k pneumoniae  (ATCC)

Journal: Nucleic Acids Research

Article Title: PhoP-regulated VirK acts as an accessory factor to maintain virulence in polymyxin-resistant Klebsiella pneumoniae

doi: 10.1093/nar/gkag290

Figure Lengend Snippet: Sequence and structure comparison of VirK (from K. pneumoniae ATCC BAA2146) and YbjX (from E. coli K-12 ) proteins. ( A ) Alignment of the amino acid sequence of VirK ( Q ) with that of YbjX ( T ); ( B ) Comparison of the protein structures of VirK and YbjX. Amino acid sequences and structures were compared using the foldseek server . The protein structure of YbjX was obtained from the AFDB database (AFDB accession: AF- P75829 -F1).

Article Snippet: The effects of virK on bacterial pathogenicity were further evaluated in a mouse systemic infection model using virK mutants and complemented strains under K. pneumoniae ATCC BAA2146 (wild type) or Mut-S ( mgrB truncated strain) backgrounds.

Techniques: Sequencing, Comparison

Journal: Nucleic Acids Research

Article Title: PhoP-regulated VirK acts as an accessory factor to maintain virulence in polymyxin-resistant Klebsiella pneumoniae

doi: 10.1093/nar/gkag290

Figure Lengend Snippet: Sequence and structure comparison of VirK (from K. pneumoniae ATCC BAA2146) and YbjX (from E. coli K-12 ) proteins. ( A ) Alignment of the amino acid sequence of VirK ( Q ) with that of YbjX ( T ); ( B ) Comparison of the protein structures of VirK and YbjX. Amino acid sequences and structures were compared using the foldseek server . The protein structure of YbjX was obtained from the AFDB database (AFDB accession: AF- P75829 -F1).

Article Snippet: Results from K. pneumoniae ATCC BAA2146 serial strains suggested that virK deficiency resulted in a modest reduction in bacterial virulence, while complementation partially restored this phenotype.

Techniques: Sequencing, Comparison

Journal: Nucleic Acids Research

Article Title: PhoP-regulated VirK acts as an accessory factor to maintain virulence in polymyxin-resistant Klebsiella pneumoniae

doi: 10.1093/nar/gkag290

Figure Lengend Snippet: PhoP directly regulates the expression of virK in K. pneumoniae . ( A ) The ability of PhoP to bind to the virK promoter was determined by EMSA. His-tagged PhoP was incubated with virK and 16S rDNA (negative control) in a concentration gradient. The experiments were repeated three times. An upward arrow marks bound DNA fragments, a middle arrow indicates free DNA fragments, and the bottom arrow represents the 16S rDNA fragment.( B ) Mapping of PhoP binding sites in K. pneumoniae ATCC BAA 2146 by ChIP-seq. IGV genome browser view showing PhoP binding regions around the virK gene across the K. pneumoniae genome. IP: Experimental group, namely the IP samples; IN: Control group, namely the IN sample; numbers represent three independent replicate trials. ( C ) ChIP and real-time PCR assays were used to investigate the binding of PhoP to the putative binding site in the promoter region of the virK gene. The experiments were independently repeated three times. The PhoQ gene was used as a positive control. The ChIP DNA was enriched using an IgG antibody and a Flag antibody and quantified by qPCR. ( D ) DNase I footprinting analysis of PhoP binding to the virK promoter. The intergenic fragment was labeled with 6-carboxyfluorescein (FAM) dye and incubated with 10 μg of PhoP (upper curve) or without PhoP (lower curve). The region protected by PhoP from DNase I cleavage is indicated with a black dotted box (ACACCTCAATCAATTTTAA).

Article Snippet: During preliminary investigations of a polymyxin-resistant mutant (Mut-S) of K. pneumoniae ATCC BAA-2146 (Kpn2146) [ ], we detected highly upregulated expression of the Kpn2146:RS17285 gene.

Techniques: Expressing, Incubation, Negative Control, Concentration Assay, Binding Assay, ChIP-sequencing, Control, Real-time Polymerase Chain Reaction, Positive Control, Footprinting, Labeling