENSOARG00000011087,ENSOARG00000011663, ENSOARG00000013700 | 0.0053 |
核酸剪切修复 Nucleotide excision repair | Novel00167,Novel01238,Novel00501 | 0.0215 |
卵巢类固醇生成Ovarian steroidogenesis | ENSOARG00000009277,ENSOARG00000011087,ENSOARG00000011663 | 0.0393 |
细胞因子受体相互作用 Cytokine-cytokine receptor interaction | FLT4,KDR,IL6ST,LIFR,TGFBR1,FLT1,IFNAR1E,TGFBR2,IL13RA1,CSF2RB,CSF3R,ENSOARG00000019477 | 0.0011 |
DEGs显著富集通路(LPL90 vs. NPL90) Significantly enriched pathway based on the DEGs(LPL90 vs. NPL90) | ||
酪氨酸代谢Tyrosine metabolism | ENSOARG00000007808 | 0.0057 |
表5 差异表达基因KEGG通路富集分析
Table 5 KEGG pathway enrichment analysis of different expressed genes
KEGG通路 KEGG pathway | 差异表达基因 DEGs | P |
---|---|---|
DEGs显著富集通路(LPL60 vs. NPL60) Significant enrichment pathway based on the DEGs(LPL60 vs. NPL60) | ||
化学物致癌作用 Chemical carcinogenesis | CYP2E1,GSTA1,CCBL1,MGST1,Novel01136,ENSOARG00000007128, ENSOARG00000013700,ENSOARG00000014759,ENSOARG00000019285, ENSOARG00000019297 | 5.07E-09 |
细胞色素P450对外源物质代谢 Metabolism of xenobiotics by cytochrome P450 | MGST1,GSTA1,CYP2E1,Novel01136,ENSOARG00000007128, ENSOARG00000013700,ENSOARG00000014759,ENSOARG00000019285, ENSOARG00000019297 | 1.47E-08 |
细胞色素P450对药物代谢 Drug metabolism-cytochrome P450 | MGST1,GSTA1,CYP2E1,Novel01136,ENSOARG00000014759, ENSOARG00000019285,ENSOARG00000019297 | 3.65E-06 |
谷胱甘肽代谢 Glutathione metabolism | MGST1,GSTA1,ENSOARG00000014759,ENSOARG00000019285, ENSOARG00000019297 | 4.61E-04 |
类固醇激素生物合成 Steroid hormone biosynthesis | CYP2E1. Novel01136,ENSOARG00000009277,ENSOARG00000011087, ENSOARG00000011663 | 9.85E-04 |
花生四烯酸代谢 Arachidonic acid metabolism | CYP2E1,ENSOARG00000009277,ENSOARG00000011087,ENSOARG00000011663, ENSOARG00000013700 | 0.0016 |
甘氨酸、丝氨酸和苏氨酸代谢 Glycine,serine,and threonine metabolism | GLYCTK,ALAS1,PSPH,PHGDH | 0.0017 |
代谢通路 Metabolic pathways | CYP2E1,NADSYN1,PEMT,GLYCTK,ALAS1,CCBL1,PSPH,DCTPP1,TM7SF2, ALDH1A1,PHGDH,Novel01136,ENSOARG00000005352,ENSOARG00000007808, ENSOARG00000009277,ENSOARG00000011087,ENSOARG00000011663, ENSOARG00000013700 | 0.0053 |
核酸剪切修复 Nucleotide excision repair | Novel00167,Novel01238,Novel00501 | 0.0215 |
卵巢类固醇生成Ovarian steroidogenesis | ENSOARG00000009277,ENSOARG00000011087,ENSOARG00000011663 | 0.0393 |
细胞因子受体相互作用 Cytokine-cytokine receptor interaction | FLT4,KDR,IL6ST,LIFR,TGFBR1,FLT1,IFNAR1E,TGFBR2,IL13RA1,CSF2RB,CSF3R,ENSOARG00000019477 | 0.0011 |
DEGs显著富集通路(LPL90 vs. NPL90) Significantly enriched pathway based on the DEGs(LPL90 vs. NPL90) | ||
酪氨酸代谢Tyrosine metabolism | ENSOARG00000007808 | 0.0057 |
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