Mining of the Pyrrolamide Antibiotics Analogs in <i>Streptomyces netropsis</i> Reveals the Amidohydrolase-Dependent “Iterative Strategy” Underlying the Pyrrole Polymerization

<div><p>In biosynthesis of natural products, potential intermediates or analogs of a particular compound in the crude extracts are commonly overlooked in routine assays due to their low concentration, limited structural information, or because of their insignificant bio-activities. This may lead into an incomplete and even an incorrect biosynthetic pathway for the target molecule. Here we applied multiple compound mining approaches, including genome scanning and precursor ion scan-directed mass spectrometry, to identify potential pyrrolamide compounds in the fermentation culture of <i>Streptomyces netropsis</i>. Several novel congocidine and distamycin analogs were thus detected and characterized. A more reasonable route for the biosynthesis of pyrrolamides was proposed based on the structures of these newly discovered compounds, as well as the functional characterization of several key biosynthetic genes of pyrrolamides. Collectively, our results implied an unusual “iterative strategy” underlying the pyrrole polymerization in the biosynthesis of pyrrolamide antibiotics.</p></div

NiO Matrix Decorated by Ru Single Atoms: Electron-Rich Ru-Induced High Activity and Selectivity toward Electrochemical N₂ Reduction

Developing a single-atom catalyst with electron-rich active sites is a promising strategy for catalyzing the electrochemical N2 reduction reaction (NRR). Herein, we choose NiO(001) as a model template and deposit a series of single transition metal (TM) atoms with higher formal charges to create the electron-rich active centers. Our first-principles calculations show that low-valent Ru (+2) on NiO(001) can significantly activate N2, with its oxidation states varying from +2 to +4 throughout the catalytic cycle. The Ru/NiO(001) catalyst exhibits the best activity with a relatively low limiting potential of −0.49 V. Furthermore, under NRR operating conditions, the Ru site is primarily occupied by *N2 rather than *H, indicating that NRR overwhelms the hydrogen evolution reaction and thus exhibits excellent selectivity. Our work highlights the potential of designing catalysts with electron-rich active sites for NRR

Illustration of the “iterative strategy” underlying pyrrolamide biosynthesis.

<p>The putative amidohydrolase Pya25 catalyzed the deacetylation of PCP-tethered pyrrolamide biosynthesis intermediates and determined the number of the pyrrole groups assembled into various pyrrolamides. A, adenylation domain; C, condensation domain; PCP, peptidyl carrier protein.</p

Identification of the novel pyrrolamide compounds 4 (A), 5 (B), 6 (C), and 7 (D).

<p>High resolution mass spectrum and MS/MS patterns of each compound are shown.</p

Organization of the pyrrolamides biosynthesis-related genes identified from <i>S. ambofaciens</i> (a congocidine producer) and <i>S. netropsis</i>.

<p>The deduced functions of each gene are summarized in Table S1 in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099077#pone.0099077.s001" target="_blank">File S1</a>. Homologies in sequence are indicated by plain and dashed lines (the latter pattern is for the separate gene cluster).</p

In-frame deletion of <i>pya25</i> and <i>pya26</i> in <i>S. netropsis</i>.

<p>HPLC analysis of pyrrolamides production in <i>S. netropsis</i> wild-type strain, the mutant strains WDY002 (Δ<i>pya25</i>) and WDY003 (Δ<i>pya26</i>), and the complementation strains WDY004 (negative control) and WDY005. Congocidine, Compound <b>3</b>, and Distamycin are indicated. The characteristic absorbance wave-length for pyrrolamides is 297 nm.</p

Identification of Congocidine (1), Distamycin (2), and a novel pyrrolamide compound (3) in <i>S. netropsis</i>.

<p>(A) High resolution mass spectrum of Congocidine and Distamycin. (B) Precursor ion scan-directed mass spectrum to identify compound <b>3</b>. Base peak chromatograms of precursor ion scan are shown. Ions of <i>m</i>/<i>z</i> 273 and 247 are daughter ions of compound <b>3</b>, and were used as the queries.</p

Soil pH value (a) and electrical conductivity (EC us.cm^-1) (b) (mean±SE) in the 0-5cm and 5-20cm soil layers of <i>H</i>. <i>ammodendron</i> plantations planted in different decades across 50 years (CK-mobile sand dune).

<p>(Different uppercase letters indicate significant differences in soil properties between two soil depths in the same plantation age at <i>p</i><0.05. Different lowercase letters indicate significant differences in soil properties among different plantation ages with the same soil depth at <i>p</i><0.05).</p

Changes in soil crust characteristics on mobile sand dunes (CK) and of <i>H</i>. <i>ammodendron</i> plantations established in each decade over 50 years.

<p>Changes in soil crust characteristics on mobile sand dunes (CK) and of <i>H</i>. <i>ammodendron</i> plantations established in each decade over 50 years.</p

Herbaceous species diversity indices, coverage and species number (mean±SE) of life-form in <i>H</i>. <i>ammodendron</i> plantations established each decade over 50 years.

<p>Herbaceous species diversity indices, coverage and species number (mean±SE) of life-form in <i>H</i>. <i>ammodendron</i> plantations established each decade over 50 years.</p