Transcriptomics as a tool to discover new antibacterial targets

Abstract

The emergence of antibiotic-resistant pathogens, multiple drug-resistance, and extremely drug-resistant strains demonstrates the need for improved strategies to discover new drug-based compounds. The development of transcriptomics, proteomics, and metabolomics has provided new tools for global studies of living organisms. However, the compendium of expression profiles produced by these methods has introduced new scientific challenges into antimicrobial research. In this review, we discuss the practical value of transcriptomic techniques as well as their difficulties and pitfalls. We advocate the construction of new databases of transcriptomic data, using standardized formats in addition to standardized models of bacterial and yeast similar to those used in systems biology. The inclusion of proteomic and metabolomic data is also essential, as the resulting networks can provide a landscape to rationally predict and exploit new drug targets and to understand drug synergies.

Ceragenins and Antimicrobial Peptides Kill Bacteria through Distinct Mechanisms

“…To gain insights into the mechanism of action of CAMPs and ceragenins, we determined the global transcriptional responses of E. coli exposed to colistin, LL37, CSA13, and CSA131 using RNAseq, as similarly used for other antibacterial compounds ( 17 , 18 ). Bacteria were grown to log phase and then treated with supra-MICs of antibiotics for 1 h before RNA extraction and sequencing (see Materials and Methods).…”

Transcriptome-Based Molecular Networks Uncovered Interplay Between Druggable Genes of CD8+ T Cells and Changes in Immune Cell Landscape in Patients With Pulmonary Tuberculosis

“…However, polymorphism studies were unable to provide full insight into the complex molecular crosstalk between thousands of host genes involved in innate and adaptive immune responses. In this context, high throughput transcriptome approaches have shown great promise in dissecting the host-pathogen interactions thereby helping to develop a novel vaccine and therapeutic targets for several infectious diseases (39)(40)(41). Therefore, we explored host immune system response through integrated systems biology approach based on immune cell subtyping and differential gene expression profiles of patients with PTB to normal controls.…”

Antifungal Metabolites as Food Bio-Preservative: Innovation, Outlook, and Challenges

“…The effects of diverse antifungal drugs should be determined using microarray or other 'omics' technologies, as most of these targets are unknown. Future research should improve our understanding of the genetic mechanisms and metabolic pathways of antifungal synthesis [122].…”