Heavy metal-based NPs and ions increased transformation frequency
A naturally competent opportunistic pathogen A. baylyi was used to evaluate the effects of heavy metal-based NPs (including Ag NPs, CuO NPs and ZnO NPs) and their ionic forms (Ag+, Cu2+ and Zn2+) on the transformation of plasmid pWH1266 encoded ARGs. The tested heavy metal and NP concentrations were included the environmentally relevant concentrations (e.g., 0.1 and 1 mg/L). In general, all the tested heavy metal-based NPs and ions could significantly (* p < 0.05, ** p < 0.01) promote the transformation of pWH1266 plasmid into A. baylyi at certain exposure levels (Fig. 1A, B and C). For example, the transformation frequencies under 0.1 mg/L Ag+ (7.5 ± 1.1 × 10− 6 per recipient cell, Fig. 1A), 100 mg/L CuO NPs (1.5 ± 0.04 × 10− 5 per recipient cell, Fig. 1B) and 10 mg/L Zn2+-treated group (2.9 ± 0.2 × 10− 5 per recipient cell, Fig. 1C) were 2.8, 5.6 and 11.0-folds higher than that of the control groups (2.7 ± 0.5 × 10− 6 per recipient cell), respectively. Various NPs and ion types resulted in different trends in terms of transformation frequencies. For Ag and CuO NPs/ions-treated groups, the increments of the natural transformation frequency were concentration-independent when compared to the control groups. For the ZnO NPs/ions-treated groups, a concentration-dependent increase was observed for the natural transformation frequencies when compared to the control groups. From 0.1 mg/L to 100 mg/L, the ZnO NPs/ions-mediated transformation frequencies increased with the increments of ZnO NPs/ions concentrations (Fig. 1C). However, it should be noted that the transformation frequencies of plasmid pWH1266 were significantly (* p < 0.05, ** p < 0.01) decreased under 100 mg/L Ag NPs, 10 and 100 mg/L Ag+, and 10 and 100 mg/L Cu2+ concentrations (Fig. 1A, B and C).
Multiple approaches were conducted to confirm the uptake of plasmid pWH1266 by A. baylyi. Firstly, the minimum inhibitory concentrations (MICs) of recipient wild-type A. baylyi and transformants against both Amp and Tet antibiotics were scanned. Since the plasmid pWH1266 encodes resistance genes against ampicillin (Amp) and tetracycline (Tet), transformants should have obtained the resistance against Amp and Tet from the plasmid. As expected, all the transformants exhibited around 15 and 5 folds higher MICs to Amp and Tet, compared to the recipient (Fig. 1D). Secondly, plasmids extracted from the transformants were compared with the donor plasmid by gel electrophoresis. Clear bands from transformants were shown with approximate sizes to the donor (Fig. 1E), indicating that the transformants have received pWH1266 plasmids. Thirdly, the Polymerase chain reaction (PCR) amplification with long amplicons was employed to confirm if the transformants have carried both blaTEM−1 and tetA genes. All the amplified products from transformants exhibited similar sizes to that of the donor (Fig. 1E), demonstrating that the transformants have harbored plasmid pWH1266.
Collectively, these results confirmed that heavy metal-based NPs and ions could promote the transformation of pWH1266 plasmid into A. baylyi at environmentally relevant concentrations.
ROS over-production under the exposure of heavy metal-based nanoparticles and ions
All of the tested Ag, CuO and ZnO NPs/ions were able to increase the intracellular ROS generation of A. baylyi. Based on flow cytometer detection results, the recipient strain showed significant (* p < 0.05, ** p < 0.01) concentration-dependent increases of intracellular ROS generation from 0.01 mg/L Ag NPs and CuO NPs, and from 0.1 mg/L Ag+ and Cu2+, to 100 mg/L Ag and CuO NPs/ions (Fig. 2A and B). More importantly, it was found that the Ag and CuO NPs/ions-increased transformation was correlated with the increase of ROS levels below a certain threshold (approximately around 2-fold of ROS increase compared to the control). For instance, the transformation frequencies of pWH1266 plasmid started to decrease from 10 mg/L of Ag+, Ag NPs and CuO NPs (Fig. 1A and B), at which the ROS generation mediated by the corresponding heavy metal-based NPs and ions was over 2-fold higher than the control groups (Fig. 2A and B). In contrast, the ZnO NPs/ions-facilitated transformation frequencies did not correlate with the ROS generation mediated by ZnO NPs/ions (Fig. 1C and 2C). Moreover, although the ROS generation increased under the exposure of ZnO NPs/ions from 0.01 mg/L, the fold-changes were below 1.3-fold (Fig. 2C), which is much lower than the increment of ROS mediated by Ag and CuO NPs/ions (e.g., 2.7-fold increase under 100 mg/L Ag+, Fig. 2A).
The molecular responses of A. baylyi against heavy metal-based NPs/ions were further investigated by using whole-genome RNA sequencing and proteomic analysis. In terms of ROS response, under all heavy metal-based NPs/ions treatments, the expression levels of the 12 known antioxidant system-related genes were mostly up-regulated, especially for the expression of the alkyl hydroperoxide reductase-coding genes ahpC and ahpF (Fig. 2D, Table S2). To illustrate, in response to the exposures of 1 mg/L Cu2+, the expression level of ahpC gene were 42.8-fold (i.e., Log2 fold change (LFC) = 5.42) higher than that of the control. To further validate the oxidative stress response in translational levels, proteomic sequencing was performed and indicated a similar enhancement of the antioxidant system (Fig. 2E, Table S3). Apart from the increased translations of alkyl hydroperoxide reductase AhpC and AhpF, there is also an upregulation in the translation of catalase KatA under all heavy metal-based NPs/ions, in which up to 7.1-fold (i.e., LFC = 2.8) increase was observed when treated with 10 mg/L Zn2+ (Fig. 2E).
