BLASTn and BLASTp [80, 82] were used initially to search the open

BLASTn and BLASTp [80, 82] were used initially to search the open reading frames and protein databases with known PLC, PLA1, and PLA2 genes and protein sequences. Using this approach we were not able to identify any significant hits. To make sure that the gene was not missed by the gene predicting software, we used tBLASTn [82] to search the ureaplasma full genomes translated nucleotide database.

PLC assay Amplex® Red Phosphatidylcholine-Specific Phospholipase C Assay Kit (Invitrogen Cat.No.A12218) was used to detect activity of the enzyme in whole cell lysates, membrane, cytosolic, and media fractions of exponential and stationary phase cultures. The Amplex® Red Assay provides lecithin as substrate for PLC that when cleaved forms phosphocholine. Phosphocholine is modified

to choline by alkaline phosphatase, which in the presence of choline oxidase produces betaine and H2O2. The Amplex red reagent in randurls[1|1|,|CHEM1|]# turn reacts in the presence of H2O2 and horseradish peroxidase to produce the red fluorescent compound resorufin. However, if the test sample contains PLD, PLD will cleave lecithin to produce choline, Poziotinib in vivo which bypasses the alkaline phosphatase step of the assay’s cascade; therefore, this assay would give a combined readout of PLC and PLD. Due to the potential presence of a PLD gene in ureaplasmas, to make the assay PLC specific we modified the assay by repeating it for each test sample, but omitting alkaline phosphatase from the reaction, in order to be able to subtract

any activity by the putative PLD enzyme in the ureaplasma genomes. Everything else followed the manufacturer’s assay protocol. ATCC UPA3 and UUR8 cultures were grown in 10B or Trypticase Soy Broth to exponential phase. Cells were harvested through centrifugation and subjected to osmotic lysis. Cell membranes were collected through ultracentrifugation. The cleared cell lysates and the cell membranes were tested for PLC activity with the Amplex Red assay and with the previously published assay by DeSilva and Quinn [20, 21, 23]. Phylogenetic trees Multiple sequence alignments (MSA) and phylogenetic tree constructions were performed using ClustalX 2.1 [85]. Phylogenetic trees were visualized with Dendroscope [86]. Multi-gene phylogenetic trees were generated by aligning the nucleotide sequences of 82 genes: the 7 genes encoding the urease subunits (ureA-G), 47 genes encoding ribosomal proteins, 12 genes encoding RNA and DNA polymerase subunits, and 16 genes encoding tRNA ligases. The MSAs of all genes were concatenated and edited with Jalview 2.6.1 [87] to remove the non-informative positions (100% conserved in all 19 genomes) from the alignment. This was needed because the extreme similarity among the strains generated multiple sequence alignments containing approximately 5% informative positions.

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