Phylogenomic analysis of the diversity of graspetides and proteins involved in their biosynthesis.

BACKGROUND: Bacteria and archaea produce an enormous diversity of modified peptides that are involved in various forms of inter-microbial conflicts or communication. A vast class of such peptides are Ribosomally synthesized, Postranslationally modified Peptides (RiPPs), and a major group of RiPPs are graspetides, so named after ATP-grasp ligases that catalyze the formation of lactam and lactone linkages in these peptides. The diversity of graspetides, the multiple proteins encoded in the respective Biosynthetic Gene Clusters (BGCs) and their evolution have not been studied in full detail. In this work, we attempt a comprehensive analysis of the graspetide-encoding BGCs and report a variety of novel graspetide groups as well as ancillary proteins implicated in graspetide biosynthesis and expression. RESULTS: We compiled a comprehensive, manually curated set of graspetides that includes 174 families including 115 new families with distinct patterns of amino acids implicated in macrocyclization and further modification, roughly tripling the known graspetide diversity. We derived signature motifs for the leader regions of graspetide precursors that could be used to facilitate graspetide prediction. Graspetide biosynthetic gene clusters and specific precursors were identified in bacterial divisions not previously known to encode RiPPs, in particular, the parasitic and symbiotic bacteria of the Candidate phyla radiation. We identified Bacteroides-specific biosynthetic gene clusters (BGC) that include remarkable diversity of graspetides encoded in the same loci which predicted to be modified by the same ATP-grasp ligase. We studied in details evolution of recently characterized chryseoviridin BGCs and showed that duplication and horizonal gene exchange both contribute to the diversification of the graspetides during evolution. CONCLUSIONS: We demonstrate previously unsuspected diversity of graspetide sequences, even those associated with closely related ATP-grasp enzymes. Several previously unnoticed families of proteins associated with graspetide biosynthetic gene clusters are identified. The results of this work substantially expand the known diversity of RiPPs and can be harnessed to further advance approaches for their identification.

New gastroprotective ferruginol derivatives with selective cytotoxicity against gastric cancer cells.

The diterpene ferruginol has shown a strong protective effect in animal gastric ulcer models. In the present work, we report the gastroprotective effect and cytotoxicity of 16 new semisynthetic ester derivatives of ferruginol. The gastroprotective effect of these compounds was assessed with the HCl/EtOH-induced gastric lesions model in mice and the cytotoxicity was measured using MRC-5 fibroblasts, gastric adenocarcinoma (AGS) and liver hepatoma Hep G2 cells. The compounds were tested for a gastroprotective effect at a single oral dose of 20 mg/kg. The best gastroprotective effect was elicited by ferruginyl nicotinate ( 13), reducing the lesion index by 71 %, while the derivatives ferruginyl chloroacetate ( 2), ferruginyl palmitate ( 6), ferruginyl oleate ( 7), ferruginyl 3,5-dinitrobenzoate ( 11), ferruginyl 3-methylbenzofuran-2-carbonyl ester ( 12), ferruginyl indoleacetate ( 14), ferruginyl indolebutyrate ( 15) and ferruginyl pthalate ( 16) reduced the lesions by 49 - 66 %. The most promising compounds were 11, 13 and 14, presenting a gastroprotective effect higher or similar to that of ferruginol but with a high selectivity towards the tumor AGS cells. Among the three products, the most selective towards AGS cells was 14, followed by 13, and 11 (IC (50) values of 12, 22 and 29 microM, respectively). The isobutyrate 4, inactive as a gastroprotective agent, showed selective cytotoxicity against AGS and Hep G2 cells (IC (50) values of 60 and 39.2 microM, respectively). The cytotoxicity of the above cited compounds towards fibroblasts was >1000 microM. Considering the aliphatic esters of ferruginol, the best gastroprotective activity was found in the C (16) and C (18) derivatives but tended to decrease with increasing aliphatic chain unsaturation. For short-chain esters, the gastroprotective effect could be observed when the chain contained a chlorine atom. For aromatic esters, the presence of nitro groups or a nitrogen atom in the aromatic ring enhanced the gastroprotective activity. The compounds with the best gastroprotective effect and the highest selectivity against tumor cells bear an amino group (indoleacetate and nicotinate) or nitro group (3,5-dinitrobenzoate).