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53. Wilson K: Preparation of genomic DNA from bacteria. Curr Protoc Mol Biol 2001, 00:2.4.1–2.4.5. Competing interests The authors declare they have no competing interests. Authors’ contributions TLW designed the data analysis approach, interpreted results and wrote the manuscript. SH performed the data analysis for Figure  1, Tables  1, 2, 3 and Additional file 1: Table S1, Additional file 2: Table S2 and Additional file 6: Table S4. IA conceived and supervised the study and edited the paper. II supervised the bioinformatics analyses and edited the paper. All authors have read and approved the manuscript.”
“Background Salmonella enterica serovar Typhimurium is an enteroinvasive bacterial

pathogen typically encountered by ingesting contaminated food or water. S. Typhimurium causes self-limiting gastroenteritis in humans and typhoid-like fever in mice [1, 2]. Greater than 99% of the bacteria in murine salmonellosis are killed in the stomach or passed out of the gut [2], but S. Typhimurium that survive passage through the acidic stomach environment enter into the small intestine, where upon they transverse the intestinal epithelial barrier. The bacteria are then phagocytosed by macrophages Dactolisib mouse or they can actively invade both phagocytic and non-phagocytic cells using a type III secretion system [1]. Following invasion, Anidulafungin (LY303366) Salmonella disseminates throughout the body leading to a systemic typhoid-like infection [2]. Salmonella forms biofilms on abiotic selleck screening library surfaces such as plastic and egg conveyer belts, which may have a role in environmental survival of this organism [3, 4]. Biofilm formation and aggregation in S. enterica serovar Typhimurium is exemplified by the rdar colony morphology, where colonies grown on media containing Congo red are red, dry, and rough [5, 6]. This morphology requires the production of curli fimbriae and multiple exopolysaccharides [7,

8]. S. Typhimurium also grows enmeshed in EPS rich biofilms on the surface of gallstones, which may contribute to inefficient antibiotic treatment and facilitates typhoid carriage [9, 10]. Biofilm shedding from colonized gallstones is likely a source of recurring infections [11]. The PhoPQ two-component system is important for intracellular survival within macrophages. Limiting Mg2+, low pH and the presence of antimicrobial peptides are PhoPQ-activating signals in culture [12, 13] but low pH and antimicrobial peptides are important activating signals during intracellular macrophage growth [14]. The PmrAB two component system responds to Fe3+ and low pH, and is activated under Mg2+ limiting conditions by a post-translational mechanism involving PmrD, a PhoPQ-regulated protein.

A total of 771 BAY 1895344 solubility dmso proteins were matched to proteins found within the P. chlororaphis gp72 reference genome [19]. Fifty nine of these proteins

were differentially expressed between the two strains, exhibiting a vector difference (Vdiff) greater than or equal to +1.65 and less than or equal to −1.65, corresponding to proteins in the upper or lower 10% of the population distribution (Table 1). The 59 proteins could be classified into 16 clusters of orthologous groups (COGs) based on their predicted function. Figure 3 summarizes the classification of the identified proteins, indicating significant up- or downregulation of protein expression. The largest COG category was the unknown function group, suggesting that many yet-to-be-identified proteins play a role in the loss of biocontrol exhibited by PA23-443. Table 1 Differentially expressed proteins in mutant PA23-443 compared to the PA23 wild type PF-02341066 solubility dmso CX-4945 in vivo COG Category Locus Tag Predicted Function Fold Changea VdiffScore Amino acid transport and metabolism MOK_00491 4-aminobutyrate aminotransferase and related aminotransferases 1.59 2.24   MOK_03651 Monoamine oxidase −2.39 −2.7   MOK_04019 ornithine carbamoyltransferase −1.48 −1.67 Nucleotide transport and metabolism MOK_04929 hypothetical protein −3.13 −2.54 Carbohydrate transport and metabolism

MOK_03378 Chitinase −3.30 −3.76   MOK_05029 Glucose/sorbosone dehydrogenases −1.68 −2.04   MOK_05478 Chitinase −2.61 −1.66 Lipid transport and metabolism MOK_04573 Acyl dehydratase −2.16 −2.42 Translation, ribosomal structure and biogenesis MOK_00565 Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) 1.61 1.94   MOK_01324 ribosomal protein L32 2.33 2.77   MOK_02337 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C subunit 2.09 1.7   MOK_04471 ribosomal protein S19, bacterial/organelle 1.49 1.7 Transcription MOK_02056 cold shock domain protein

Progesterone CspD −2.31 −1.81   MOK_02888 Cold shock proteins 2.30 2.44   MOK_03359 Cold shock proteins 1.26 1.65 Replication, recombination and repair MOK_00606 competence protein ComEA helix-hairpin-helix repeat region −2.78 −3.04 Cell wall, membrane and envelope biogenesis MOK_05137 Outer membrane protein and related peptidoglycan-associated (lipo)proteins −1.65 −1.79 Cell motility MOK_01499 Flagellin and related hook-associated proteins 2.71 3.26 Post-translational modification, protein turnover and chaperones MOK_00750 monothiol glutaredoxin, Grx4 family 1.20 1.81   MOK_01830 peroxiredoxin, OsmC subfamily −2.61 −2.69   MOK_05742 Peroxiredoxin −1.84 −1.78   MOK_05953 Peptidyl-prolyl cis-trans isomerase (rotamase) – cyclophilin family 2.00 1.73 Inorganic ion transport and metabolism MOK_05447 Predicted periplasmic lipoprotein involved in iron transport 1.42 1.