中国农业科学

• 植物保护 • 上一篇    

枯草芽孢杆菌NCD-2对棉花根系分泌物L-脯氨酸响应的转录-蛋白组学联合分析

赵卫松,郭庆港,董丽红,王培培,苏振贺,张晓云,鹿秀云,李社增,马平   

  1. 河北省农林科学院植物保护研究所/河北省农业有害生物综合防治工程技术研究中心/农业农村部华北北部作物有害生物综合治理重点实验室, 河北保定 071000
  • 收稿日期:2021-03-21 接受日期:2021-05-31 出版日期:2021-06-21 发布日期:2021-06-21

Transcriptome and proteome analysis of Bacillus subtilis NCD-2 response to L-proline from cotton root exudates

ZHAO WeiSong, GUO QingGang, DONG LiHong, WANG PeiPei, SU ZhenHe, ZHANG XiaoYun, LU XiuYun, LI SheZeng, MA Ping   

  1. IPM Center of Hebei Province/Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture/Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Baoding 071000, Hebei
  • Received:2021-03-21 Accepted:2021-05-31 Published:2021-06-21 Online:2021-06-21

摘要: 【目的】棉花根系分泌物L-脯氨酸是影响生防菌株定殖的关键因素之一,前期研究发现L-脯氨酸能够提高枯草芽孢杆菌(Bacillus subtilisNCD-2生物膜形成能力。通过高通量测序技术分析L-脯氨酸调控枯草芽孢杆菌NCD-2生物膜形成和生防潜力相关的基因,为深入认识棉花根系分泌物与生防菌株的分子互作关系打下基础。【方法】以枯草芽孢杆菌NCD-2菌株为供试材料,外源添加浓度为10 mg·mL-1L-脯氨酸共培养24 h后,分别进行转录组(RNA-seq)和同位素标记相对定量蛋白组技术(iTRAQ)分析,对所获得的转录组和蛋白组数据进行生物信息学分析,利用RT-qPCR验证不同代谢通路中部分差异基因的表达情况。【结果】转录组分析发现,L-脯氨酸和NCD-2菌株共培养后,获得1 071个差异表达基因(DEG),其中602个基因上调,469个基因下调。GO分析发现在生物过程、细胞组分和分子功能方面分别有49、14和30个功能条目显著富集。KEGG代谢通路主要富集在化合物代谢、鞭毛组装、细菌运动和趋化作用。蛋白组学分析发现,筛选到211个差异表达蛋白(DEP),其中118个蛋白显著上调,93个蛋白显著下调。GO分析发现在生物过程和分子功能方面分别有13和8个功能条目显著富集。KEGG代谢通路主要富集在氨基酸代谢、碳水化合物类代谢、鞭毛组装和ABC转运蛋白。进一步转录-蛋白组学联合分析发现,在L-脯氨酸作用下,检测到共有的显著差异表达基因(或蛋白)112个,其中38个下调基因(或蛋白)和74个上调基因(或蛋白)。GO功能显著富集主要集中在营养库活性、催化活性、细胞膜、定位、细胞脂质代谢过程、氧化还原过程、sigma因子活性、转运活性、芽孢形成9个方面。KEGG代谢通路主要富集在能量代谢、ABC转运蛋白、抗生素生物合成、鞭毛组装、运动或趋化作用和双组分系统方面。RT-qPCR验证了26个差异表达显著基因,结果发现在表达量上存在一定的差异,但表达趋势与 RNA-seq和iTRAQ组学分析结果基本一致。【结论】 棉花根系分泌物L-脯氨酸与枯草芽孢杆菌NCD-2之间的互作存在一个复杂的生物过程,依赖于不同代谢通路网络中的多个基因。双组分系统、抗生素生物合成、能量代谢、运动或趋化作用、鞭毛组装和ABC转运蛋白通路中的差异基因(或蛋白)可能在棉花根系分泌物与枯草芽孢杆菌互作过程方面发挥着重要作用。


关键词: L-脯氨酸, 枯草芽孢杆菌, 转录组, 蛋白组, 互作关系

Abstract: 【Objective】L-proline in root exudates of cotton is one of the key factors affecting the colonization of biocontrol microorganisms. Previous studies showed that L-proline could improve the biofilm formation ability of Bacillus subtilis NCD-2. Through high-throughput sequencing technology, we explored the regulatory genes related to the biofilm formation and biocontrol potential of strain NCD-2, which laid a foundation for further understanding the molecular interaction between cotton root exudates and the strain.MethodTranscriptome (RNA-seq) and isotope labeled relative quantitative proteomics (iTRAQ) were analyzed after 24 hours of co-culture with 10 mg·mL-1 L-proline and strain NCD-2, respectively. RT-qPCR was used to verify the expression of some differential genes in different metabolic pathways.ResultTranscriptome analysis showed that 1 071 DEGs were obtained after L-proline and NCD-2 co-culture, of which 602 genes were up-regulated and 469 genes were down regulated. Go analysis showed that 49, 14 and 30 functional items were significantly enriched in biological processes, cell components and molecular functions, respectively. KEGG pathway is mainly enriched in compound metabolism, flagellum assembly, bacterial motility or chemotaxis. Proteomic analysis showed that total of 211 differentially expressed proteins were detected compared to the control. Hierarchical cluster analysis was carried out to group proteins, among which 118 proteins were up-regulated, which 93 proteins were down-regulated. Go analysis showed that 13 and 8 functional items were significantly enriched in biological process and molecular function, respectively. KEGG pathway is mainly enriched in amino acid metabolism, carbohydrate metabolism, flagellum assembly and ABC transporter. Further transcriptional-proteomics analysis revealed that 112 differentially expressed genes (or proteins), including 38 down-regulated genes (or proteins) and 74 up-regulated genes (or proteins), were detected. Go was enriched in 9 aspects, including nutrient reservoir activity, catalytic activity, cell membrane, localization, cellular lipid metabolic process,  oxidation-reduction process, sigma factor activity, transport activity and spore formation. KEGG pathway is mainly enriched in energy metabolism, ABC transporters, antibiotic biosynthesis, flagellum assembly, motility or chemotaxis and two-component system. 26 differentially expressed genes was verified by RT-qPCR, the results showed that there were some differences in the expression level, but the expression trend was basically consistent with that of RNA-seq and iTRAQ.ConclusionThe interaction between L-proline in cotton root exudates and Bacillus subtilis NCD-2 was a complex biological process, which depended on multiple genes in different metabolic pathway networks. It was clear that differential expressed genes (or proteins) of the two-component system, antibiotic biosynthesis, energy metabolism, motility or chemotaxis, flagellum assembly and in ABC transporter pathway may play an important role in the interaction between cotton root exudates and Bacillus subtilis. The results lay a foundation for further study on the molecular interaction between L-proline and B. subtilis NCD-2.


Key words: L-proline, Bacillus subtilis, transcriptome, proteome, interaction relationship