Open AccessMALDI ‐ TOF MS analysis of ribosomal proteins coded in S 10 and spc operons rapidly classified the S phingomonadaceae as alkylphenol polyethoxylate‐degrading bacteria from the environment
Author(s) -
Hotta Yudai,
Sato Hiroaki,
Hosoda Akifumi,
Tamura Hiroto
Publication year - 2012
Publication title -
fems microbiology letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.899
H-Index - 151
eISSN - 1574-6968
pISSN - 0378-1097
DOI - 10.1111/j.1574-6968.2012.02525.x
Subject(s) - alkylphenol , operon , bacteria , ribosomal rna , biology , computational biology , microbiology and biotechnology , chemistry , genetics , gene , escherichia coli , alkyl , organic chemistry
Matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry ( MALDI ‐ TOF MS ) using ribosomal subunit proteins coded in the S 10–spc‐alpha operon as biomarkers was applied for the classification of the S phingomonadaceae from the environment. To construct a ribosomal protein database, S 10‐spc‐alpha operon of type strains of the S phingomonadaceae 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 S 10‐spc‐alpha operon, L 18, L 22, L 24, L 29, L 30, S 08, S 14, S 17, and S 19, could successfully distinguish the S phingopyxis terrae NBRC 15098 T and APEO n ‐degrading bacteria strain BSN 20, despite only one base difference in the 16 S r RNA gene sequence. This method, named the S 10 ‐ GERMS ( S 10‐spc‐alpha operon gene‐encoded ribosomal protein mass spectrum) method, is a significantly useful tool for bacterial discrimination of the S phingomonadaceae at the strain level and can detect and monitor the main APEO n ‐degrading bacteria in the environment.