Proteomic dataset of Listeria monocytogenes exposed to sublethal concentrations of free and nanoencapsulated nisin

The cellular proteins of L. monocytogenes exposed to free and liposome-encapsulated nisin at sublethal concentration were hydrolyzed by trypsin and examined by tandem mass spectrometry (MS/MS) to obtain proteomic data. In the present study, we use the STRING v11.05 database analyze the interactions among the 78 upregulated proteins from L. monocytogenes obtained after treatment with sublethal concentrations of free and nanoliposome-encapsulated nisin. As result, from the upregulated proteins by free nisin was determined a network with 140 edges with two relevant nodes, containing ribosomal proteins and transmembrane transport proteins (SecD and ABC transport system). These two sets of proteins present biological connection as a group, with strong interactions and are related to detoxification and other Listeria response mechanisms. In addition, a high amount of membrane proteins was identified in the free nisin treatment. On the other hand, in the interaction analysis of upregulated proteins by liposome-loaded nisin, was found 156 edges with a single protein network, the same observed in free nisin, related to ribosomal proteins. Therefore, according with this analysis, the encapsulation of nisin into liposomes cause upregulation of ribosomal and decrease of L. monocytogenes response proteins as compared with free nisin.


a b s t r a c t
The cellular proteins of L. monocytogenes exposed to free and liposome-encapsulated nisin at sublethal concentration were hydrolyzed by trypsin and examined by tandem mass spectrometry (MS/MS) to obtain proteomic data. In the present study, we use the STRING v11.05 database analyze the interactions among the 78 upregulated proteins from L. monocytogenes obtained after treatment with sublethal concentrations of free and nanoliposome-encapsulated nisin. As result, from the upregulated proteins by free nisin was determined a network with 140 edges with two relevant nodes, containing ribosomal proteins and transmembrane transport proteins (SecD and ABC transport system). These two sets of proteins present biological connection as a group, with strong interactions and are related to detoxification and other Listeria response mechanisms. In addition, a high amount of membrane proteins was identified in the free nisin treatment. On the other hand, in the interaction analysis of upregulated proteins by liposome-loaded nisin, was found 156 edges with a single protein network, the same observed in free nisin, related to ribosomal proteins. Therefore, according with this analysis, the encapsulation of nisin into liposomes cause upregulation of ribosomal and decrease of L. monocytogenes response proteins as compared with free nisin.
© 2022 The Author(s

Value of the Data
• This dataset contains unique information on proteome of L. monocytogenes exposed to nanostructured antimicrobial peptide nisin. • The data may be valuable for scientists of different fields, including microbiology, protein science, food science, and nanotechnology. • The data can be useful to understand the effect of natural antimicrobials on pathogenic bacteria at molecular level. • The analysis of data may be used for development of innovative strategies to combat pathogenic bacteria.

Data Description
The proteomics data analyzed in this article is related to our previous research article titled "Proteomic analysis reveals differential responses of Listeria monocytogenes to free and nanoencapsulated nisin" [1] . The data of this article includes the set proteins identified using UniProt, with VIP (Variable Importance in Projection) score ≥1.0, obtained from of L. monocytogenes ATCC 7644 cells incubated for 1 h with sublethal concentrations of either free or liposomeencapsulated nisin. The set of proteins showing upregulation as compared with the control cells are summarized in Table 1 . This set of proteins denotes the global mechanism, in terms of protein expression and triggered by L. monocytogenes cells after treatment with free and nanoencapsulated nisin. These two groups of proteins were selected to explore the interactions among    proteins that showed differential expression. An in silico analysis was conducted using the free available software STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) version 11.05. For each set of proteins that were upregulated in response to free nisin and/or nanoencapsulated nisin, it was determined the number of protein-protein interactions documented in the database and the network functional enrichment. The complete set of proteins obtained from the STRING enrichment analysis for both free and liposome encapsulated nisin, are showed in the supplementary Table S1 and Table S2, respectively (available in the on-line repository MSV0 0 0 089076). In addition, a graph linking proteins symbolized by nodes with known interactions with the encoded genes of the identified proteins was assembled for visualization purposes. Different colors were used to evaluate the functional characteristics of proteins that were present in the nodes observed for upregulated proteins in treatments with free nisin ( Fig. 1 ) and nanoencapsulated nisin ( Fig. 2 ). A network with 140 edges with two relevant nodes was obtained with the analysis of proteins upregulated by free nisin, including a great quantity of membrane proteins. These protein clusters present biological connection and are related to stress response mechanisms in L. monocytogenes . The interaction analysis of upregulated proteins by liposome-loaded nisin showed 156 edges with a single protein network, the same observed in free nisin, related to ribosomal proteins.

