<em>S. aureus</em> strain functional diversity as observed through pan-proteomics: an emerging approach for proteome measurement within a background of genetic heterogeneity — ASN Events
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  2. Symposium Nine: Microbial Proteomics
  3. S. aureus strain functional diversity as observed through pan-proteomics: an emerging approach for proteome measurement within a background of genetic heterogeneity

S. aureus strain functional diversity as observed through pan-proteomics: an emerging approach for proteome measurement within a background of genetic heterogeneity (#038)

James A Broadbent 1 2 , Imalka UK Tennakoon 1 , Daniel A Broszczak 2 , Flavia Huygens 1
  1. Microbial Molecular Pathogenesis Group, Infection Disease Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
  2. Omics and Systems Biology Group, Tissue Repair and Regeneration Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia

Background

Pan-proteome analysis is an emerging method that seeks to qualitatively and quantitatively compare the proteomes of genetically heterogeneous microorganisms. This approach has been reported in a single paper within the scientific literature;(1) however, there are major technical considerations that need to be addressed in order for this method to progress towards a valuable and accessible analytical technology.

Experimental Approach

FIve unique strains of Staphylococcus aureus, four of which are unsequenced, were grown under standard conditions and harvested at mid-exponential and stationary points on the growth curve. Cells were processed and comprehensive proteome samples subjected to data-independent acquisition LC-MS/MS as well as data-dependant acquisition LC-MS/MS, following deep proteome fractionation.

Qualitative mass spectrometry data were searched against all S. aureus sequences (~125,000) found within the UniProt database (Sept, 2014) using the Paragon algorithm. The resulting data were used to generate a spectral library of empirical S. aureus peptide mass spectra; the library was used to extract peptide ion areas from within the data-independent mass spectra. Peak area data were exported and processed in R in order to compare the summed protein abundance information under a set of unified pan-protein identifiers, based on protein sequence homology. Pan-protein abundances were normalized then compared across all strains using permutation statistics. Global protein abundance ratios between strains were compared to matched RNAseq quantification data.

Results and discussion

Pan-proteomics offers new opportunities to measure and interpret microorganisms’ biochemistry within the context of genetic diversity. In this example, the contribution of protein abundance to unsequenced S. aureus strain types were measured and interpreted to reveal potential metabolic and virulence advantages that may underpin pathogenic observation. With robust development, pan-proteomics may prove valuable in the areas of drug development and/or industrial strain selection and, furthermore, could be applied to the proteome measurement of genetically-diverse but related plants and invertebrates.

  1. 1. Zhang, L.; Xiao, D.; Pang, B.; Zhang, Q.; Zhou, H.; Zhang, L.; Zhang, J.; Kan, B., The core proteome and pan proteome of Salmonella Paratyphi A epidemic strains. PLoS One 2014, 9, (2), e89197.