Phylogenetics and mass spectrometry enabled microbial identification
Although much progress has been made in microbial taxonomy over the years, there remains a need for the development of fast, low-cost, and robust methods for classifying different microbial species at the molecular level where fine-grained differentiation between closely-related species and strains is possible. My current research focus centres on the development of new approaches for understanding the phylogenetics of microbial species as well as gaining a deeper understanding of the biological basis of mass spectrometry enabled microbial identification. Sub-topics in this area include the development of ribosomal protein mass fingerprinting approach to microbial identification, understanding the biological basis of mass spectrometry enabled microbial identification, and elucidating the evolutionary significance of ribosomal proteins.
Theoretical ribosomal protein mass fingerprinting
Ribosomal proteins are known to be conserved and thus useful for understanding the evolutionary divergence of different species. However, observations of distinct molecular mass of the same ribosomal proteins in different species across the three domains of life revealed that ribosomal proteins are more varied than previously thought, and likely encode deeper information on how natural selection exerts selective pressure on the evolution of ribosomal proteins’ amino acid sequence. Given the presence of large number of ribosomal proteins in the large and small ribosome subunit, unique ribosomal protein mass fingerprint likely exists for each species. Thus, the goal of this project is to understand the possibility of developing ribosomal protein mass fingerprinting as a tool for microbial identification and classification.
Representative publications
Wenfa Ng, “Theoretical ribosomal protein mass distribution of Pseudomonas aeruginosa PAO1”, PeerJ Preprints, Link to preprint
Wenfa Ng, “Existence of theoretical ribosomal protein mass fingerprints in bacteria, archaea and eukaryotes”, PeerJ Preprints, Link to preprint
Wenfa Ng, “Theoretical ribosomal protein mass fingerprint database” PeerJ Preprint, Link to preprint
Understanding the biological basis of MALDI-TOF MS microbial identification
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a proven technique for microbial identification. Specifically, the mass spectrum fingerprinting approach utilizes the comparison of mass spectrum of unknown microbe with those of known microorganisms catalogued in a reference database for identification purposes. However, the method lacks a firm biological basis given the comparison of mass peaks of unknown origins. Hence, the goal of this research is to uncover the possible biological basis embedded in the approach of MALDI-TOF MS microbial identification.
Specifically, the research is directed towards the identification of conserved mass peaks in MALDI-TOF mass spectra at the species and genus level that could lend a firmer biological basis to the method. Results from profiling MALDI-TOF mass spectra from SpectraBank revealed the existence of conserved mass peaks in mass spectra of different strains of the same species. Additionally, conserved mass peaks were also found at the genus level for many genus, but not Bacillus and Staphylococcus.
Representative publications
Wenfa Ng, “Conserved mass peaks in MALDI-TOF mass spectra of bacterial species at the genus and species levels”, PeerJ Preprints, Link to preprint
Wenfa Ng, “Annotation of ribosomal protein mass peaks in MALDI-TOF mass spectra of bacterial species and their phylogenetic significance”, bioRxiv, Link to preprint
Evolutionary significance of ribosomal proteins
Ribosomal proteins are housekeeping proteins that constitute part of the ribosome, the protein factory of the cell. Thus, ribosomal proteins could serve as markers that chronicles the evolutionary events that impact on all three domains of life. More importantly, ability to chronicle molecular evolutionary events through the eons also meant that ribosomal proteins could serve as phylogenetic markers in microbial taxonomy. However, the degree of concordance between phylogenetic trees based on ribosomal proteins and that based on the gold standard phylogenetic marker, 16S rRNA gene, remain partially understood. Hence, this research aims to explore the phylogenetic significance of ribosomal proteins in different phylogenetic families in Bacteria, Archaea, and Eukaryotes, as well as understand the potential utility of ribosomal protein profiling in building unique mass spectrum fingerprints for individual microbial species in the emerging method of mass spectrometry-based microbial identification.
Representative publication
Wenfa Ng, “Ribosomal proteins could explain the phylogeny of Bacillus species”, bioRxiv, Link to preprint
Looking at life with a scientific lens 