Bacterial strains and their culture
Escherichia coli strains were cultured in LB broth at 37°C with ampicillin 100 μg/ml.
M. genitalium wild type strain (G37) was grown in 100 ml of SP-4 medium at 37°C for 72 h in 150 cm2 tissue culture flasks (Corning, NY). M. genitalium transposon mutant strains TIM207 and TIM262, (kindly provided by Dr. John Glass, J. Craig Venter Institute, Rockville, MD) were also grown similarly in SP-4 medium with 4 μg/ml tetracycline or 50 μg/ml gentamicin.
Adherent M. genitalium from culture flasks was washed three times with PBS (pH 7.2) and scraped with cell scrapers (39 cm handle/3 cm blade; Corning, NY). The suspension was centrifuged at 20,000xg for 20 min at 4°C in Sorvall RC 5B centrifuge. The pellets were resuspended in PBS and passed through 18G needles and then through 23G needles to disperse bacterial clumps. The suspensions, diluted to OD600=1.0 (which is equivalent to 1 X107 CFU/ml) with PBS, were used to infect cell lines with different multiplicity of infection (MOI).
Cell lines and their culture
Human cell lines THP-1 (TIB-202) and HeLa (CCL-2) were purchased from American Type Culture Collection (ATCC, Manassas, VA). THP-1 and HeLa cells were cultured in RPMI and Dulbecco’s modified Eagle’s medium (DMEM), respectively, with 10% FBS at 37°C in a humid chamber with 5% CO2.
Plasmids from E. coli were isolated using QIAprep Spin kit (Qiagen). Genomic DNA from mycoplasma was isolated using DNA isolation kit (Invitrogen). Primers for amplification of MG_207 gene and subsequent site directed mutagenesis were synthesized at the DNA core facility, The University of Texas Health Science Center at San Antonio (UTHSCSA). The whole gene encoding MG207 was amplified by PCR using primers MG_207EX1 (5´-ACGCATATGCAAAACAAACTGATTAAGGTT-3´) and MG_207EX2 (5´-CAGTCGGATCCGTTAACTAACTTTTGAAGCTTG-3´) and M. genitalium genomic DNA as template. This fragment was cloned into pCR 2.1 to result in pMG207. The gene MG_207 has a TGA codon for tryptophan residue, which will be recognized as stop codon by E. coli, and this needed modification into TGG to express the gene in E. coli. To do this modification (point mutation), we used QuikChange Site-Directed Mutagenesis Kit (Stratagene) and primers MG_207M1 (5´-CAAAATGCTACTTTTTGGGTGGCAGGTAACAAC-3´) and MG_207M2 (5´-GTTGTTACCTGCCACCCAAAAAGTAGCATTTTG-3´). Plasmid pMG207 served as the template for point mutation. Subsequent to point mutation, the newly synthesized plasmid DNA (pMG207A) was transformed into E. coli, plasmid isolated and the sequence of the insert region was verified to confirm the point mutation. The coding region of MG_207 from pMG207A was digested with NdeI and BamHI and the fragment cloned into similarly cut pET16b expression vector. This plasmid (pMG207EX) was transformed into E. coli BL21 (DE3) strain to overexpress His10MG207 protein.
To reconfirm the insertion of transposon Tn4001 in MG_207, we performed Southern hybridization. Briefly, chromosomal DNA from M. genitalium G37 and TIM207 was cut with SpeI and separated in 1% agarose gels. The separated DNA fragments were transferred to Zeta probe membranes (Bio-Rad) by Southern blotting and crosslinked with UV. Prehybridization of the membranes was performed in a solution containing 50% formamide, 0.12 M Na2HPO4, 0.25 M NaCl, and 7% (wt/vol) sodium dodecyl sulfate (SDS) for 4 h. Hybridization of the membranes was done in the same solution with [α-32P]dCTP labeled probe DNA of MG_207 or gentamicin gene for overnight at 42°C. The membranes were washed at 42°C (each wash for 15 min with solutions A (2X SSC with 0.1% SDS), B (0.5X SSC with 0.1% SDS) and C (0.1X SSC with 0.1% SDS) for three times. Afterwards, the membranes were exposed to X-ray films for autoradiography.
