Natural products serve important roles as drug candidates and as tools for chemical biology. However, traditional natural product discovery, largely based on bioassay-guided approaches, is biased towards abundant compounds and rediscovery rates are high. Orthogonal methods to facilitate discovery of new natural products are thus needed, and herein we describe an isotope tag-based expansion of reactivity-based natural product screening to address these shortcomings. Reactivity-based screening is a directed discovery approach in which a specific reactive handle on the natural product is targeted by a chemoselective probe to enable its detection by mass spectrometry. In this study, we have developed an aminooxy-containing probe to guide the discovery of aldehyde- and ketone-containing natural products. To facilitate the detection of labeling events, the probe was dibrominated, imparting a unique isotopic signature to distinguish labeled metabolites from spectral noise. As a proof of concept, the probe was then utilized to screen a collection of bacterial extracts, leading to the identification of a new analog of antipain, deimino-antipain. The bacterial producer of deimino-antipain was sequenced and the responsible biosynthetic gene cluster was identified by bioinformatic analysis and heterologous expression. These data reveal the previously undetermined genetic basis for a well-known family of aldehyde-containing, peptidic protease inhibitors, including antipain, chymostatin, leupeptin, elastatinal, and microbial alkaline protease inhibitor (MAPI), which have been widely used for over 40 years.

A total of 288 crossbred (Duroc×Landrace×Yorkshire) growing pigs were used in two experiments to investigate the effects of adding β-mannanase to corn-soybean meal-based diets on pig performance and apparent total tract digestibility (ATTD). Both experiments lasted 28 d and were split into two phases namely 1 to 14 days (phase 1) and 15 to 28 days (phase 2). In Exp. 1,144 pigs weighing 23.60±1.59 kg BW were assigned to one of four corn-soybean meal-based diets containing 0, 200, 400 or 600 U/kg β-mannanase. Increasing the level of β-mannanase increased weight gain (quadratic effect; p<0.01) and feed efficiency (linear and quadratic effect; p<0.01) during the second phase and the overall experiment. However, performance was unaffected (p>0.05) by treatment during phase 1. Increasing the amount of β-mannanase in the diet improved (linear and quadratic effect; p<0.05) the ATTD of CP, NDF, ADF, calcium, and phosphorus during both phases. Based on the results of Exp. 1, the optimal supplementation level was determined to be 400 U/kg and this was the level that was applied in Exp. 2. In Exp. 2, 144 pigs weighing 23.50±1.86 kg BW were fed diets containing 0 or 400 U/kg of β-mannanase and 3,250 or 3,400 kcal/kg digestible energy (DE) in a 2×2 factorial design. β-Mannanase supplementation increased (p<0.01) weight gain and feed efficiency while the higher energy content increased (p<0.01) feed intake and feed efficiency during both phases and overall. Increased energy content and β-mannanase supplementation both increased (p<0.05) the ATTD of DM, CP, NDF, ADF, phosphorus, and GE during both phases. There were no significant interactions between energy level and β-mannanase for any performance or digestibility parameter. In conclusion, the β-mannanase used in the present experiment improved the performance of growing pigs fed diets based on corn and soybean. The mechanism through which the improvements were obtained appears to be related to improvements in ATTD.

Graspetides are a class of ribosomally synthesized and post-translationally modified peptide natural products featuring ATP-grasp ligase-dependent formation of macrolactones/macrolactams. These modifications arise from serine, threonine, or lysine donor residues linked to aspartate or glutamate acceptor residues. Characterized graspetides include serine protease inhibitors such as the microviridins and plesiocin. Here, we report an update to Rapid ORF Description and Evaluation Online (RODEO) for the automated detection of graspetides, which identified 3,923 high-confidence graspetide biosynthetic gene clusters. Sequence and co-occurrence analyses doubled the number of graspetide groups from 12 to 24, defined based on core consensus sequence and putative secondary modification. Bioinformatic analyses of the ATP-grasp ligase superfamily suggest that extant graspetide synthetases diverged once from an ancestral ATP-grasp ligase and later evolved to introduce a variety of ring connectivities. Furthermore, we characterized thatisin and iso-thatisin, two graspetides related by conformational stereoisomerism from Lysobacter antibioticus. Derived from a newly identified graspetide group, thatisin and iso-thatisin feature two interlocking macrolactones with identical ring connectivity, as determined by a combination of tandem mass spectrometry (MS/MS), methanolytic, and mutational analyses. NMR spectroscopy of thatisin revealed a cis conformation for a key proline residue, while molecular dynamics simulations, solvent-accessible surface area calculations, and partial methanolytic analysis coupled with MS/MS support a trans conformation for iso-thatisin at the same position. Overall, this work provides a comprehensive overview of the graspetide landscape, and the improved RODEO algorithm will accelerate future graspetide discoveries by enabling open-access analysis of existing and emerging genomes.

Linaridins are members of the ribosomally synthesized and post-translationally modified peptide (RiPP) family of natural products. Five linaridins have been reported, which are defined by the presence of dehydrobutyrine, a dehydrated threonine residue. This work describes the development of a linaridinspecific scoring module for Rapid ORF Description and Evaluation Online (RODEO), a genome-mining tool tailored towards RiPP discovery. Upon mining publicly accessible genomes available in the NCBI database, RODEO identified 561 (382 non-redundant) linaridin biosynthetic gene clusters (BGCs). Linaridin BGCs with unique gene architectures and precursor sequences markedly different from previous predictions were uncovered during these efforts. To aid in dataset validation, two new linaridins, pegvadin A and B, were detected through reactivity-based screening (RBS) and isolated from Streptomyces noursei and Streptomyces auratus, respectively. RBS involves the use of a reactive chemical probe that chemoselectively modifies a functional group present in the natural product. The dehydrated amino acids present in linaridins as a/b-unsaturated carbonyls were appropriate electrophiles for nucleophilic 1,4addition using a thiol-functionalized probe. The data presented within significantly expands the number of predicted linaridin BGCs and serves as a road map for future work in the area. The combination of bioinformatics and RBS is a powerful approach to accelerate natural product discovery.