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Chemistry World. Education in Chemistry. Open Access. Historical Collection. You do not have JavaScript enabled. Please enable JavaScript to access the full features of the site or access our non-JavaScript page. From the journal: Natural Product Reports. Piperazic acid-containing natural products: structures and biosynthesis. Kalindi D. Covering: up to the end of Piperazic acid is a cyclic hydrazine and a non-proteinogenic amino acid found in diverse non-ribosomal peptide NRP and hybrid NRP—polyketide PK structures.

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DOI: Download Citation: Nat. Piperazic acid-containing natural products: structures and biosynthesis K.

Morgan, R. Andersen and K. Ryan, Nat. Search articles by author Kalindi D. Raymond J. Katherine S. Back to tab navigation This article has not yet been cited. Back to tab navigation. A Organization of the biosynthetic genes, as exemplified by that for nosiheptide utilized as the reference in this study. Some thiopeptide gene clusters contain several up to5 almost identical precursor peptide genes.

Grey, genes that are not conserved between gene clusters, presumably creating the remarkable diversity of thiopeptides. B Enzymatic reactions resulting in the highly modified, circular, precursor of a typical thiopeptide. A macro-circular structure, joined at the 6-membered nitrogen heterocycle yellow is found in all thiopeptides. Shapes: orange oval with capital letter, natural amino acid; blue pentagon, azole; red square with parallel lines indicating the double bond, dehydroamino acid; yellow hexagon, and six-membered nitrogen ring.

Lower case letters indicate the original amino acid residue. C Classification of thiopeptide biosynthetic gene clusters. MIA indolyl; QA, quinaldic acid. See Figure 4 for more details. The ThioFinder web server rapidly processes one complete or partial genome sequence per run.

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Each run is assigned a job ID and the associated output files are stored on the server for 7 days. Presently, ThioFinder takes 2 minutes to identify a thiocillin biosynthetic gene cluster in the 5.

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The detailed reports along with graphical representation are shown in Figure 2. After running the local version of ThioFinder by command line, we had predicted 65 putative biosynthetic gene clusters of thiopeptides in complete and draft bacterial genomes available at NCBI on April 13, Table S1. Among them, 11 were known with chemical and genetic experimental results, 54 were firstly reported and pending to be verified whether known or new thiopeptides are produced. Most of the obtained biosynthetic gene clusters of thiopeptides carried both the thiosf -like cassettes and the precursor peptide genes prep, in agreement with the above criteria for constituting a thiopeptide biosynthetic machinery; whereas 4, in each of which prep is missing, only have the thiosf -like cassette.

The latter suggests that the genetic locus of prep can be beyond the 25 kb analyzed DNA region or that the gene clusters are incomplete for thiopeptide biosynthesis. These strains represented species and genera of variable origin and diverse habitats, such as GC-rich Streptomyces versus AT-rich Bacillus , natural human vaginal strain Lactobacillus gasseri versus human pathogen Streptococcus pneumoniae, and Thermobispora bispora isolated from decaying manure versus Verrucosispora maris from deep marine sediment.

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As of May 25, , the open-access database ThioBase includes the following information. The GBrowse viewer [36] was employed for manipulating and displaying annotations on biosynthetic gene clusters of thiopeptides. The ThioBase reference collection is also searchable using the combination of distinct retrieval method, such as by the name of thiopeptide, author, title, journal, year and PubMed ID.

As the dramatic pace of expansion in bacterial genome data obtained by next-generation sequencing, the putative thiopeptide biosynthetic gene clusters are being identified in increasing numbers by using the in silico tools, like ThioFinder. According to the current understanding of thiopeptide biosynthesis, it is becoming feasible to classify the genotypes of thiopeptides, towards establishing the relationship to chemotypes, by taking the specific genes for diversity into account of the resulting structural manners via the biosynthetic reactions.

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We investigated the correlation between the 11 reported biosynthetic gene clusters of thiopeptides and their verified metabolite structures. These specific genes are involved in the thiopeptide side ring system in structure, the formation of which is independent of the precursor peptide. Despite sharing a similar macrocyclic framework, the members in thiopeptide family differ in the substitution of the six-membered central ring, installation of the side ring system, decoration of the core system, and C-terminal functionalization of the extended side chain [1] Figure 4.

Biochemical investigations indicated that the functionalization utilizes L-tryptophan as a common substrate but can proceed in completely different ways [37] , to afford variable groups as the indolic acid IA moiety of nosiheptide and the quinaldic acid QA moiety of thiostrepton. As for IA formation, we have recently characterized a radical S -adenosylmethionine SAM 3-methylindolic acid synthase e. Comparative analysis of the corresponding gene s for L-tryptophan processing among the available 11 biosynthetic gene clusters revealed i that formations of IA and QA are common in each moiety-containing bi-macrocyclic members, consistent with the nosL homologue for IA in the nocathiacin gene cluster and the tsrT and tsrD homologues for QA in the siomycin gene cluster, respectively; and ii that the gene clusters of the members without the L-tryptophan-derivative moiety, most of which are mono-macrocyclic, apparently lack the above counterparts.

