Gene Expression in Escherichia coli O157∶H7 Biofilms

doi:10.13304/j.nykjdb.2021.1029

Abstract

Abstract:

Biofilm is a special extracellular structure of bacteria to adapt environmental stress. The physiological and metabolic activities of bacteria will change during the transition from the planktonic state to a biofilm. To investigate the changes of physiological metabolic pathways and the molecular regulation mechanism of biofilm formation， RNA-Seq technology was used in this study to examine the global gene expression profiles of Escherichia coli O157∶H7 during biofilm and planktonic growth states. The results showed that， in comparison to the planktonic growth state， there were 1 652 differentially expressed genes in biofilm growth state of E. coli O157∶H7， including 821 up-regulated genes and 831 downregulated genes. Genes involved in flagella assembly， bacterial chemotaxis in connection with bacterial motility， and bacterial two-component system regulatory system relating to environmental factors were up-regulated during E. coli O157∶H7 biofilm formation， while the genes involved in ABC transporters of nutrients and signal molecules were downregulated. In addition，changes in carbon metabolism， nitrogen metabolism， fatty acid metabolism and other metabolic pathways were found during E. coli O157∶H7 biofilm formation. Above results provided a scientific basis for the further study of biofilm formation mechanisms.

Key words: Escherchia coli, biofilm, RNA-Seq, differentially expressed genes, enrichment analysis

摘要：

生物被膜是细菌适应不良环境形成的一种特殊胞外结构，当细菌从浮游状态转换成生物被膜状态后其生理代谢活动也会随之发生改变。为了研究细菌形成生物被膜后生理代谢途径的变化及生物被膜形成的分子调控机制，以食源致病性大肠杆菌O157∶H7为试验对象，对其在浮游状态和生物被膜形成状态下的转录组进行测序分析。结果表明，与浮游状态相比，大肠杆菌O157∶H7在生物被膜形成状态有1 652个显著差异表达的基因（上调821个，下调831个），其中鞭毛组装、细菌趋化性和双组分系统调控蛋白基因等在生物被膜形成阶段表达上调；ABC转运系统调控蛋白基因等表达下调。同时，碳代谢、氮代谢、脂肪酸代谢等多个代谢途径也发生了变化。上述结果为深入研究生物被膜形成的分子机制提供数据支持。

关键词: 大肠杆菌, 生物被膜, 转录组, 差异基因, 富集分析

CLC Number:

R378.2+1

Lan MA, Qing PENG, Xiaoqing XU, Shuo YANG, Yuwei ZHANG, Dandan TIAN, Linbo SHI, Bo SHI, Yu QIAO. Gene Expression in Escherichia coli O157∶H7 Biofilms[J]. Journal of Agricultural Science and Technology, 2023, 25(6): 71-88.

马蓝, 彭晴, 徐小轻, 杨硕, 张宇微, 田丹丹, 施琳波, 石波, 乔宇. 大肠杆菌O157∶H7生物被膜状态下基因表达分析[J]. 中国农业科技导报, 2023, 25(6): 71-88.

Figures/Tables 14

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样品 Sample	原始数据 Raw read	有效数据 Clean read	比对率 Rate of mapping/%	Q20/%	Q30/%	GC含量 GC content/%
PLA_1	7 764 802	7 687 384	95.14	98.28	94.68	52.73
PLA_2	8 499 610	8 413 248	96.04	98.21	94.50	52.83
PLA_3	7 898 142	7 806 976	93.57	98.07	94.24	52.65
BIO_1	7 595 958	7 482 884	96.41	98.21	94.51	52.83
BIO_2	8 355 944	8 252 782	97.22	98.21	94.44	52.94
BIO_3	7 995 002	7 902 000	97.51	98.31	94.73	52.88

样品 Sample	原始数据 Raw read	有效数据 Clean read	比对率 Rate of mapping/%	Q20/%	Q30/%	GC含量 GC content/%
PLA_1	7 764 802	7 687 384	95.14	98.28	94.68	52.73
PLA_2	8 499 610	8 413 248	96.04	98.21	94.50	52.83
PLA_3	7 898 142	7 806 976	93.57	98.07	94.24	52.65
BIO_1	7 595 958	7 482 884	96.41	98.21	94.51	52.83
BIO_2	8 355 944	8 252 782	97.22	98.21	94.44	52.94
BIO_3	7 995 002	7 902 000	97.51	98.31	94.73	52.88

