MALDI-TOF MS analysis of ribosomal proteins coded in S10 and spc operons rapidly classified the Sphingomonadaceae as alkylphenol polyethoxylate-degrading bacteria from the environment.
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) using ribosomal subunit proteins coded in the S10-spc-alpha operon as biomarkers was applied for the classification of the Sphingomonadaceae from the environment. To construct a ribosomal protein database, S10-spc-alpha operon of type strains of the Sphingomonadaceae and their related alkylphenol polyethoxylate (APEO(n) )-degrading bacteria were sequenced using specific primers designed based on nucleotide sequences of genome-sequenced strains. The observed MALDI mass spectra of intact cells were compared with the theoretical mass of the constructed ribosomal protein database. The nine selected biomarkers coded in the S10-spc-alpha operon, L18, L22, L24, L29, L30, S08, S14, S17, and S19, could successfully distinguish the Sphingopyxis terrae NBRC 15098(T)  and APEO(n) -degrading bacteria strain BSN20, despite only one base difference in the 16S rRNA gene sequence. This method, named the S10-GERMS (S10-spc-alpha operon gene-encoded ribosomal protein mass spectrum) method, is a significantly useful tool for bacterial discrimination of the Sphingomonadaceae at the strain level and can detect and monitor the main APEO(n) -degrading bacteria in the environment.
Department of Environmental Bioscience, Meijo University, Nagoya, Aichi, Japan. n0861503@ccalumni.meijo-u.ac.jp
Yudai
Y
Hotta
Hiroaki
H
Sato
Akifumi
A
Hosoda
Hiroto
H
Tamura
D001426:Bacterial Proteins / Q000032:analysis / Q000235:genetics; D001431:Bacteriological Techniques / Q000379:methods*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004783:Environmental Microbiology; D008969:Molecular Sequence Data; D011092:Polyethylene Glycols / Q000378:metabolism*; D012269:Ribosomal Proteins / Q000032:analysis* / Q000235:genetics; D017422:Sequence Analysis, DNA; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*; D042301:Sphingomonadaceae / Q000737:chemistry* / Q000145:classification / Q000302:isolation & purification* / Q000378:metabolism
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D012269:Ribosomal Proteins; C023354:alkylpolyethoxylates; D011092:Polyethylene Glycols