title: Verification of Ribosomal Proteins ofAspergillus fumigatusfor Use as Biomarkers in MALDI-TOF MS Identification.
abstract: We have previously proposed a rapid identification method for bacterial strains based on the profiles of their ribosomal subunit proteins (RSPs), observed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). This method can perform phylogenetic characterization based on the mass of housekeeping RSP biomarkers, ideally calculated from amino acid sequence information registered in public protein databases. With the aim of extending its field of application to medical mycology, this study investigates the actual state of information of RSPs of eukaryotic fungi registered in public protein databases through the characterization of ribosomal protein fractions extracted from genome-sequencedAspergillus fumigatusstrains Af293 and A1163 as a model. In this process, we have found that the public protein databases harbor problems. The RSP names are in confusion, so we have provisionally unified them using the yeast naming system. The most serious problem is that many incorrect sequences are registered in the public protein databases. Surprisingly, more than half of the sequences are incorrect, due chiefly to mis-annotation of exon/intron structures. These errors could be corrected by a combination ofin silicoinspection by sequence homology analysis and MALDI-TOF MS measurements. We were also able to confirm conserved post-translational modifications in eleven RSPs. After these verifications, the masses of 31 expressed RSPs under 20,000 Da could be accurately confirmed. These RSPs have a potential to be useful biomarkers for identifying clinical isolates ofA. fumigatus.
authors.affiliation: Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST).
authors.forename: Sayaka
authors.initials: S
authors.lastname: Nakamura
authors.affiliation: Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST); Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST).
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Sato
authors.affiliation: Medical Mycology Research Center, Chiba University.
authors.forename: Reiko
authors.initials: R
authors.lastname: Tanaka
authors.affiliation: Medical Mycology Research Center, Chiba University.
authors.forename: Takashi
authors.initials: T
authors.lastname: Yaguchi
keywords: Aspergillus fumigatus; MALDI-TOF MS; protein database; ribosomal protein; sequence correction