Integrative analysis of outer membrane vesicles proteomics and whole-cell transcriptome analysis of eravacycline
DineshKumar Kesavan1,2, Aparna Vasudevan2, Liang Wu2
1International Genomics Research Centre (IGRC), Jiangsu University, Zhenjiang, 212013, China.
Background:
Acinetobacter baumannii is a multidrug-resistant (MDR) hazardous bacterium with very high antimicrobial resistance profiles. Outer membrane vesicles (OMVs) help directly and/or indirectly towards antibiotic resistance in these organisms. The present study aims to look on the proteomic profile of OMV as well as on the bacterial transcriptome upon exposure and induction with eravacycline, a new synthetic fluorocycline. RNA sequencing analysis of whole-cell and LC-MS/MS proteomic profiling of OMV proteome abundance were done to identify the differential expression among the eravacycline-induced A. baumannii ATCC 19606 and A. baumannii clinical strain JU0126.
Results:
The differentially expressed genes from the RNA sequencing were analysed using R package and bioinformatics software and tools. Genes encoding drug efflux and membrane transport were upregulated among the DEGs from both ATCC 19606 and JU0126 strains. As evident with the induction of eravacycline resistance, ribosomal proteins were upregulated in both the strains in the transcriptome profiles and also resistance pumps, such as MFS, RND, MATE and ABC transporters. High expression of stress and survival proteins were predominant in the OMVs proteome with ribosomal proteins, chaperons, OMPs OmpA, Omp38 upregulated in ATCC 19606 strain and ribosomal proteins, toluene tolerance protein, siderophore receptor and peptidases in the JU0126 strain. The induction of resistance to eravacycline was supported by the presence of upregulation of ribosomal proteins, resistance-conferring factors and stress proteins in both the strains of A. baumannii ATCC 19606 and JU0126, with the whole-cell gene transcriptome towards both resistance and stress genes while the OMVs proteome enriched more with survival proteins.
Conclusion:
The induction of resistance to eravacycline in the strains were evident with the increased expression of ribosomal and transcription related genes/proteins. Apart from this resistance-conferring efflux pumps, outer membrane proteins and stress-related proteins were also an essential part of the upregulated DEGs. However, the expression profiles of OMVs proteome in the study was independent with respect to the whole-cell RNA expression profiles with low to no correlation. This indicates the possible role of OMVs to be more of back-up additional protection to the existing bacterial cell defence during the antibacterial stress.
Insights
Outer membrane vesicles (OMVs) in multidrug-resistant Acinetobacter baumannii contribute to eravacycline resistance by upregulating stress and survival proteins. OMVs provide additional protection independent of bacterial cell gene expression during antibiotic stress.
Area of Science:
- Microbiology
- Genomics
- Proteomics
Background:
- Acinetobacter baumannii is a multidrug-resistant (MDR) bacterium with significant antimicrobial resistance.
- Outer membrane vesicles (OMVs) play a role in antibiotic resistance mechanisms.
- Eravacycline is a novel synthetic fluorocycline antibiotic used to treat MDR bacterial infections.
Purpose of the Study:
- To investigate the proteomic profile of OMVs and the bacterial transcriptome of A. baumannii upon exposure to eravacycline.
- To identify differentially expressed genes and proteins in response to eravacycline induction in both a reference and a clinical strain.
Main Methods:
- RNA sequencing of whole-cell A. baumannii strains (ATCC 19606 and JU0126) exposed to eravacycline.
- LC-MS/MS proteomic profiling of OMVs isolated from the same bacterial strains.
- Bioinformatic analysis of differentially expressed genes (DEGs) and proteins.
Main Results:
- Upregulation of genes involved in drug efflux and membrane transport in both strains.
- Increased expression of ribosomal proteins, stress, and survival proteins in both transcriptome and OMV proteome.
- OMV proteome showed enrichment of survival proteins, with distinct profiles between the two strains.
- Low correlation observed between whole-cell RNA expression and OMV proteome profiles.
Conclusions:
- Eravacycline resistance induction in A. baumannii involves increased expression of ribosomal, transcription, efflux pump, and stress-related genes/proteins.
- OMVs appear to function as a supplementary protective mechanism, independent of direct transcriptional changes in the bacterial cell during antibiotic stress.
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