No abstract

The gut microbiota synthesize hundreds of molecules, many of which are known to impact host physiology. Among the most abundant metabolites are the secondary bile acids deoxycholic acid (DCA) and lithocholic acid (LCA), which accumulate at ~500 µM and are known to block C. difficile growth 1 , promote hepatocellular carcinoma 2 , and modulate host metabolism via the GPCR TGR5 3 . More broadly, DCA, LCA and their derivatives are a major component of the recirculating bile acid pool 4 ; the size and composition of this pool are a target of therapies for primary biliary cholangitis and nonalcoholic steatohepatitis. Despite the clear impact of DCA and LCA on host physiology, incomplete knowledge of their biosynthetic genes and a lack of genetic tools in their native producer limit our ability to modulate secondary bile acid levels in the host. Here, we complete the pathway to DCA/LCA by assigning and characterizing enzymes for each of the steps in its reductive arm, revealing a strategy in which the A-B rings of the steroid core are transiently converted into an electron acceptor for two reductive steps carried out by Fe-S flavoenzymes. Using anaerobic in vitro reconstitution, we establish that a set of six enzymes is necessary and sufficient for the 8-step conversion of cholic acid to DCA. We then engineer the pathway into Clostridium sporogenes, conferring production of DCA and LCA on a non-producing commensal and demonstrating that a microbiome-derived pathway can be expressed and controlled heterologously. These data establish a complete pathway to two central components of the bile acid pool, and provide a road map for deorphaning and engineering pathways from the microbiome as a critical step toward controlling the metabolic output of the gut microbiota.

Meroterpenoids are a class of fungal natural products that are produced from polyketide and terpenoid precursors. An understanding of meroterpenoid biosynthesis at the genetic level should facilitate engineering of second-generation molecules and increasing production of first-generation compounds. The filamentous fungus Aspergillus nidulans has previously been found to produce two meroterpenoids, austinol and dehydroaustinol. Using targeted deletions that we created, we have determined that, surprisingly, two separate gene clusters are required for meroterpenoid biosynthesis. One is a cluster of four genes including a polyketide synthase gene, ausA. The second is a cluster of ten additional genes including a prenyltransferase gene, ausN, located on a separate chromosome. Chemical analysis of mutant extracts enabled us to isolate 3,5-dimethylorsellinic acid and ten additional meroterpenoids that are either intermediates or shunt products from the biosynthetic pathway. Six of them were identified as novel meroterpenoids in this study. Our data, in aggregate, allow us to propose a complete biosynthetic pathway for the A. nidulans meroterpenoids.

The hallmark trait of fungal secondary-metabolite gene clusters is well established, consisting of contiguous enzymatic and often regulatory gene(s) devoted to the production of a metabolite of a specific chemical class. Unexpectedly, we have found a deviation from this motif in a subtelomeric region of Aspergillus fumigatus. This region, under the control of the master regulator of secondary metabolism, LaeA, contains, in its entirety, the genetic machinery for three natural products (fumitremorgin, fumagillin, and pseurotin), where genes for fumagillin and pseurotin are physically intertwined in a single supercluster. Deletions of 29 adjoining genes revealed that fumagillin and pseurotin are coregulated by the supercluster-embedded regulatory gene with biosynthetic genes belonging to one of the two metabolic pathways in a noncontiguous manner. Comparative genomics indicates the fumagillin/pseurotin supercluster is maintained in a rapidly evolving region of diverse fungal genomes. This blended design confounds predictions from established secondary-metabolite cluster search algorithms and provides an expanded view of natural product evolution.gene regulation | Zn(II) 2 Cys 6 transcription factor | FapR | biosynthesis | cluster evolution F ilamentous fungi are well known for their ability to produce a variety of natural products, so-called secondary metabolites that are not essential for growth under laboratory conditions (reviewed in refs. 1 and 2). However, the maintenance of the genetic information allowing fungi to produce secondary metabolites suggests that these small molecules provide essential benefits in environmental niches ranging from protection from fungivory (reviewed in ref.3) to chemical shields from UV radiation (4). Apart from providing evolutionary fitness to the producing organism in their natural habitat, many secondary metabolites are of major importance to humans because of their beneficial and deleterious effects as drugs and toxins, respectively.Fungal secondary metabolism has been characterized by physical linkage of the genes required for synthesis of specific metabolites and the distinct enzymatic machinery encoded by these genes (1, 2, 5). For instance, most fungal secondary metabolites belong to one of four chemical classes that are characterized based on the key or backbone enzymes that consist of polyketide synthases (PKSs), nonribosomal peptide synthetases (NRPSs), terpene cyclases (TCs), and prenyltransferases (PTs). Typically, cluster genes adjacent to these backbone genes code for accessory enzymes involved in either modification of the chemical scaffold, transcriptional control of cluster genes, transport of substrates and/or products, and resistance mechanisms. The most common regulatory genes of clusters encode fungal-specific C6 zinc binuclear cluster (Zn(II) 2 Cys 6 ) transcription factors (6), which, in general, exert positive transcriptional regulation of most of the genes within a single cluster (7). In addition to cluster-specific transcription factors, a higher order...

Epipolythiodioxopiperazines (ETPs) are a class of fungal secondary metabolites derived from diketopiperazines. Acetylaranotin belongs to one structural subgroup of ETPs characterized by the presence of a seven-membered 4,5-dihydrooxepine ring. Defining the genes involved in acetylaranotin biosynthesis should provide a means to increase production of these compounds and facilitate the engineering of second-generation molecules. The filamentous fungus Aspergillus terreus produces acetylaranotin and related natural products. Using targeted gene deletions, we have identified a cluster of nine genes including one nonribosomal peptide synthetase gene, ataP, which is required for acetylaranotin biosynthesis. Chemical analysis of the wild type and mutant strains enabled us to isolate seventeen natural products from the acetylaranotin biosynthesis pathway. Nine of the compounds identified in this study are previously not reported natural products. Our data allow us to propose a biosynthetic pathway for acetylaranotin and related natural products.