Data on nucleoid-associated proteins isolated from Mycoplasma gallisepticum after intracellular infection

Mycoplasma gallisepticum (M. gallisepticum) belongs to the class of Mollicutes. It causes chronic respiratory disease in avian species. It is characterized by lack of cell wall and reduced genome size. As a result of genome reduction, M. gallisepticum has a limited variety of DNA-binding proteins (DBP) and transcription factors. Consequently, the diversity of DNA-binding proteins and transcription factors (TF) in M. gallisepticum is limited in comparison with related bacteria such as Bacillus subtilis. Studies have shown, however, that mycoplasmas demonstrate a wide range of differential expression of genes in response to various stress factors, which promotes effective adaptation to unfavorable conditions. We assume that in the case of mycoplasmas, which are characterized by a combination of the reduction of known gene expression regulation systems and a high adaptive potential, the coordination of gene expression can be provided due to local changes in the structure and spatial organization of the chromosome. The study of the dynamic changes of the proteomic profile of M. gallisepticum nucleoid may assist in revealing its mechanisms of functioning, regulation of chromosome organization and stress adaptation including its changes upon invasion of the host cells.


a b s t r a c t
Mycoplasma gallisepticum (M. gallisepticum) belongs to the class of Mollicutes. It causes chronic respiratory disease in avian species. It is characterized by lack of cell wall and reduced genome size. As a result of genome reduction, M. gallisepticum has a limited variety of DNA-binding proteins (DBP) and transcription factors. Consequently, the diversity of DNA-binding proteins and transcription factors (TF) in M. gallisepticum is limited in comparison with related bacteria such as Bacillus subtilis . Studies have shown, however, that mycoplasmas demonstrate a wide range of differential expression of genes in response to various stress factors, which promotes effective adaptation to unfavorable conditions. We assume that in the case of mycoplasmas, which are characterized by a combination of the reduction of known gene expression regulation systems and a high adaptive potential, the coordination of gene expression can be provided due to local changes in the structure and spatial organization of the chromosome. The study of the dynamic changes of the proteomic profile of M. gallisepticum nucleoid may assist in revealing its mechanisms of functioning, regulation of chromosome organization and stress adaptation including its changes upon invasion of the host cells.

Value of the Data
• This dataset contains detailed proteomic profiles of M. gallisepticum nucleoids obtained from cell culture with synchronized cell division after intracellular infection. • This dataset can be used in research to investigate new nucleoid-associated proteins in genome-reduced organisms. • The data are valuable for researchers interested in M. gallisepticum proteomics.

Data Description
Lately more and more evidence has appeared that one of the mechanisms of regulation of gene expression in bacteria can be local rearrangements of the structure and spatial organization of the chromosome [1 , 2] . This is most important for mycoplasmas because a small set of transcription factors cannot fully capture the regulation of gene expression. To understand the significance of the structural organization of the chromosome in the processes of regulation of genes and adaptation to stress, it is necessary to identify new TF and DBPs that can take part in dynamic changes in the structure of the chromosome. We previously demonstrated phase transition of the M. gallisepticum upon invasion of eukaryotic cells. Proteomic changes affected a broad range of processes including metabolism, translation and oxidative stress response [3] . To search for new potential DBPs that may play a role in the infection process, we isolated nucleoids from M. gallisepticum cells before and after infection of the HD3 chicken erythroblast cell line and performed a comparative proteomic analysis of these nucleoids and their corresponding cell lysates. The list of samples is presented in Table 1 . LC-MS/MS analysis was carried out on an Ultimate 30 0 0 RSLC nano HPLC system connected to a QExactive Plus mass spectrometer (Thermo Fisher Scientific, USA) [4] . Identification and label-free quantification analysis were performed with MaxQuant 1.6.10.43 software with default settings. The data was searched against M. gallisepticum S6 NCBI database partner repository with the dataset identifier PXD025107. ( https://www.ebi.ac.uk/pride/archive/projects/PXD025107 ). Further calculations , along with Uniport protein and gene names and gene ontology information is presented in the supplementary file S1. The resulting Pearson correlation matrix (Table S1, LFQ values) show good reproducibility between biological replicas ( Fig. 1 ). Volcano plots ( Fig. 2 , Table S1, LFQ and corrected p values) show the number of DNA-binding proteins that change their representation in the nucleoid relative to the cell lysate for acute ( Fig. 2 A) and chronic infection ( Fig. 2 B). Lists of proteins enriched (Log2FC > 1, adjusted p-value < 0.05) in nucleoid fractions relative to cell lysate for acute and chronic infections are presented in Table  S2 (A-B). The range of protein enriched in M. gallisepticum nucleoids before and after acute and chronic infection of HD3 cells is shown in Fig. 2 C and D. Table S3 lists differential proteins, the level of which changes by 2 or more times in the nucleoides isolated from cells of M. gallisepticum after acute (Table S3, C) and chronic (Table S3, D) infection relative to control nucleoids (before infection).

