The higher the number, the better the match. Individual ions with scores greater than the threshold Caspase inhibitor level (in brackets) indicates identity or extensive homology (p < 0.05). The band that had the highest probability of a match was Band 13. Its Mowse score for 30 S ribosomal protein S5 was 246 with a threshold level of 38. Since 5 fragments from this band matched to this protein the identification is highly probable. Other bands with high match identities were Band 5 (aerobic glycerol-3-phosphate dehydrogenase), Band 8 (30 S ribosomal protein S2), Band 15 (50 S ribosomal protein L17) and Band 16 (30 S ribosomal protein
S10) (Table 1). YsxC, the protein originally tagged, was also identified as a high match band (Band 9, 227(36)). All these proteins matched at least 2 fragments from the band. For 2 parent ions with a score of 95% or better, one can assume that the proteins has been identified. Other interacting bands identified with a score indicative of extensive homology (i.e., 36, See Methods) were bands 2 and 7, and XAV-939 ic50 corresponded to the DNA-directed RNA https://www.selleckchem.com/PD-1-PD-L1.html polymerase beta’
chain protein and putative elongation factor Tu. However, although the former matched 2 fragments, the latter, like SecA and PflB, were one hit matches, which would require further validation
to be considered as legitimate YsxC partners. Similarly, Bands 3 and 4 corresponded to casein, a protein not present in S. aureus but a common preparation contaminant. TAP tagging has not previously been reported in S. aureus therefore it was important to eliminate the possibility that any of the proteins identified, corresponded to purification artefacts. An independent purification of an unrelated TAP-tagged protein of S. aureus most likely 5FU participating in phospholipid metabolism and also purifying with the membrane fraction was carried out (YneS/PlsY; García-Lara and Foster, unpublished). It revealed interactions with proteins also encountered in our search for YsxC partners: 30 S ribosomal protein S5, elongation factor Tu and aerobic glycerol-3-phosphate dehydrogenase (data not shown). Although these data do not exclude the corresponding proteins as legitimate interacting partners of YsxC and YneS/PlsY, the involvement of these two proteins in different aspects of bacterial physiology suggests the common partners as likely artefacts of the purification procedure. Overall, the protein partners resulting from our experiments suggest YsxC as a ribosome-interacting protein.