CDA: Calcium‐Dependent Peptide Antibiotics from <i>Streptomyces coelicolor</i> A3(2) Containing Unusual Residues

Kempter, Christoph; Kaiser, Dietmar; Haag, Sabine; Nicholson, Graeme; Gnau, Volker; Walk, T.; Gierling, Karl Heinz; Decker, Heinrich; Zähner, Hans; Jung, Günther; Metzger, Jörg W.

doi:10.1002/anie.199704981

Cited by 61 publications

(54 citation statements)

References 9 publications

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“…1, included homologs of enzymes required for the synthesis of tryptophan, an amino acid incorporated twice into the structure of CDA (32). These enzymes included TrpE, TrpG, TrpD, and TrpC, which would be expected to carry out three of the four reactions required to convert chorismate to indole-3-glycerol phosphate, with the exception being the reaction carried out by N-phosphoribosylanthranilate isomerase (TrpF).…”

Section: Vol 184 2002mentioning

confidence: 99%

“…Chemical analysis of CDA had shown that it was a cyclic lipopeptide composed of 11 amino acid residues linked to a six-carbon fatty acid chain (32), which in previous studies had been shown to require calcium ions for its mode of action (33). In experiments based on the premise that CDA was likely to be synthesized by a nonribosomal peptide synthetase, degenerate primers designed against conserved regions of nonribosomal peptide synthetases from other species were used to amplify two sections of S. coelicolor chromosomal DNA using PCR (18).…”

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confidence: 99%

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Regulation of the Streptomyces coelicolor Calcium-Dependent Antibiotic by absA , Encoding a Cluster-Linked Two-Component System

2002

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The Streptomyces coelicolor absA two-component system was initially identified through analysis of mutations in the sensor kinase absA1 that caused inhibition of all four antibiotics synthesized by this strain. Previous genetic analysis had suggested that the phosphorylated form of AbsA2 acted as a negative regulator of antibiotic biosynthesis in S. coelicolor (T. B. Anderson, P. Brian, and W. C. Champness, Mol. Microbiol. 39:553-566, 2001). Genomic sequence data subsequently provided by the Sanger Centre (Cambridge, United Kingdom) revealed that absA was located within the gene cluster for production of one of the four antibiotics, calcium-dependent antibiotic (CDA). In this paper we have identified numerous transcriptional start sites within the CDA cluster and have shown that the original antibiotic-negative mutants used to identify absA exhibit a stronger negative regulation of promoters upstream of the proposed CDA biosynthetic genes than of promoters in the clusters responsible for production of actinorhodin and undecylprodigiosin. The same antibiotic-negative mutants also showed an increase in transcription from a promoter divergent to that of absA, upstream of a putative ABC transporter, in addition to an increase in transcription of absA itself. Interestingly, the negative regulation of the biosynthetic transcripts did not appear to be mediated by transcriptional regulation of cdaR (a gene encoding a homolog of the pathway-specific regulators of the act and red clusters) or by any other recognizable transcriptional regulator associated with the cluster. The role of absA in regulating the expression of the diverse antibiotic biosynthesis clusters in the genome is discussed in light of its location in the cda cluster.

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Section: Vol 184 2002mentioning

confidence: 99%

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confidence: 99%

Regulation of the Streptomyces coelicolor Calcium-Dependent Antibiotic by absA , Encoding a Cluster-Linked Two-Component System

2002

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“…The primary structure of 8D1-1 is highly similar to that of the cyclic depsipeptide calcium-dependent antibiotic CDA3b produced by S. coelicolor and S. lividans, in which the Trp3, Hpg6, and 3-OH-Asn residues are epimerized to a D-configuration during their incorporation into the final product by the CDA nonribosomal peptide synthetase (NRPS) assembly line (39). To determine the configuration of these residues in the linear lipopeptides, 8D1-1 was hydrolyzed, derivatized with FDAA, and analyzed by LC-MS in parallel with standard stereoisomeric monomers.…”

