Antibacterial mechanism and transcriptome analysis of ultra-small gold nanoclusters as an alternative of harmful antibiotics against Gram-negative bacteria

In this work, a well-known Au₂₅ NCs with high purity was prepared by simple one-pot reducing method. The as-synthesized Au₂₅ NCs exhibited excellent antibacterial efficiency toward Gram-negative bacteria in a dose- and time-dependent manner, which could be used as nanoantibiotics to replace harmful antibiotics. The antibacterial assays showed that almost 100% bacteria were killed at lower concentration (100–150 μM) within a short time (30–60 min), providing a rapid and effective killing outcome for Gram-negative bacteria. After that, antibacterial mechanism was mainly investigated at cellular level via destruction of membrane integrity, disruption of antioxidant defense system, metabolic inactivation, DNA damage, as well as at molecular level via transcriptome analysis (RNA sequencing) for the first time. RNA sequencing results showed that differentially expressed genes (DEGs) related to biosynthesis of cell wall and membrane, glycolysis and TCA cycle, oxidative phosphorylation and DNA replication and repair were significantly affected. It was concluded that synergetic effect of membrane damage, oxidative stress, DNA damage and energy metabolism eventually led to the Gram-negative bacteria growth inhibition and death.