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Microbial genome mining is a rapidly developing approach to discover new and novel secondary metabolites for drug discovery. Many advances have been made in the past decade to facilitate genome mining, and these are reviewed in this Special Issue of the Journal of Industrial Microbiology and Biotechnology. In this Introductory Review, we discuss the concept of genome mining and why it is important for the revitalization of natural product discovery; what microbes show the most promise for focused genome mining; how microbial genomes can be mined; how genome mining can be leveraged with other technologies; how progress on genome mining can be accelerated; and who should fund future progress in this promising field. We direct interested readers to more focused reviews on the individual topics in this Special Issue for more detailed summaries on the current state-of-the-art.

The biosynthetic gene cluster for the enediyne antitumor antibiotic maduropeptin (MDP) from Actinomadura madurae ATCC 39144 was cloned and sequenced. Cloning of the mdp gene cluster was confirmed by heterologous complementation of enediyne polyketide synthase (PKS) mutants from the C-1027 producer Streptomyces globisporus and the neocarzinostatin producer Streptomyces carzinostaticus using the MDP enediyne PKS and associated genes. Furthermore, MDP was produced, and its apo-protein isolated and N-terminal sequenced; the encoding gene, mdpA, was found to reside within the cluster. The biosynthesis of MDP is highlighted by two iterative type I PKSs -the enediyne PKS and a 6-methylsalicylic acid PKS; generation of (S)-3-(2-chloro-3-hydroxy-4-methoxyphenyl)-3-hydroxypropionic acid derived from L-α-tyrosine; a unique type of enediyne apo-protein; and a convergent biosynthetic approach to the final MDP chromophore. The results demonstrate a platform for engineering new enediynes by combinatorial biosynthesis and establish a unified paradigm for the biosynthesis of enediyne polyketides.

The enzyme YkvM from Bacillus subtilis was identified previously along with three other enzymes (YkvJKL) in a bioinformatics search for enzymes involved in the biosynthesis of queuosine, a 7-deazaguanine modified nucleoside found in tRNA GUN of Bacteria and Eukarya. Genetic analysis of ykvJKLM mutants in Acinetobacter confirmed that each was essential for queuosine biosynthesis, and the genes were renamed queCDEF. QueF exhibits significant homology to the type I GTP cyclohydrolases characterized by FolE. Given that GTP is the precursor to queuosine and that a cyclohydrolase-like reaction was postulated as the initial step in queuosine biosynthesis, QueF was proposed to be the putative cyclohydrolase-like enzyme responsible for this reaction. We have cloned the queF genes from B. subtilis and Escherichia coli and characterized the recombinant enzymes. Contrary to the predictions based on sequence analysis, we discovered that the enzymes, in fact, catalyze a mechanistically unrelated reaction, the NADPHdependentreductionof7-cyano-7-deazaguanineto7-aminomethyl-7-deazaguanine, a late step in the biosynthesis of queuosine. We report here in vitro and in vivo studies that demonstrate this catalytic activity, as well as preliminary biochemical and bioinformatics analysis that provide insight into the structure of this family of enzymes.tRNA ͉ modified base T he avalanche of new protein structures that have been reported over the last decade (see summary at www.rcsb. org͞pdb͞holdings.html) has made it clear that the number of scaffolds that are used to produce all of the proteins in a cell is surprisingly limited, with Ϸ80% of the proteins using one of the 400 structural folds identified to date (1, 2). Specific functions evolve by duplication, recombination, and divergence of this core repertoire (3). Analysis of the functions of the different members of a protein structural family reveal that, in general, catalytic mechanisms and chemistries are conserved in a given family whereas substrate specificity changes (4). Much rarer are the cases in which the reactions catalyzed differ among members of the family (3); the best characterized examples being the TIM barrel superfamilies (5) and the enolase superfamily (6). Understanding the molecular paths that lead to the evolution of one function from another in a given superfamily is one of the next challenges of structural biology, impacting not only our understanding of how proteins evolve, but also the task of correctly annotating the genes identified by whole-genome sequencing (7,8).We recently used comparative genomic techniques (9) to discover four previously uncharacterized bacterial genes families (queCDEF) involved in the biosynthesis of the modified nucleoside queuosine (10). Three of these families (queCDE) have homologs in Archaea and are therefore implicated in the biosynthesis of the related modified nucleoside archaeosine (Fig. 1). Both nucleosides share an unusual 7-deazaguanosine core structure but diverge in their phylogenetic distribution, location in the ...