Journal: bioRxiv

Article Title: Evolution of PqsE as a Pseudomonas aeruginosa -specific regulator of LuxR-type receptors: insights from Pseudomonas and Burkholderia

doi: 10.1101/2024.12.09.627592

Figure Lengend Snippet: Phylogenetic analysis and conservation of PqsE and the pqsABCDE operon. (a) Conservation of the pqsABCDE and the orthologous hhqABCDEFG operon. Maximum-likelihood tree of PqsE/HhqE protein sequences ( n = 7) (left). Filled and open circles represent bootstrap support values of 100% and >95%, respectively. Schematic of the pqsABCDE and hhqABCDEFG operons (right). Values represent percent identity of pqsABCDE from P. fluorescens strain NCTC 10783 compared to P. aeruginosa PA14 using BLASTP within the Pseudomonas Genome DB and B. thailandensis E264, B. pseudomallei K96243 compared to B. cepacia ATCC 25416. (b) Maximum-likelihood tree of orthologous PqsE protein sequences from P. aeruginosa and HhqE from B. cepacia ( n = 764 sequences). Triangles indicate collapsed clades with 100 % sequence identity. Black circles represent bootstrap support values of 100%. A full list of sequences can be found in Data S1. (c) Cartoon representation of PqsE (PDB ID: 7KGW) colored by conservation compared with 300 homologs, estimated using the ConSurf-DB . Purple residues are highly conserved and green residues are highly variable. (d) 2D projection highlighting the conserved 69 HXHXDH 74 motif that constitute the PqsE active site. Water molecules are depicted as black spheres, residue labels are colored dark purple based on PqsE numbering or salmon for HhqE numbering. All structure images were generated in ChimeraX – .

Article Snippet: Genes encoding hhqE and cepR were amplified from B. cepacia (ATCC 25416) genomic DNA using traditional PCR-based methods.

Techniques: Sequencing, Residue, Generated

Journal: bioRxiv

Article Title: Evolution of PqsE as a Pseudomonas aeruginosa -specific regulator of LuxR-type receptors: insights from Pseudomonas and Burkholderia

doi: 10.1101/2024.12.09.627592

Figure Lengend Snippet: Sequence and structural comparison of PqsE and HhqE orthologs. (a) Multiple-sequence alignment of full-length protein sequences of PqsE from P. aeruginosa PA14 and P. fluorescens NCTC 10783 or HhqE in B. cepacia ATCC 25416, B. pseudomallei K96243, and B. thailandensis E264. Active site residues H69, H71, D73, and H74 (numbering according to PA14 PqsE) are highlighted in red. Residues involved in PqsE dimerization are highlighted in blue; residues unique to PqsE that are required for the PqsE-RhlR interaction are highlighted in green. Secondary structure assignments are represented above the sequence, determined from the PA14 PqsE experimental structure (PDB: 7KGW 3 ). (b) Structural overlay of PA14 PqsE (PDB: 7KGW 3 ) with predicted structures of the Pseudomonas and Burkholderia orthologs. For clarity, structures are depicted as ribbons, with the color scheme corresponding to the alignment in (a). All structure images were generated in ChimeraX 4-6 .

Article Snippet: Genes encoding hhqE and cepR were amplified from B. cepacia (ATCC 25416) genomic DNA using traditional PCR-based methods.

Techniques: Sequencing, Comparison, Generated

Journal: bioRxiv

Article Title: Evolution of PqsE as a Pseudomonas aeruginosa -specific regulator of LuxR-type receptors: insights from Pseudomonas and Burkholderia

doi: 10.1101/2024.12.09.627592

Figure Lengend Snippet:

Article Snippet: Genes encoding hhqE and cepR were amplified from B. cepacia (ATCC 25416) genomic DNA using traditional PCR-based methods.

Techniques: Sequencing

Journal: bioRxiv

Article Title: Evolution of PqsE as a Pseudomonas aeruginosa -specific regulator of LuxR-type receptors: insights from Pseudomonas and Burkholderia

doi: 10.1101/2024.12.09.627592

Figure Lengend Snippet: HhqE from Burkholderia cepacia is a monomer. (a) Cartoon representation of the PqsE homodimerization interface. Close-up view of the C-terminal interaction interface between opposing monomers. Residues E187, R243, R246, and R247 of chain A (light pink) and residues on the opposing chain (purple) are highlighted in gray and colored by heteroatom. (b) Cartoon representation of two HhqE Bc monomers (salmon) overlayed on top of the PqsE homodimer (pink). Close-up view of the HhqE Bc residues on the C-terminal α-helix that correspond to the necessary residues for PqsE dimerization. Residues Q187, A244, A247, and D248 are highlighted in gray and colored by heteroatom. (c) Size exclusion chromatography (SEC) analysis of PqsE and HhqE proteins using a Superdex-200 column, with protein elution volumes measured by absorbance at 280 nM ( A 280 , y-axis) as a function of retention volume (mL, x-axis). Chromatogram traces are representative of six independent purifications for PqsE and HhqE Bc or three purifications for HhqE Bp . Traces are normalized to a maximum value of 1 for clarity. The mean retention volume and standard deviation (σ) are indicated above each peak. (d) Mass histograms of PqsE and HhqE Bc after manual or (e) automated dilution measured by mass photometry. Mass photometry mass distribution of 10 nM PqsE and HhqE Bc proteins diluted in PBS. 50 μM PqsE was measured with mass photometry after rapid dilution to 50 nM using the MassFluidix HC system (Refeyn). All structure images were generated in ChimeraX – .

