Roles of Ala-149 in the catalytic activity of diadenosine tetraphosphate phosphorylase from <i>Mycobacterium tuberculosis</i> H37Rv

<div><p>Diadenosine 5′,5′′′-<i>P</i>¹,<i>P</i>⁴-tetraphosphate (Ap₄A) phosphorylase from <i>Mycobacterium tuberculosis</i> H37Rv (MtAPA) belongs to the histidine triad motif (HIT) superfamily, but is the only member with an alanine residue at position 149 (Ala-149). Enzymatic analysis revealed that the Ala-149 deletion mutant displayed substrate specificity for diadenosine 5′,5′′′-<i>P</i>¹,<i>P</i>⁵-pentaphosphate and was inactive on Ap₄A and other substrates that are utilized by the wild-type enzyme.</p></div

Comparative Metabolomics Reveals a Bifunctional Antibacterial Conjugate from Combined-Culture of Streptomyces hygroscopicus HOK021 and Tsukamurella pulmonis TP-B0596

To investigate the potential for secondary metabolite biosynthesis by Streptomyces species, we employed a coculture method to discover natural bioactive products and identified specific antibacterial activity from a combined-culture of Streptomyces hygroscopicus HOK021 and Tsukamurella pulmonis TP-B0596. Molecular networking using ultrahigh performance liquid chromatography-quadrupole time-of-flight tandem mass spectrometry (UPLC-QTOF-MS/MS) data revealed a specific clade of metabolites in this combined-culture that were not detected in both monocultures. Using the chemical profiles, a previously unidentified conjugate between FabF inhibitor and catechol-type siderophore was successfully identified and named harundomycin A. Harundomycin A was a conjugate between the 2,4-dihydroxy-3-aminobenzoate moiety of platensimycin and N,N′-bis(2,3-dihydroxybenzoyl)-O-seryl-cysteine (bisDHBA-Ser-Cys) with a thioester linkage. Along with the production of harundomycin A, platensimycin, its thiocarboxylic acid form thioplatensimycin, enterobactin, and its degradation product N,N′-bis(2,3-dihydroxybenzoyl)-O-l-seryl-dehydroalanine (bisDHBA-Ser-Dha) were also induced in the combined-culture. Genomic data of S. hygroscopicus HOK021 and T. pulmonis TP-B0596 indicated that strain HOK021 possessed biosynthetic gene clusters for both platensimycin and enterobactin, and thereby revealed that T. pulmonis stimulates HOK021 and acts as an inducer of both of these metabolites. Although the harundomycin A was modified by bulky bisDHBA-Ser-Cys, responsible for the binding to the target molecule FabF, it showed a similar antibacterial spectrum to platensimycin, including against methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci, suggesting that the pharmacophore is platensimycin. Additionally, Chrome Azurol S assay showed that harundomycin A possesses ferric iron-chelating activity comparable to that of enterobactin. Our study demonstrated the transformation of existing natural products to bifunctional molecules driven by bacterial interaction

Population dynamics of Prn⁻ strains in in vitro growth competition assay.

<p>Prn⁺ back-mutants and parental Prn⁻ strains were mixed in the ratio 4∶1 (Prn⁺-BP59Sm^r versus BP59Sm^r or Prn⁺-BP202Sm^r versus BP202Sm^r) and cocultured in mSS broth at 36°C. The bacterial cultures were collected at 0, 36, 72 and 144 h, and plated on CSM agar plates. The representation of Prn⁻ strains among 40 colonies was examined by colony-PCR. Data are means and standard deviations from 3 independent experiments.</p

Molecular mechanisms of loss of Prn expression.

<p>(A) Deletion of the Prn signal sequence (<i>prn1</i>ΔSS). Prn⁻ isolates (<i>n</i> = 24) have an 84-bp deletion, resulting in a 28-amino acid deletion (Val⁹ to Trp³⁶) in the N-terminal region. (B) IS<i>481</i> insertion mutation in Prn1 gene (<i>prn1</i>::IS<i>481</i>). Eight Prn⁻ isolates have an IS<i>481</i> insertion in the forward direction at the 6-bp direct repeats (ACTAGG, 1593–1598 bp) of <i>prn1</i>, and 1 isolate had the insertion in the reverse.</p

Geographical distribution of Prn⁻ isolates in Japan during 2001–2009.

<p>Blue and red circles indicate Prn⁻ isolates harboring <i>prn1</i>ΔSS and <i>prn1</i>::IS<i>481</i>, respectively. Numbers of isolates tested are indicated in parentheses.</p

Minimum spanning tree of MLVA of Prn⁻ and Prn⁺ isolates.

<p>Total 121 <i>B. pertussis</i> isolates, collected during 1990–2009 in Japan, were subjected to MLVA: Prn⁻ isolate harboring <i>prn1</i>ΔSS, 24 isolates; Prn⁻ isolate harboring <i>prn1</i>::IS<i>481</i>, 9 isolates; Prn⁺ isolate, 88 isolates. Each circle in the tree represents a different MLVA type with the MLVA type number. The distance between neighboring genotypes is expressed as the similarity value. Prn⁻ isolates belong to MLVA-186, -194, and -226.</p

Schematic representation of multiple drug-resistance determinants.

<p>Pairwise comparison of plasmid regions around the <i>bla</i>_NDM-1 gene in pNDM-1_Dok01, pNDM-HK, and pKpANDM-1 in <i>K. pneumoniae</i> KP-05-506 and <i>E. coli</i> strain 271 by a BLASTN homology search and visualized with the ACT program. The <i>bla</i>_NDM-1 genes are identical among the aligned sequences. The red and blue bars between the DNA represent individual nucleotide matches in the forward and inverted directions, respectively. BLASTN match scores of <300 are not shown.</p

ORFs in NDM-1 composite transposon.

<p>ORFs in NDM-1 composite transposon.</p

Circular representation of the <i>E. coli</i> NDM-1_Dok01 plasmid pNDM-1_Dok01.

<p>From the outside inwards, the outer circle indicates the homologous regions to the <i>E. coli</i> strain AR060302 plasmid pAR060302 (red) and <i>E. coli</i> strain HK-01 plasmid pNDM-HK (orange). The second circle shows the size in base pairs (bp). The third and fourth circles show the positions of the CDSs transcribed in the clockwise and anti-clockwise directions, respectively (using color codes according to the clusters of orthologous groups (COG) classification table and additional customized categories). The fifth circle shows a plot of the G + C content (in 0.5 kb windows).</p

Phylogenetic tree of the whole amino acid sequences of chaperonin GroEL homologs.

<p>The amino acid sequences were selected and retrieved with a BLASTP search against the refseq_protein database with a cut-off value of 75% identity. The tree was constructed using the maximum likelihood method with 1,000 bootstrap replicates. The scale indicates that a branch length of 0.03 is 3 times as long as one that would show a 1% difference between the amino acid sequences at the beginning and end of the branch. The number at each branch node represents the bootstrapping value. The chromosomal GroEL in <i>E. coli</i> NDM-1_Dok01 is highlighted in blue. The GC percentage of the respective nucleotide sequences is shown on the right-hand side of the figure.</p