Overexpression of MG207 in E. coli
Overexpression and purification of recombinant MG207 protein using pET16b were performed as detailed before [55, 56]. Briefly, E. coli strain BL21 (DE3) harboring the pMG207EX was induced with 0.5 mM IPTG at 37°C to overexpress the protein. The overexpressed protein was purified with Ni-NTA affinity column chromatography (Qiagen). The E. coli extracts and purified protein were separated on 12% SDS-PAGE to assess the expression and purification. The purified recombinant protein was designated as His10MG207. All purification and desalting procedures were performed with buffers based on Tris–HCl pH8.0 and use of phosphate buffer was avoided.
To determine if the overexpressed and purified His10MG207 was functional, we performed phosphatase assay with p-nitrophenyl phosphate (pNPP) as substrate (Sigma-Aldrich, St. Louis, MO). The assay was conducted in 96 well plates and the assay mixture (120 μl) contained 1 mM pNPP in 20 mM Tris–HCl pH 8.0, 5 mM MgCl2 and His10MG207 protein. Control reactions had no protein or heat inactivated His10MG207. Each reaction was done in triplicate wells. The reaction mixtures were incubated at 37°C for 1 h and the yellow color, developed due to the hydrolysis of pNPP, was read at 405 nm using a Spectramax plate reader (Molecular Devices, Sunnyvale, CA).
To determine the specificity of His10MG207 towards serine or threonine residue, we used Alkaline/Acid Phosphatase assay kit (Millipore, Temecula, CA). This uses synthetic peptides for serine phosphate (RRApSSVA) and threonine phosphate (KRpTIRR) as substrates for the enzyme assay. The reactions were done as described by the manufacturer in 96 well plates, except that the reaction mixture had MgCl2 instead of NiCl2. Amount of phosphate released was calculated using phosphate reference standards supplied with the kit.
SDS-PAGE and immunoblot
Premade SDS-PAGE gels (NuPAGE 12% Bis-Tris gel, Invitrogen, Carlsbad, CA) were used to separate proteins from E. coli and M. genitalium for coomassie staining of proteins and for Western blot. In these gels 50 μg of total protein was loaded per well. Protein concentration was determined by BCA method (Pierce). Western blots were probed with anti-MG207 rabbit antiserum (1:500 dilutions) to detect MG207 protein of M. genitalium strains. This rabbit antiserum was generated against purified His10MG207 protein using a commercial source (Alpha Diagnostic International Inc., San Antonio).
Two-dimensional gel analysis of proteins
Two-dimensional (2-D) gel analyses of total proteins of M. genitalium G37 and TIM207 strains were performed by Kendrick Lab Inc., (Madison, WI). Fifty μg of total proteins were separated by isoelectric focusing [IEF] in glass tubes with an inner diameter of 2.0 mm. The IEF gel contained 2% pH 4–6 ampholines (Servalytes, Serva, Heidelberg, Germany) and 2% pH 5–8 ampholines (GE Healthcare). After IEF, gels were equilibrated for 10 min in buffer “0” (10% glycerol, 50 mm dithiothreitol, 2.3% SDS and 0.0625 M Tris, pH 6.8). Thereafter, each tube gel was sealed to the top of a stacking gel that was overlaid above 10% SDS-PAGE acrylamide gels (slab gels, 0.75 mm thick) and gels were run for about 4 h at 15 mA/gel. The gels were then fixed twice in 50% methanol 10% acetic acid solution and stained with Pro-Q Diamond for phosphoproteins. Images of the gels were acquired by scanning the gels with Bio-Rad Molecular Imager FX ProPlus scanner. After destaining, the gels were stained with Sypro Ruby (Molecular Probes) and again scanned with Bio-Rad Molecular Imager FX ProPlus scanner to obtain the images of total proteins. The following proteins (Sigma Chemical Co., St. Louis, MO) were used as molecular weight standards: myosin (22,000), phosphorylase A (94,000), catalase (60,000), actin (43,000), carbonic anhydrase (29,000) and lysozyme (14,000).