GO功能条目 GO term	差异基因总数 Total DEGs	上调差异基因数 Up-regulated DEGs	下调差异基因数 Down-regulated DEGs
运动Locomotion	15	14	1
膜蛋白复合物Membrane protein complex	10	5	5
氧化还原过程Oxidation-reduction process	118	65	53
磷代谢过程Phosphorus metabolic process	41	31	10
小分子分解代谢过程Small molecule catabolic process	8	6	2
阳离子跨膜转运Cation transmembrane transport	8	7	1
无机离子跨膜转运Inorganic ion transmembrane transport	8	7	1
无机阳离子跨膜转运Inorganic cation transmembrane transport	8	7	1
质子跨膜转运Proton transmembrane transport	7	7	0
单糖代谢过程Monosaccharide metabolic process	11	11	0
蛋白质折叠Protein folding	9	9	0
纤毛或鞭毛依赖性细胞运动 Cilium or flagellum-dependent cell motility	8	7	1
细胞或亚细胞成分的运动 Movement of cell or subcellular component	8	7	1
细胞运动Cell motility	8	7	1
细胞定位Localization of cell	8	7	1
细菌型鞭毛依赖性细胞运动 Bacterial-type flagellum-dependent cell motility	8	7	1
含嘧啶化合物代谢过程 Pyrimidine-containing compound metabolic process	8	5	3
古菌或细菌型鞭毛依赖性细胞运动 Archaeal or bacterial-type flagellum-dependent cell motility	8	7	1
磷酸化Phosphorylation	14	11	3
葡萄糖代谢过程Glucose metabolic process	7	7	0
含磷化合物代谢过程 Phosphate-containing compound metabolic process	36	31	5
含嘌呤化合物代谢过程 Purine-containing compound metabolic process	15	14	1
含嘌呤化合物生物合成过程 Purine-containing compound biosynthetic process	12	12	0
碳水化合物生物合成过程Carbohydrate biosynthetic process	13	8	5
谷氨酰胺家族氨基酸代谢过程 Glutamine family amino acid metabolic process	7	2	5
嘌呤核苷酸代谢过程Purine nucleotide metabolic process	14	13	1
磷酸核苷代谢过程Nucleoside phosphate metabolic process	20	18	2
多生物过程Multi-organism process	13	6	7
嘌呤核苷酸生物合成过程Purine nucleotide biosynthetic process	11	11	0
硫化合物代谢过程Sulfur compound metabolic process	11	4	7

GO功能条目 GO term	差异基因总数 Total DEGs	上调差异基因数 Up-regulated DEGs	下调差异基因数 Down-regulated DEGs
运动Locomotion	15	14	1
膜蛋白复合物Membrane protein complex	10	5	5
氧化还原过程Oxidation-reduction process	118	65	53
磷代谢过程Phosphorus metabolic process	41	31	10
小分子分解代谢过程Small molecule catabolic process	8	6	2
阳离子跨膜转运Cation transmembrane transport	8	7	1
无机离子跨膜转运Inorganic ion transmembrane transport	8	7	1
无机阳离子跨膜转运Inorganic cation transmembrane transport	8	7	1
质子跨膜转运Proton transmembrane transport	7	7	0
单糖代谢过程Monosaccharide metabolic process	11	11	0
蛋白质折叠Protein folding	9	9	0
纤毛或鞭毛依赖性细胞运动 Cilium or flagellum-dependent cell motility	8	7	1
细胞或亚细胞成分的运动 Movement of cell or subcellular component	8	7	1
细胞运动Cell motility	8	7	1
细胞定位Localization of cell	8	7	1
细菌型鞭毛依赖性细胞运动 Bacterial-type flagellum-dependent cell motility	8	7	1
含嘧啶化合物代谢过程 Pyrimidine-containing compound metabolic process	8	5	3
古菌或细菌型鞭毛依赖性细胞运动 Archaeal or bacterial-type flagellum-dependent cell motility	8	7	1
磷酸化Phosphorylation	14	11	3
葡萄糖代谢过程Glucose metabolic process	7	7	0
含磷化合物代谢过程 Phosphate-containing compound metabolic process	36	31	5
含嘌呤化合物代谢过程 Purine-containing compound metabolic process	15	14	1
含嘌呤化合物生物合成过程 Purine-containing compound biosynthetic process	12	12	0
碳水化合物生物合成过程Carbohydrate biosynthetic process	13	8	5
谷氨酰胺家族氨基酸代谢过程 Glutamine family amino acid metabolic process	7	2	5
嘌呤核苷酸代谢过程Purine nucleotide metabolic process	14	13	1
磷酸核苷代谢过程Nucleoside phosphate metabolic process	20	18	2
多生物过程Multi-organism process	13	6	7
嘌呤核苷酸生物合成过程Purine nucleotide biosynthetic process	11	11	0
硫化合物代谢过程Sulfur compound metabolic process	11	4	7

