利用基因组学和MALDI-TOF MS技术鉴定放线菌纲细菌的核糖体蛋白质标志物

Characterization of the ribosomal protein biomarkers of Actinobacteria via genomics and MALDI-TOF MS techniques

摘要:

【目的】基质辅助激光解吸电离飞行时间质谱(MALDI-TOF MS)法基于微生物的特征蛋白指纹图谱鉴定菌种，本研究利用基因组学和MALDI-TOF MS技术鉴定放线菌纲细菌的核糖体蛋白质标志物。【方法】从MALDI-TOF MS图谱数据库选取放线菌纲代表菌种，在基因组数据库检索目标菌种，获取目标菌株或其参比菌株的核糖体蛋白质序列，计算获得分子质量理论值，用于注释目标菌株MALDI-TOF MS指纹图谱中的核糖体蛋白质信号。【结果】从8目，24科，53属，114种，142株放线菌的MALDI-TOF MS图谱中总共注释出31种核糖体蛋白质。各菌株的指纹图谱中核糖体蛋白质信号数量差异显著。各种核糖体蛋白质信号的注释次数差异显著。总共15种核糖体蛋白质在超过半数图谱中得到注释，注释次数最高的是核糖体大亚基蛋白质L36。【结论】本研究找到了放线菌纲细菌MALDI-TOF MS图谱中常见的15种核糖体蛋白质信号，可为通过识别核糖体蛋白质的质谱特征峰鉴定放线菌的方法建立提供依据。

Abstract:

[Objective] Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) technique provides mass spectral fingerprints of characteristic proteins for microbial identification. This study aims to characterize the ribosomal protein biomarkers from Actinobacteria via genomics and MALDI-TOF MS techniques. [Methods] Actinobacteria representatives were chosen from MALDI-TOF MS spectral library. By searching against genome database, we acquired the ribosomal protein sequences from the target or reference strains of target species and calculated the theoretical molecular masses. The mass peaks in the MALDI-TOF mass spectra of target strains were annotated with the calculated molecular masses of ribosomal proteins. [Results] Mass peaks annotated in the spectra of 142 strains of 114 species, 53 genera, 24 families from 8 orders were assigned to 31 ribosomal proteins. The number of annotated ribosomal proteins varied significantly among strains. The number of mass peak annotations also varied considerably among different subunit proteins. A total of 15 ribosomal proteins were annotated in over half of the spectra, and the ribosomal protein with the most mass peak annotations was L36. [Conclusion] This study identified 15 common ribosomal protein mass peaks in MALDI-TOF mass spectra of Actinobacteria. The results can support the establishment of a method for the identification of Actinobacteria by matching characteristic mass peaks of ribosomal protein biomarkers in MALDI-TOF mass spectra.