Mass spectrometry analyses were conducted in our core facility at UTHSCA. Pro-Q Diamond-stained gel spots were manually excised and digested in situ with trypsin (Promega, modified) in 40 mM NH4HCO3 overnight at 37°C. The digests were analyzed by capillary HPLC-electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS) using a Thermo Fisher LTQ linear ion trap mass spectrometer fitted with a New Objective PicoView 550 nanospray interface. On-line HPLC separation was accomplished with an Eksigent NanoLC micro HPLC: column, PicoFrit™ (New Objective; 75 μm i.d.) packed to 11 cm with Vydac 218MSB5 (5 μm, 300 Å) using a scan strategy in which a survey scan was acquired followed by data-dependent collision-induced dissociation (CID) of the seven most intense ions in the survey scan above a set threshold. The uninterpreted CID spectra were searched by means of Mascot (Matrix Science) against the Swiss-Prot database [2011_03 (525,997 sequences; 185,874,894 residues)] as follows: enzyme, trypsin, one missed cleavage allowed; precursor and fragment ion mass tolerances, ± 1.5 Da and ± 0.8 Da, respectively; variable modifications, methionine oxidation and phosphorylation of serine, threonine and tyrosine. Cross correlation of the Mascot results with X! Tandem and determination of probabilities for peptide assignments and protein identities were accomplished by Scaffold™ (Proteome Software).
Attachment of mycoplasmas to the HeLa cells: HeLa cells (2.5 × 105) were grown on square cover slides in 6 well tissue culture plates (Corning, NY). M. genitalium strains were labeled with Fluorescein isothiocyanate isomer I (FITC: Sigma-Aldrich, St. Louis, MO) as described before  and infected with an MOI of 1:25 for 1 h at 37°C. The cell monolayer was then washed three times with PBS and images captured using at 488 nm in an inverted laser microscope (Olympus FV1000) with 20 X objective (NA 0.75).
Cytotoxicity of M. genitalium strains was assessed by infecting HeLa cell line as reported earlier . Briefly, HeLa cells (2.5 × 105) were grown on coverslips in 6 well plates for 24 h and then infected with wild type G37 and mutant (TIM207 and TIM262) M. genitalium strains with MOI=50 for 2–3 h. Heat killed M. genitalium (HKG37) was used as control. Cytotoxic effect was determined by evaluating the integrity of the infected cells using differential interference contrast  at 488 nm in an inverted laser scanning confocal microscope (Olympus FV1000) with 20X objective.
Determination of H2O2 in M. genitalium strains
Production of H2O2 by mycoplasma strains was measured by colorimetric ferrous ion oxidation in xylenol orange [FOX] method [58, 59]. Protein samples from strains of M. genitalium were used as the source for H2O2. Protein content of samples was determined using Pierce BCA Protein Assay Kit (Pierce). Equal amount of protein samples (each 25 μl) and cold FOX reagent (250 μl) were mixed and incubated for 30 min at room temperature. After incubation, absorbance was measured at 560 nm. The amount of hydrogen peroxide in each sample was determined using a standard curve generated with known amounts of H2O2. The results were expressed as μmoles H2O2/per μg protein.
Differentiation of monocytic THP-1 cells by M. genitalium strains
THP-1 cells were labeled with carboxyfluorescein diacetate succinimidyl ester (CFSE) and cells (0.5X105) were plated on 4 chamber 1.5 German cover glass slides (Nunc, Rochester, NY). The cells were then infected with (MOI 1:5) M. genitalium (G37 or TIM207 or TIM262 or HKG37) for 1 h. After incubation, the chambers were washed with PBS to remove non-adherent cells. Cells adhering to the cover slips were examined under FV1000 laser scanning inverted confocal microscope (Olympus, Japan) with 20X objective. Images were acquired and labeled cells in each image was counted using the NIH analyze particle plug-in of Image J software.
The data were analyzed by paired t-test using graphpad prism software.