Section: Resultsmentioning

confidence: 92%

Functional Genome Mining for Metabolites Encoded by Large Gene Clusters through Heterologous Expression of a Whole-Genome Bacterial Artificial Chromosome Library in Streptomyces spp

Wang

Zhao

et al. 2016

Appl Environ Microbiol

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Genome sequencing projects in the last decade revealed numerous cryptic biosynthetic pathways for unknown secondary metabolites in microbes, revitalizing drug discovery from microbial metabolites by approaches called genome mining. In this work, we developed a heterologous expression and functional screening approach for genome mining from genomic bacterial artificial chromosome (BAC) libraries in Streptomyces spp. We demonstrate mining from a strain of Streptomyces rochei, which is known to produce streptothricins and borrelidin, by expressing its BAC library in the surrogate host Streptomyces lividans SBT5, and screening for antimicrobial activity. In addition to the successful capture of the streptothricin and borrelidin biosynthetic gene clusters, we discovered two novel linear lipopeptides and their corresponding biosynthetic gene cluster, as well as a novel cryptic gene cluster for an unknown antibiotic from S. rochei. This high-throughput functional genome mining approach can be easily applied to other streptomycetes, and it is very suitable for the large-scale screening of genomic BAC libraries for bioactive natural products and the corresponding biosynthetic pathways. IMPORTANCEMicrobial genomes encode numerous cryptic biosynthetic gene clusters for unknown small metabolites with potential biological activities. Several genome mining approaches have been developed to activate and bring these cryptic metabolites to biological tests for future drug discovery. Previous sequence-guided procedures relied on bioinformatic analysis to predict potentially interesting biosynthetic gene clusters. In this study, we describe an efficient approach based on heterologous expression and functional screening of a whole-genome library for the mining of bioactive metabolites from Streptomyces. The usefulness of this function-driven approach was demonstrated by the capture of four large biosynthetic gene clusters for metabolites of various chemical types, including streptothricins, borrelidin, two novel lipopeptides, and one unknown antibiotic from Streptomyces rochei Sal35. The transfer, expression, and screening of the library were all performed in a high-throughput way, so that this approach is scalable and adaptable to industrial automation for next-generation antibiotic discovery. Microbial natural products have been a main source of drugs during the last century due to their diverse structures and bioactivities (1). The natural product drug pipeline seems to have stalled in the last 3 decades, even though recent Streptomyces genome sequencing projects have uncovered multiple biosynthetic gene clusters (BGCs) for undiscovered natural products (secondary metabolites), far exceeding the number of known metabolites (2-4). However, those BGCs are usually cryptic under laboratory conditions, producing very little or no corresponding secondary metabolites, which are needed for biological testing (5, 6).Different approaches have been developed to activate the cryptic BGCs for coelichelin, clostrubin, stambomycin, and...

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“…4A). The mutant MT1110-DasnO, however, does not produce any CDA that is common to the MT1110 or 2377 strains (Hojati et al, 2002;Kempter et al, 1997), but instead exhibits a major new product with a retention time of 6.90 min, which exhibited protonated, sodiated and potassiated ([M+H] + , [M+Na] + and [M+K] + ) molecular ions in the ESI-MS consistent molecular weight (mw) 1478.5 Da (Fig. 4B).…”

Section: Analysis Of S Coelicolor Dhasp and Dasnomentioning

confidence: 99%

“…The calcium-dependent antibiotics (CDAs) from Streptomyces coelicolor (Hojati et al, 2002;Kempter et al, 1997) belong to the group of structurally related acidic lipopetide antibiotics, which include A54145 (Fukuda et al, 1990; Miao et al, 2006), daptomycin (Baltz et al, 2005;Miao et al, 2005;Raja et al, 2003), friulimicins and amphomycins (Vértesy et al, 2000). All of these nonribosomally biosynthesized lipopeptides contain N-terminal fatty acid side chains, which is a trans-2,3-epoxyhexanoyl moiety in the case of CDA (Fig.…”