Article Snippet: Genes encoding hhqE and cepR were amplified from B. cepacia (ATCC 25416) genomic DNA using traditional PCR-based methods.

Techniques: Size-exclusion Chromatography, Standard Deviation, Generated

Journal: bioRxiv

Article Title: Evolution of PqsE as a Pseudomonas aeruginosa -specific regulator of LuxR-type receptors: insights from Pseudomonas and Burkholderia

doi: 10.1101/2024.12.09.627592

Figure Lengend Snippet: Structural similarities of LuxR-type receptors. Structural overlay of AlphaFold-Multimer predicted structures of CepR from B. cepacia and PmlR from B. pseudomallei compared to the experimental structure of RhlR (PDB ID: 8DQ0 7 ). The percentage amino acid identity and root mean square deviation (rmsd) values of CepR and PmlR relative to PA14 RhlR are indicated. The inset highlights the universally conserved YXXXW motif within the ligand binding pocket (LBP) of LuxR-type receptors (numbering based on PA14 RhlR). The solvent-accessible volume of the RhlR LBP, shown in light blue is included to provide structural context. All structure images were generated in ChimeraX.

Article Snippet: Genes encoding hhqE and cepR were amplified from B. cepacia (ATCC 25416) genomic DNA using traditional PCR-based methods.

Techniques: Ligand Binding Assay, Solvent, Generated

Journal: bioRxiv

Article Title: Evolution of PqsE as a Pseudomonas aeruginosa -specific regulator of LuxR-type receptors: insights from Pseudomonas and Burkholderia

doi: 10.1101/2024.12.09.627592

Figure Lengend Snippet: HhqE does not complement pyocyanin production in a Δ pqsE strain of P. aeruginosa . (a) Pyocyanin production in Δ pqsE strains of P. aeruginosa expressing plasmid-borne pqsE or hhqE Bc was quantified by OD 695 /OD 600 and LC-MS. OD 695 /OD 600 values were normalized to levels observed in the strain expressing WT pqsE (center bar). (b) Growth of Δ pqsE strains carrying plasmids as in (a) on LB agar. Complementation of pyocyanin production was observed with WT pqsE but not with hhqE from B. cepacia .

Article Snippet: Genes encoding hhqE and cepR were amplified from B. cepacia (ATCC 25416) genomic DNA using traditional PCR-based methods.

Techniques: Expressing, Plasmid Preparation, Liquid Chromatography with Mass Spectroscopy

Journal: bioRxiv

Article Title: An investigation of carbapenemase-encoding genes in Burkholderia cepacia and Aeromonas sobria nosocomial infections among Iraqi patients

doi: 10.1101/2024.11.28.625853

Figure Lengend Snippet:

Article Snippet: After cultivating pure single colonies of B. cepacia and A. sobria isolates on brain heart infusion broth overnight under strictly sterile conditions, the entire DNA of 75 B. cepacia and 20 A. sobria isolates was extracted using specific DNA extraction kits (Sacace, Italy), in accordance with the directions and guidelines of the manufacture company [ , ].

Techniques:

Journal: bioRxiv

Article Title: An investigation of carbapenemase-encoding genes in Burkholderia cepacia and Aeromonas sobria nosocomial infections among Iraqi patients

doi: 10.1101/2024.11.28.625853

Figure Lengend Snippet:

Article Snippet: According to the criteria defined by the Clinical and Laboratory Standards Institute (CLSI) the antibiotic susceptibilities of B. cepacia and A. sobria isolates were tested using the VITEK-2 System (BioMérieux, Marcyl’Étoile, France) [ ].

Techniques:

Journal: Nanomaterials

Article Title: Green Synthesis of Silver Oxide Nanoparticles from Mauritia flexuosa Fruit Extract: Characterization and Bioactivity Assessment

doi: 10.3390/nano14231875

Figure Lengend Snippet: Minimal inhibitory concentration (MIC) for different bacterial strains.

Article Snippet: The Gram-negative bacteria P. aeruginosa ATCC 27853 and B. cepacia ATCC 25416 exhibited the lowest MIC values at 11.25 µg/mL, indicating higher sensitivity to the Mf-Ag 2 ONPs.

Techniques: Concentration Assay