Samples
The influence of free and nanoliposome-encapsulated nisin on the proteomic profile of L. monocytogenes was investigated using the strain ATCC 7644 (American Type Culture Collection, Manassas, VA, USA). The bacterial strain was retrieved from the stock culture maintained in Brain Heart Infusion (BHI) broth (Kasvi, São José dos Pinhais, Paraná, Brazil) containing 20% (v/v) glycerol for long-standing storage. To acclimatize the strain to the experimental conditions, an aliquot of the culture (0.1 mL) was inoculated into 9.9 mL BHI broth and incubated overnight in a shaker at operating 37 °C and 125 rpm. Afterwards, the bacterial cells were cultivated in BHI broth for 24 h at 37 °C using a 1% (v/v) inoculum. For the analysis, cells were then cultivated at 37 °C until they reached the mid-exponential growth phase (at hour 6 and OD 600 about 0.4). At this time, either free or liposome-encapsulated nisin were added at 0.3 μg/mL final concentration in separate treatments [1] . The liposomes were prepared by the thin film hydration method using purified phosphatidylcholine (Phospholipon 90G, provided by Lipoid, Ludwigshafen, Germany) as detailed in a previous work [2] . This method result in stable liposomes with entrapment efficiency of nisin superior to 90% [3] . Cells of L. monocytogenes incubated under the same conditions but without any treatment were used as control. The bacterial cells were incubated at 37 °C for 1 h, then harvested by centrifugation at 50 0 0 g at 4 °C for 10 min, and the pellets were washed three times with 2 mL of PBS pH 7.4 and then reserved for protein extraction [4] . Each treatment was performed in triplicate (biological replicates). For the analysis, samples of L. monocytogenes treated with free and liposome-encapsulated nisin were compared with control L. monocytogenes cultures.

Protein digestion and preparation of peptides
Protein digestion was performed according to standard protocols for complex protein mixtures [5] . In summary, the protocol consisted of the following steps: Afterwards, samples were centrifuged at 14,0 0 0 g for 20 min, and the supernatants were collected and applied to C18 reverse phase Stage Tips for desalination [6] . Stage Tips were previously conditioned with methanol and equilibrated with 0.1% (v/v) formic acid. Samples were loaded and 0.1% (v/v) formic acid was used to wash the salt residues. Peptides were then eluted with 60% (v/v) acetonitrile containing 0.1% (v/v) formic acid and the samples were freeze-dried and stored at −20 °C until LC-MS/MS analysis.
Instrumental procedures: set up in the data-dependent acquisition (DDA) mode; nanoelectrospray voltage 2.2 kV; source temperature 275 °C; resolution r = 60,0 0 0; collision energy of 35% for CID (collision-induced dissociation) fragmentation of most abundant ions with charge ≥2, sequentially isolated to a target value of 50 0 0; dynamic exclusion enabled at size list of 500 peptides, exclusion duration of 60 s and a repetition count of 1.

Data processing
Raw MS files were processed with the MaxQuant software version v1.3.0.3 [7] , and the Andromeda engine was employed to match MS/MS spectra against the Listeria monocytogenes UniProt protein sequence database and contaminant protein sequence ( https://www.uniprot. org/ ). The following parameters were used for MaxQuant: trypsin digestion, with maximum 2 missed cleavages and minimum peptide length of 7; cysteine carbamidomethylation as a fixed modification, while variable modifications were methionine oxidation and acetylation (Protein N-term); mass tolerance for peptides and fragments was set to ±20 ppm and ±0.1 Da; peptide and protein false discovery rate (FDR) cut-off was set to 0.01. The statistical analysis was performed using MetaboAnalyst 3.068. Only proteins with valid intensity values of label-free quantification (LFQ) detected in ≥50% of the samples were considered for analysis. The data was subjected to partial least squares discriminate statistical analysis (PLS-DA), then was established the cutoff value VIP (Variable Importance in Projection) and proteins with VIP score ≥1.0 were considered as upregulated [8] . All the proteins with VIP score ≥1.0 were characterized using UniProt and regrouped as upregulated proteins.
From the treatments, two groups of proteins (free and nanoencapsulated-encapsulated nisin) were selected for examination of the interactions among proteins showing differential expression (upregulation). An in silico analysis was conducted using the free available software STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) database version 11.05 [9] . The number of protein-protein interactions registered in the database were determined for the proteins that were differentially over expressed. For visualization purposes, a diagram was assembled linking proteins depicted by nodes with recognized connections with the identified proteins. At the same time, proteins with common gene ontology terms were identified by different colors.

Ethics Statements
This work does not involve human subjects, animal experiments or data collected from social media platforms.

Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.