Rapid identification of Saccharothrix spp. based on ribosomal protein biomarkers and matrix-assisted laser desorption/ionization-time of flight mass spectrometry

Abstract:

[Objective] Saccharothrix is a genus of rare filamentous actinomycetes showing great application values in the biopharmaceutical field, industrial enzyme preparations, and environmental remediation. This study aims to establish a method to identify Saccharothrix spp. based on ribosomal protein biomarkers and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). [Methods] We searched two public genome databases to obtain the sequences of 15 ribosomal proteins from the genome-sequenced strains of Saccharothrix and calculated the theoretical molecular weights. We then compared the molecular weights to investigate the matching of 15 ribosomal proteins between different species of Saccharothrix and that between the type strains of Saccharothrix and its closely related three genera (Umezawaea, Actinosynnema, and Lentzea). The criteria for identifying Saccharothrix at the species and genus levels were proposed based on the number of ribosomal protein matches. Subsequently, the identification criteria were tested by MALDI-TOF MS with target and non-target organisms and improved. [Results] MALDI-TOF MS peaks from an unknown organism were compared with the weight list of 15 ribosomal protein biomarkers from each Saccharothrix type strain and the number of peaks that matched each strain’s biomarkers was obtained. Based on the maximum matches, peak intensity mode, and characteristic peaks, the organism can be identified at the genus or species level. [Conclusion] This study established a method for identifying Saccharothrix spp. based on 15 ribosomal protein biomarkers and MALDI-TOF MS, which can be used in directed screening and rapid identification of Saccharothrix spp.