Pan-Proteomic Analysis and Elucidation of Protein Abundance among the Closely Related Brucella Species, Brucella abortus and Brucella melitensis

Abstract

Brucellosis is a zoonotic infection caused by bacteria of the genus Brucella. The species, B. abortus and B. melitensis, major causative agents of human brucellosis, share remarkably similar genomes, but they differ in their natural hosts, phenotype, antigenic, immunogenic, proteomic and metabolomic properties. In the present study, label-free quantitative proteomic analysis was applied to investigate protein expression level differences. Type strains and field strains were each cultured six times, cells were harvested at a midlogarithmic growth phase and proteins were extracted. Following trypsin digestion, the peptides were desalted, separated by reverse-phase nanoLC, ionized using electrospray ionization and transferred into an linear trap quadrapole (LTQ) Orbitrap Velos mass spectrometer to record full scan MS spectra (m/z 300–1700) and tandem mass spectrometry (MS/MS) spectra of the 20 most intense ions. Database matching with the reference proteomes resulted in the identification of 826 proteins. The Cluster of Gene Ontologies of the identified proteins revealed differences in bimolecular transport and protein synthesis mechanisms between these two strains. Among several other proteins, antifreeze proteins, Omp10, superoxide dismutase and 30S ribosomal protein S14 were predicted as potential virulence factors among the proteins differentially expressed. All mass spectrometry data are available via ProteomeXchange with identifier PXD006348.

Dichloromethane Degradation Pathway from Unsequenced Hyphomicrobium sp. MC8b Rapidly Explored by Pan-Proteomics

“…The pan-proteomics concept [4,7] can be applied to a relatively large number of prokaryotic isolates, as the genomes of many types of microorganisms have now been sequenced. While the small number of available genomes for eukaryotes still represents a limitation for the application of pan-proteomics, the similar concept of "homology-driven proteomics" [42,43] has proved helpful for the analysis of proteomes of unsequenced animals and plants [44,45].…”

“…The proteome of closely-related bacterial strains can be compared unifying all the genome sequences into a single protein database for interpreting shotgun proteomic data [4]. This pan-proteomics concept allows better quantitative proteome measurements and was recently applied to characterize the proteome of Lactococcus lactis strains [5], Streptococcus agalactiae strains [6], and mid-exponentially grown Brucella representatives [7], thereby promoting information attributions about unified groups of proteins within a given branch of the Tree of Life. The concept can be further extended to still uncharacterised isolates.…”

Proteomics of Brucella: Technologies and Their Applications for Basic Research and Medical Microbiology

“…However, if the instrument is present and after training, it is relatively easy to operate daily, it offers several advantages such as improved accuracy and precision, retrieves an important amount of information from samples in a short time and has a higher selectivity. Liquid chromatography coupled to a tandem mass spectrometry (LC-MS/MS) has recently become a more popular alternative for the quantitative pan-proteome analysis of Brucella [12].…”

“…This lack of data results in a somewhat sketchy picture of the whole proteome of Brucella and needs to be closed by pan-proteomics studies. Thus, the future of Brucella proteomics should focus on whole and pan proteomes [12]. Comparative and comprehensive proteomics analysis of several types and wild strains of brucellae from different host populations may help to discover crucial virulence proteins, unravel the secrets behind host specificity and the host-pathogen interaction phenomena, as well as to identify virulence mechanisms.…”

“…Brucella lacks classical virulence factors and several aspects of its biology e.g., pathogenesis, survival in macrophages, and host specificity, are still not well understood. To explain its virulence and host specificity, a better understanding at the proteome and metabolome level could be helpful [12].…”