These findings supported that the specific gene s involved in L-tryptophan processing can serve as a new strategy for classifying the biosynthetic gene clusters of thiopeptides into three types and prediction of the metabolite structures Figure 4. The correlation of these gene cluster types with their associated chemicals will facilitate new thiopeptide discovery.

Selected examples of thiopeptides of different types exhibit distinct chemical signatures. MR denotes macrocyclic ring; SR, light grey, side ring.

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In classical classification , Thiopeptides are classified into series a-e according to the oxidative state of the central heterocyclic ring Pink, 6-membered N heterocycle, including pyrimidine. Three types of thiopeptide gene cluster biosynthetic we proposed makes use of the conserved amino acid sequences of enzyme that produce characteristic indolyl MIA or quinolinic acid QA residues, which are often found in the side rings of some thiopeptides. Type I, characterized by a side ring containing the indolyl structure blue, MIA. Type II thiopeptides contain side rings with quinaldic acid orange, QA , which is formed by two enzymes, a hypothetical amidotransferase and a putative ester cyclase for the epoxide ring intermediate.

The thiopeptides had been classically classified by their chemical structures as five series a—e , and especially by the oxidation state of the 6-membered nitrogen heterocycle Figure 4 [1]. Yet this classification cannot be applied to the new thiopeptides predicted from DNA sequence information, long before the substance is characterized chemically. The three gene cluster types we proposed make use of the conserved amino acid sequences of enzyme that produce characteristic indolyl MIA or quinolinic acid QA residues, which are often found in the side rings of some thiopeptides.

Interestingly, when considering the resultant thiopeptide structures, we found the gene cluster types could match to the chemical signatures as well as classical series classification Figure 4. This suggests the genotypes can be responsible for the chemotypes, and may be deduced from the chemotypes in turn.

ThioFinder thus grouped the identified gene clusters into the three types along with the products. These specific genetic features can hint the structural manners of their potential products.

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  • The remaining 53 Type III clusters lacking type-specific gene s of L-tryptophan processing may involve in the production of the members without the L-tryptophan-derived side ring. We also reversely deduced the genetic types of the only structurally known thiopeptides. Of the ThioBase-archived 99 structurally known thiopeptides, 14 were grouped into Type I that features a nosL-like gene encoding IA moiety formation, 21 into Type II that possesses tsrT and tsrD -like genes for QA moiety biosynthesis, and 64 into Type III that contains none of the above to afford the side ring system.

    Remarkably, the above genotypes are consistent with the classical thiopeptide classification which is according to the oxidative state of the central heterocyclic domain Figure 4. The genotypes of Types I and III are completely in line with the thiopeptides of series e as the monocyclic members with a trissubstituted pyridine central ring and d as the bi-macrocyclic members with a hydroxypyridine central ring and an indolic side ring system , respectively.

    The Type II genotypes are in agreement with the members of series a, b and c, all of which share a piperidine central ring and a QA moiety in the side ring system Figure 4. The prediction strategy we proposed has the advantage in grouping the genotypes of some members that are structurally almost identical but different only in the central ring, such as thiopeptins, 8 members of which have to be classified into distinct series of chemotypes [1].

    Currently the classification is established on the observation of a relative small sample, but it can be further improved by the future characterization of thiopeptide genotypes and chemotypes. We have provided a user-friendly interactive tool ThioFinder to quickly and precisely detect thiopeptide biosynthetic gene clusters in the user-supplied nucleotide sequences.

    The back-end database ThioBase maintains a growing variety of thiopeptide antibiotic related data extracted and curated from experimental literature. Additionally, ThioFinder grouped the identified gene clusters into the three types, towards deducing thiopeptide side ring structure from the type-specific genes. Ultimately, we propose the thiopeptide-specific resource could be of interest to a broad community of the researchers with multidisciplinary backgrounds, to facilitate the further investigation into thiopeptides, the potential candidates in antibacterial and anticancer drug development, both in genetics and chemistry.

    A List of the known thiopeptides. B Detailed information of thiopeptides, regarding the chemical structure, analogue, biological activity, producing strain, biosynthetic gene cluster, structure peptide sequence and reference, as exemplified by that for nosiheptide. Browse Subject Areas? Click through the PLOS taxonomy to find articles in your field. Abstract Thiopeptides are a growing class of sulfur-rich, highly modified heterocyclic peptides that are mainly active against Gram-positive bacteria including various drug-resistant pathogens.

    Introduction Thiopeptides are a growing family of sulfur-rich and highly modified heterocyclic peptide antibiotics produced in various bacterial strains [1]. Download: PPT. Table 1. List of the HMM-profiles of the protein families or domains involved in thiopeptide biosynthesis. Figure 2. Screenshot and examples of output results of ThioFinder. Results and Discussion Typical Features of Biosynthetic Gene Clusters of Thiopeptides Thiopeptide biosynthesis typically features one or several almost identical ribosomally synthesized precursor peptides up to 4 as reported so far and conserved posttranslational modifications [15] — [16] , [35].

    Figure 3.