To further verify whether heavy metal-based NPs and ions-mediated ARGs transformations were correlated to the ROS over-production, we then examined the effect of a ROS scavenger, thiourea, on ROS production and ARGs transformation. With 100 µM thiourea added, the ROS production levels were significantly (* p < 0.05, ** p < 0.01) reduced to the extent of control groups across most of the heavy metal-based NPs and ions dosage (Fig. 2F). Correspondingly, the Ag and CuO NPs/ions-mediated ARGs transformation frequencies were significantly (* p < 0.05, ** p < 0.01) decreased to the extent of control groups after thiourea addition, while thiourea did not reduce the ZnO NPs/ions-mediated ARGs transformation to the extent of control groups (Fig. 2G). These results further validated the correlation between ROS over-production and ARGs transformation under the exposure of Ag and CuO NPs/ions.
Heavy metal-based nanoparticles and ions increased cell membrane permeability
Cell membrane permeability of heavy metal-based NPs and ions-treated recipient was also evaluated by flow cytometer to verify whether it was associated with transformation enhanced by heavy metal-based NPs and ions (Fig. 3). Similar to the ROS generation, the concentration-dependent increases of membrane permeability could also be detected within Ag and CuO NPs/ions treated A. baylyi (Fig. 3A and B). In contrast, there was no significant change across all ZnO NPs/ions-treated A. baylyi (Fig. 3C). TEM imaging of A. baylyi was also conducted to evaluate the changes in cell membrane morphology under different concentrations of heavy metal-based NPs and ions treatment (Fig. 3D). Compared to the control groups, the increased cell membrane roughness and leakage of cytoplasm could be observed under 1 mg/L Ag+, Cu2+ and CuO NPs dosage. In comparison, no obvious changes in cell membrane morphology could be observed under 10 mg/L ZnO NPs/ions (Fig. 3D).
In terms of RNA transcription, most of the outer membrane-related genes (e.g., 20 out of 23 genes under 1 mg/L Ag+ treatment) were only moderately altered after 2 h of all heavy metal-based NPs and ions treatment (0 ≤ |LFC| ≤ 1). As exceptions, the outer membrane assembly gene bamD were 1.1 to 1.3-fold (LFC) up-regulated under Ag and CuO NPs/ions treatment, and the ACIAD0121 and adeK genes were down to -1.49 to -2.54-fold down-regulated under all heavy metal-based NPs and ions treatment (Fig. 3E, Table S4). Differently, the translation of outer membrane-related protein (e.g., 19 out of 22 proteins under 1 mg/L Cu2+) after 6 h of all heavy metal-based NPs and ions treatment were mainly up-regulated, especially when under CuO NPs/ions treatment (i.e., ACIAD1141, CvpA and OmpA, Fig. 3F, Table S5). Besides, the translation levels of outer membrane proteins were slightly up-regulated under Ag NPs/ions treatment, while fluctuated under ZnO NPs/ions treatment (Fig. 3F, Table S5).
Heavy metal-based NPs and ions stimulated transcription and translation of competence, stress response, SOS response and ATP production-related genes
The key steps involved in transformation of A. baylyi ADP1 are consist of type IV transformation pilus systems (pil gene family), translocase complex at the cytoplasmic membrane (com gene family) and recombination of exogenous DNA after the homology search [4, 5]. The heavy metal-based NPs/ions-mediated transcription and translation response of the genes involved in the competence system were further evaluated (Fig. 4A). Firstly, for competence-related genes, three genes associated with type IV transformation pilus and DNA translocase systems (comEA, pilT and pilU) showed increased transcription (e.g., LFC = 1.9 increase of comEA under 1 mg/L Cu2+, Fig. 4B), while three proteins (ComP, PilG and PilH) showed enhanced translation (e.g., LFC = 1.4 increase of ComP under 10 mg/L Zn2+, Fig. 4C), under all heavy metal-based NPs/ions dosage. Secondly, in terms of recombination-related genes, the transcription of the majority of these genes (e.g., 16 out of 20 genes under 1 mg/L Ag NPs treatment) were up-regulated under all heavy metal-based NPs/ions dosage, particularly for himA gene with LFC = 1.8 upregulation in response to CuO NPs/ions (Fig. 4B). Thirdly, we found that heavy metal-based NPs/ions dosage elevated the transcription of the majority (e.g., 28 out of 34 genes under 1 mg/L Ag+ treatment)of SOS response-associated genes (Fig. 4B) and the translation of four SOS response-associated proteins (DnaN, HupB, RecR and Ssb, Fig. 4C). More obviously, ZnO NPs/ions considerably enhanced the transcription of the stress response genes (Fig. 4B), in which the transcription of nirD genes were 9.6-fold (LFC = 3.3) higher than the control group when treated with Zn2+. Lastly, although the transcriptions of ATP-related genes were not up-regulated (Fig. 4B), the translations of those ATP-related proteins were largely promoted under CuO NPs/ions and Zn2+ treatment (Fig. 4C).