Functional analysis of genome sequences requires methods for cloning DNA of interest. However, existing methods, such as library cloning and screening, are too demanding or inefficient for high-throughput application to the wealth of genomic data being delivered by massively parallel sequencing. Here we describe direct DNA cloning based on the discovery that the full-length Rac prophage protein RecE and its partner RecT mediate highly efficient linear-linear homologous recombination mechanistically distinct from conventional recombineering mediated by Redαβ from lambda phage or truncated versions of RecET. We directly cloned all ten megasynthetase gene clusters (each 10–52 kb in length) from Photorhabdus luminescens into expression vectors and expressed two of them in a heterologous host to identify the metabolites luminmycin A and luminmide A/B. We also directly cloned cDNAs and exactly defined segments from bacterial artificial chromosomes. Direct cloning with full-length RecE expands the DNA engineering toolbox and will facilitate bioprospecting for natural products.

Four new cyclic depsipeptides termed mirabamides A-D (1-4) have been isolated from the marine sponge Siliquariaspongia mirabilis and shown to potently inhibit HIV-1 fusion. Their structures were elucidated by NMR and ESIMS, and absolute stereochemistry of the amino acids was determined using advanced Marfey's methods and NMR. Mirabamides contain two new entities, including 4-chlorohomoproline in 1-3 and an unusual glycosylated amino acid, beta-methoxytyrosine 4'-O-alpha-L-rhamnopyranoside (in 1, 2, and 4), along with a rare N-terminal aliphatic hydroxy acid. These elements proved to be useful for anti-HIV structure-activity relationship studies. Mirabamide A inhibited HIV-1 in neutralization and fusion assays with IC50 values between 40 and 140 nM, as did mirabamides C and D (IC50 values between 140 nM and 1.3 microM for 3 and 190 nM and 3.9 microM for 4), indicating that these peptides can act at the early stages of HIV-1 entry. The potent activity of depsipeptides containing the glycosylated beta-OMe Tyr unit demonstrates that beta-OMe Tyr itself is not critical for activity. Mirabamides A-C inhibited the growth of B. subtilis and C. albicans at 1-5 microg/disk in disk diffusion assays.

Lepidium meyenii, known in South America as maca, has received attention worldwide as a powerful energizer that improves physical and mental conditions and increases fertility. Because of these reports, we investigated the secondary metabolites of the tuber of maca. The methanol extract of the tuber of maca contained, in addition to free sugars and amino acids, the following: uridine, malic acid and its benzoyl derivative, and the glucosinolates, glucotropaeolin and m-methoxyglucotropaeolin. Because glucosinolates and their derived products have received increasing attention due to their biological activities, the occurrence of glucosinolate degradation products in the hexane extract was also investigated, and benzylisothiocyanate and its m-methoxy derivative were isolated. The two glucosinolates were semiquantified by HPLC, and benzylisothiocyanate was semiquantified by GC/MS. The methanol extract of maca tuber also contained (1R,3S)-1-methyltetrahydro-beta-carboline-3-carboxylic acid, a molecule which is reported to exert many activities on the central nervous system.

Releasing the cytopath: We have identified an N-myristoyl-D-asparagine (1) as the free N-terminal prodrug scaffold in cytopathogenic Escherichia coli strains expressing the colibactin gene cluster. Colibactin is released in vivo upon cleavage of precolibactin. We provide for the first time in vivo evidence of the prodrug-like release mechanism of colibactin.

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Biosynthetic pathway intermediates related to genotoxin colibactin formation: a linear compound 3 bearing a rare 7-methyl-4-azaspiro[2.4]hept-6-en-5-one residue.

Eight new antimicrobial natural products named chrysophaentins A-H belonging to a new structural class have been isolated from the chrysophyte alga Chrysophaeum taylori. Their structures were determined by extensive 2D NMR and MS techniques and are characterized by the presence of two polyhalogenated, polyoxygenated ω,ω'-diarylbutene units connected by two ether bonds to form the suite of macrocyclic natural products. Chrysophaentin A, the most potent of these antibiotics, inhibited the growth of clinically relevant Gram-positive bacteria including methicillin-resistant Staphylococcus aureus (MIC 50 1.5 ± 0.7 μg/mL), multiple drug resistant S. aureus (1.3 ± 0.4 μg/mL), and vancomycin-resistant Enterococcus faecium (MIC 50 2.9 ± 0.8 μg/ mL). In vitro enzyme assays and transmission electron microscopy showed chrysophaentin A to inhibit the GTPase activity of the bacterial cytoskeletal protein FtsZ with an IC 50 value of 6.7 ± 1.7 μg/mL, as well as GTP-induced formation of FtsZ protofilaments. Saturation Transfer Difference (STD) NMR experiments further confirmed chrysophaentin A binds to FtsZ, and NMR competition experiments with GTPγS showed chrysophaentin A and GTP to bind competitively to FtsZ. Last, molecular docking showed chrysophaentin A to bind in and occlude a large portion of the GTP binding site of FtsZ in a manner that is consistent with the binding epitope determined by STD NMR.

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