分类 Classification		基因 Gene	功能 Function	表达量变化 log₂（FoldChange）	基因 Gene	功能 Function	表达量变化 log₂（FoldChange）
细菌趋化性 Bacterial chemotaxis	趋化受体基因 Chemoreceptor gene	mglB	周质结合蛋白 Periplasmic binding protein	3.54	tap	甲基接受趋化蛋白Ⅳ Methyl-accepting chemotaxis protein Ⅳ	2.99
	趋化受体基因 Chemoreceptor gene	tar	甲基接受趋化蛋白Ⅱ Methyl-accepting chemotaxis protein Ⅱ	3.13	aer	趋氧性传感器受体 Oxygen sensor receptor	2.62
	趋化信号转导基因 Chemotactic signal transduction gene	cheA	趋化蛋白A Chemotaxis protein A	3.11	cheY	趋化反应调节蛋白 Chemotaxis response regulator	1.90
		cheR	谷氨酸O-甲基转移酶 Glutamate O-methyltransferase	3.02	cheB	谷氨酸甲酯酶 Glutamate methylesterase	1.93
		cheW	趋化蛋白 W Chemotaxis protein W	2.65
鞭毛组装 Flagellar assembly	基底蛋白基因 Basal protein gene	fliA	RNA聚合酶σ因子 RNA polymerase sigma factor	2.43	fliS	鞭毛转运分子伴侣 Flagellar export chaperone	3.99
	基底蛋白基因 Basal protein gene	fliG	鞭毛马达开关蛋白 Flagellar motor switch protein	1.40
	棒状蛋白基因 Rod protein gene	flgB	鞭毛基底棒状蛋白 Flagellar basal body rod protein	1.60	flgF	鞭毛基底棒状蛋白 Flagellar basal body rod protein	1.47
		flgC	鞭毛基底棒状蛋白 Flagellar basal body rod protein	1.70	flgG	鞭毛基底棒状蛋白 Flagellar basal body rod protein	1.25
		flgD	鞭毛组装蛋白 Flagellar hook assembly protein	2.70	flgK	鞭毛锚定相关蛋白 Flagellar hook-associated protein	2.56
		flgE	鞭毛锚定蛋白 Flagellar hook protein	3.10	flgL	鞭毛锚定相关蛋白 Flagellar hook-associated protein	1.72
	丝状帽盖基因 Filament capping gene	fliD	鞭毛丝盖蛋白 Flagellar filament capping protein	3.74	fliT	鞭毛生物合成调节蛋白 Flagella biosynthesis regulatory protein	3.45
	开关基因 Switch gene	motA	鞭毛马达固定蛋白 Flagellar motor stator protein	1.75	motB	鞭毛马达蛋白 Flagellar motor protein	1.94
	调节基因 Regulatory gene	flgM	抗σ-28因子 Anti-sigma factor	2.89	flhC	鞭毛基因转录因子 Flagellar transcriptional regulator	3.61
		flgN	鞭毛合成分子伴侣 Flagella biosynthesis chaperone	1.99	flhD	鞭毛基因转录因子 Flagellar transcriptional regulator	3.70
		rpoD	RNA聚合酶σ因子 RNA polymerase sigma factor	1.79
双组分调控系统 Two-component system	感应磷源限制基因 Phosphorus source restriction sensing gene	phoP	双组分系统反应调节器 Two-component system response regulator	2.42	phoQ	双组分系统传感器组氨酸激酶 Two-component system sensor histidine kinase	1.62