Proteomic profiling of Serratia marcescens by high-resolution mass spectrometry

Abstract

Introduction: Serratia marcescens, an opportunistic human pathogen, is reported as an important cause of nosocomial infection and outbreaks. Although the genome of S. marcescens (ATCC 13880) was completely sequenced by 2014, there are no studies on the proteomic profile of the organism. The objective of the present study is to analyze the protein profile of S. marcescens (ATCC 13880) using a high resolution mass spectrometry (MS). Methods: Serratia marcescens ATCC 13880 strain was grown in Luria-Bertani broth and the protein extracted was subjected to trypsin digestion, followed by basic reverse phase liquid chromatography fractionation. The peptide fractions were then analysed using Orbitrap Fusion Mass Spectrometry and the raw MS data were processed in Proteome Discoverer software. Results: The proteomic analysis identified 15 009 unique peptides mapping to 2541 unique protein groups, which corresponds to approximately 54% of the computationally predicted protein-coding genes. Bioinformatic analysis of these identified proteins showed their involvement in biological processes such as cell wall organization, chaperone-mediated protein folding and ATP binding. Pathway analysis revealed that some of these proteins are associated with bacterial chemotaxis and beta-lactam resistance pathway. Conclusion: To the best of our knowledge, this is the first high-throughput proteomics study of S. marcescens (ATCC 13880). These novel observations provide a crucial baseline molecular profile of the S. marcescens proteome which will prove to be helpful for the future research in understanding the host-pathogen interactions during infection, elucidating the mechanism of multidrug resistance, and developing novel diagnostic markers or vaccine for the disease.

Applications of tandem mass spectrometry (MS/MS) in antimicrobial peptides field: Current state and new applications

“…PEAKS Studio software (Waterloo, ON, Canada) is commonly used for data acquisition and analysis [ [145] , [175] , [176] , [177] , [178] ]. Additionally, software such as Proteome Discoverer [ 179 , 160 ], Mascot software [ 180 , 157 ], and ProteinLynx Global SERVER [ [148] , [181] , [182] ] are widely used in protein polypeptide analysis.…”

Molecular dynamics and simulation analysis against superoxide dismutase (SOD) target of Micrococcus luteus with secondary metabolites from Bacillus licheniformis recognized by genome mining approach

“…System inputs for MD were generated with Charmm-gui and GROMACS 2020.6 was employed to achieve SOD protein and protein–ligand complex MD simulations under the influence of the chosen CHARMM36m force field. In total, MD simulation of five ligands in complex with protein SOD were carried out for 250 ns time as reported previously ( Gangadharappa et al, 2020a , Bagewadi et al, 2023 ). The complexes include (1) SOD-Bacillibactin (SOD-BAC), (2) SOD-Paenibactin (SOD-PAE), (3) SOD-Fengycin (SOD-FEN), (4) SOD-Surfactin (SOD-SUR) and (5) SOD-Lichenysin (SOD-LIC).…”

“…Following the production MD run for 250 ns, the resultant trajectory files were analyzed using gromacs utilities such as ‘gmx rms’, ‘gmx rmsf’, ‘gmx gyrate’ and ‘gmx sasa’ for Root Mean Square Deviation (RMSD), Root Mean Square Fluctuations (RMSF), Solvent Accessible Surface Area (SASA) and Radius of Gyration (Rg) respectively ( Gangadharappa et al, 2020a ). The data was examined for a minimum steady trajectory of 60 ns in a window size of 15 ns.…”