Interaction network and mass spectrometry data of Xanthomonas citri subsp. citri surface proteins from differential proteomic analysis of infectious and non-infectious cells

Here we provide the mass-spectrometry and in silico interaction network dataset of proteins identified on our research article on surface proteomic analysis from Xanthomonas citri subsp. citri (XAC) cells grown in vivo (infectious) and in vitro (non-infectious, control) by 2D-DIGE approach. Fluorescence labeling of proteins were performed on intact cells followed by cellular lysis and labeled spots from 2D gel differing in abundance between the two conditions (ANOVA, p-value<0.05) were analyzed by a nano-electrospray tandem mass spectrometry Q-Tof Ultima API mass spectrometer (MicroMass/Waters) (LC-ESI-MS/MS). This article contains raw data of proteins detected in the 79 spots analyzed by LC-ESI-MS/MS approach and also an enrichment analysis on the resulting protein–protein interaction network performed with the Integrated Interactome System (IIS) platform and Cytoscape software. The data are supplementary to our original research article, “Xanthomonas citri subsp. citri surface proteome by 2D-DIGE: ferric enterobactin receptor and other outer membrane proteins potentially involved in citric host interaction” (Carnielli et al., 2016) [1], and raw data are available via Peptide Atlas (ftp://PASS00850:ZJ7425v@ftp.peptideatlas.org/).


Subject area
Biology More specific subject area

Plant-pathogen interaction proteomics
Type of data MS spectra raw files, Figure,

2D-DIGE proteome analysis of surface-labeled XAC cells (in vivo vs. in vitro)
Experimental features XAC cells were grown in vivo (infectious) and in vitro (non-infectious) conditions and cells were fluorescently labeled previously to cell lysis. Differential spots were isolated, trypsin-digested and peptide samples were analyzed by LC-ESI-MS/MS and proteins identified by Mascot search software.

Data source location
Campinas and São Carlos, São Paulo State, Brazil.

Data accessibility
All the raw files from mass spectrometry analysis are deposited in Peptide Atlas and can be found through the PASS00850 number or by the link ftp:// PASS00850:ZJ7425v@ftp.peptideatlas.org/.

Value of the data
Data were generated by a first study on surface proteome of XAC interacting with its citrus host and thus can provide additional information for XAC-host interaction studies in need of proteomic data In silico interaction analysis provides an overview of possible protein-protein interactions among XAC cells.

Data
Data include raw files of mass spectrometry analysis of tryptic peptides of XAC surface proteins labeled with CyDyes DIGE minimal dyes. Proteins with differential abundance in cells grown in vivo and in vitro were mapped into a protein-protein interaction network ( Fig. 1; Supplementary data). Information of overrepresented Gene Ontology (GO) biological processes and KEGG pathways is shown (Table 1).

Experimental design, material and methods
XAC genome strain (strain 306) was grown in vivo on detached Citrus aurantifolia leaves (infectious condition) and in vitro in NB medium (non-infectious condition, control), as described by Carnielli et al. [1].
Data files generated by the LC-ESI-MS/MS analysis (PeptideAtlas dataset submission PASS00850) were processed using the search engine MASCOT Distiller v.2.3.2.0, 2009 (Matrix Science Ltd.) and the sequences were searched against XAC 306 genome databank (available at NCBI) using Mascot Server v.2.3.01.0 (Matrix Science Ltd.). The following parameters were used for database searches: trypsin with 1 missed cleavage allowed, mass tolerance of 0.1 Da for the precursor ions and a tolerance of  Table 1). The network was built using the IIS software and orthologue relationship of annotated interactions from Escherichia coli database. Proteins were assigned as clusters in a circle layout according to enriched biological processes (p-value o 0.05) or enriched KEGG pathways (name written in purple color) (p-value o 0.05). Different colors were attributed to proteins according to the input (in blue) or from the database (in gray). The resultant networks were visualized using the Cytoscape 2.8.3 software.

Bioinformatic and network analysis
The identified proteins were submitted to an enrichment analysis by Integrated Interactome System (IIS) platform [2] using the functional annotation database of Escherichia coli, since Xanthomonas sp. does not have such database annotation. The resulting protein map was visualized on Cytoscape and nodes were assigned in clusters according to the most enriched (lowest enrichment pvalue) biological processes or KEGG pathway (Fig. 1). Different colors were used to display proteins from the input (orthologues proteins; in blue) or from the database (in gray). Proteins without a biological process or KEGG pathway annotation are grouped in the center of the network. The annotation table for the input list is shown in Table 1.