Bacterial strains, HD3 cells infection and cell culture synchronization
M. gallisepticum S6 was cultivated in a medium containing tryptose 20 g/l, Tris 3 g/l, NaCl 5 g/l, KCl 5 g/l, yeast extract (10%, Helicon, Russia), horse serum (10%, Biolot, Russia), glucose 1% (Sigma) and penicillin (Sintez, Russia) with a final concentration 500 units/ml (BHI medium) at pH 7.4 and 37 °C. Chicken erythroblast cell line HD3 (clone A6 of line LSCC51,52) was obtained from Professor S. V. Razin (Institute of Gene Biology, Russian Academy of Sciences) and was cultivated as described previously [5] . The gentamicin invasion assay was carried out as previously described [6] . We used the concentration of gentamicin 600 μg/ml. Cell lines were infected with the M. gallisepticum S6 in a ratio of 1:10 0 0 and cultured for 24 h (acute infection) or 4 weeks (chronic infection) at 37 °C and 5% CO 2 . After treatment with gentamicin, HD3 cells were removed from the plate, pelleted by centrifugation at 300 g for 5 min, and diluted in 1 ml of BHI medium. The resulting sample was serially diluted and plated on a semi-liquid medium. The colonies were used to obtain a culture of M. gallisepticum to isolate the nucleoid fraction. We used a culture of M. gallisepticum with synchronized division. For this, 1% of post-infectious cells were starved for 9 h in a depleted BHI medium (without serum, yeast extract, and glucose) in aerobic conditions at pH 7.4 and 37 °C. After that 10% yeast extract, 20% horse serum and 1% glucose were added. The culture was grown further at 37 °C to the logarithmic growth phase.

Nucleoid isolation and sample preparation for proteomic analysis
Nucleoid isolation was performed as described in [7] . 20 μl of 10% sodium deoxycholate and 2 μl of nuclease mix (GE HealthCare) were added to the nucleoid fraction and incubated for 1 h at 4 °C. After incubation, 80 μL of 100 mM Tris -HCl, pH 8.5 with protease inhibitor cocktail (GE HealthCare) was added to the sample. Protein concentration was estimated by BCA Assay (Sigma). Aliquots containing 300 μg of protein material were diluted to 1 μg/μL with 100 mM Tris-HCl, pH 8.5, and tris (2-carboxyethyl) phosphine hydrochloride (TCEP, Sigma) and chloroacetamide (CAA, Sigma) were added to the final concentrations of 10 and 30 mM, respectively. Cys-reduction and alkylation were achieved by 10 min heating of the sample at 85 °C. Trypsin (Promega, USA) was added at a ratio of 1:100 w/w to protein amount and incubated at 37 °C overnight. Then the second trypsin portion 1:100 w/w was added, and the sample was incubated for 4 h at 37 °C. Proteolysis was stopped by adding trifluoroacetic acid to 1%. Precipitated CDNa was removed by ethyl acetate [8] . Samples were subsequently purified on OASIS columns (Waters).

DDA LC-MS/MS analysis
LC-MS/MS analysis was carried out as described previously [7] .

Data processing
Identification and label-free quantification analysis were performed with MaxQuant 1.6.10.43 software with default settings. The data was searched against M. gallisepticum S6 NCBI database partner repository with the dataset identifier PXD025107. ( https://www.ebi.ac.uk/pride/archive/ projects/PXD025107 ). Further calculations and visualizations were made in Python 3.7.10.

Ethics Statement
This article does not contain any studies involving animals or human participants performed by any of the authors.

Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal relationships that might affect the work described in this article.

Funding
The work was funded by Russian Science Foundation , project number 19-74-10105 "The role of chromatin structure in minimal cell in the maintenance of housekeeping proteome homeostasis".

Supplementary Materials
Supplementary material associated with this article can be found in the online version at doi: 10.1016/j.dib.2021.107289 .