PagL and KdsA however, were present at reduced abundance in
AES-1R, along with several OMPs (OprD, OprG, OpmD, OprB2, OprQ and TolQ). A number of proteins related to DNA replication, cell division and transcriptional regulation were observed to be differentially abundant between AES-1R and PAO1/PA14 (Additional file 3). The majority of these were present at increased abundance in AES-1R, including DNA-directed RNA polymerase alpha, beta and beta* (RpoABC; BTSA1 PA4238, PA4269 and PA4270), FtsH cell division see more protein (PA4751), Rho transcription termination factor (PA5239), histone-like protein HU (PA3940) and DNA gyrase subunit A (GyrA; PA3168). Inspection of the AES-1R GyrA protein sequence revealed an amino acid substitution of Thr83Ile (ACC- > ATC) (data VX-680 nmr not shown), which is a reported mutation
in a number of CF clinical isolates showing quinolone resistance . This mutation is also shared with the Liverpool epidemic strain LESB58 GyrA (PLES_19001). Interestingly, AES-1R showed increased abundance of the ferric uptake regulator (Fur; PA4764) in comparison to both PAO1 and PA14, although the degree of this increase was greater in comparison to PA14. Fur is the master regulator (repressor) of iron acquisition-related genes , and increased Fur levels are consistent with decreased abundances observed for several iron acquisition proteins (PchEFG, FptA, PA5217) when
compared between AES-1R and PA14. Conversely however, we observed increased abundances of several of these proteins in AES-1R compared to PAO1, despite elevated Fur. Seven proteins were less abundant in AES-1R than in PAO1 or PA14, including 2 transcriptional regulators (MvaT [PA4315] and PA2667), and the RecG DNA helicase. All differentially abundant proteins functionally clustered into the translation category were present at increased abundance in AES-1R. These were predominantly ribosomal proteins (13 proteins), although DCLK1 both elongation factors G and Ts were also present. Chaperonins GroEL, DnaK and HtpX were also present at elevated abundance in AES-1R. Forty-two proteins functionally classified as ‘metabolic proteins’ were present at altered abundance in AES-1R compared to PAO1 and PA14. Sub-clusters within this broad functional category were also readily identified. Ten proteins involved in fatty acid biosynthesis and metabolism were altered in abundance including 7 that were more abundant in AES-1R (FabB [PA1609], FabG [PA2967], acetyl-CoA carboxylase alpha [AccA; PA3639] and beta [AccD; PA3112], acyl carrier protein AcpP [PA2966], acyl-CoA thiolase [AspC; PA4785] and (R)-specific enoyl-CoA hydratase [PhaJ4; PA4015]). Twelve of the remaining proteins were functionally classified as playing a role in amino acid biosynthesis or degradation.