Section: Introductionmentioning

confidence: 99%

An asparagine oxygenase (AsnO) and a 3-hydroxyasparaginyl phosphotransferase (HasP) are involved in the biosynthesis of calcium-dependent lipopeptide antibiotics

et al. 2007

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Nonribosomal peptides contain a wide range of unusual non-proteinogenic amino acid residues. As a result, these complex natural products are amongst the most structurally diverse secondary metabolites in nature, and possess a broad spectrum of biological activities. b-Hydroxylation of amino acid precursors or peptidyl residues and their subsequent processing by downstream tailoring enzymes are some of the most common themes in the biosynthetic diversification of these therapeutically important peptides. Identification and characterization of the biosynthetic intermediates and enzymes involved in these processes are thus pivotal in understanding nonribosomal peptide assembly and modification. To this end, the putative asparaginyl oxygenase-and 3-hydroxyasparaginyl phosphotransferase-encoding genes hasP and asnO were separately deleted from the calcium-dependent antibiotic (CDA) biosynthetic gene cluster of Streptomyces coelicolor. Whilst the parent strains produce a number of 3-hydroxyasparagine-and 3-phosphohydroxyasparagine-containing CDAs, the DhasP mutants produce exclusively non-phosphorylated CDAs. On the other hand, DasnO mutants produce several new Asn-containing CDAs not present in the wild-type, which retain calcium-dependent antimicrobial activity. This confirms that AsnO and HasP are required for the b-hydroxylation and phosphorylation of the Asn residue within CDA. INTRODUCTIONThe calcium-dependent antibiotics (CDAs) from Streptomyces coelicolor (Hojati et al., 2002;Kempter et al., 1997) belong to the group of structurally related acidic lipopetide antibiotics, which include A54145 (Fukuda et al., 1990; Miao et al., 2006), daptomycin (Baltz et al., 2005;Miao et al., 2005;Raja et al., 2003), friulimicins and amphomycins (Vértesy et al., 2000). All of these nonribosomally biosynthesized lipopeptides contain N-terminal fatty acid side chains, which is a trans-2,3-epoxyhexanoyl moiety in the case of CDA (Fig. 1), along with decapeptide lactone or lactam cores. Within the decapeptide cores are a number of conserved amino acids, including acidic residues responsible for co-ordination of calcium ions, which are essential for antimicrobial activity. Notably, daptomycin was recently approved for clinical use, becoming the first new structural class of natural antibiotic to reach the clinic in over 30 years (Baltz et al., 2005;Raja et al., 2003). As a result of this, there has been considerable interest in establishing the biosynthetic origins of the acidic lipopeptide group of antibiotics, with the specific aim of engineering new lipopeptide variants with improved therapeutic properties. To this end we have focused on engineering the biosynthesis of CDAs, using adenylation domain active site modifications to replace Asp In addition to D-HPG, CDA contains a number of other non-proteinogenic amino acids, including L-3-methylglutamic acid (3-MeGlu; at position 10), which is also present at the same relative position in the decapeptide cores of daptomycin and A54145 (Milne et al., 2006), and a Cterminal Z-dehydro...

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CDA: Calcium‐Dependent Peptide Antibiotics from Streptomyces coelicolor A3(2) Containing Unusual Residues

Cited by 61 publications

References 9 publications

Regulation of the Streptomyces coelicolor Calcium-Dependent Antibiotic by absA , Encoding a Cluster-Linked Two-Component System

Regulation of the Streptomyces coelicolor Calcium-Dependent Antibiotic by absA , Encoding a Cluster-Linked Two-Component System

Functional Genome Mining for Metabolites Encoded by Large Gene Clusters through Heterologous Expression of a Whole-Genome Bacterial Artificial Chromosome Library in Streptomyces spp

An asparagine oxygenase (AsnO) and a 3-hydroxyasparaginyl phosphotransferase (HasP) are involved in the biosynthesis of calcium-dependent lipopeptide antibiotics

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