Variochelins, Lipopeptide Siderophores from <i>Variovorax boronicumulans</i> Discovered by Genome Mining

Kurth, Colette; Schieferdecker, Sebastian; Athanasopoulou, Kalliopi; Seccareccia, Ivana; Nett, Markus

doi:10.1021/acs.jnatprod.5b00932

Cited by 22 publications

(43 citation statements)

References 62 publications

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“…6A). The products of 7 of 9 IβH Asp domains (with the exception of pyoverdine Pf0-1 and variobactin) have reported β-OHAsp stereochemistry, all 3S (29,30,33,34,(51)(52)(53). The target NRPS module of each IβH Asp domain lacks an E domain, thereby producing the L-threo (2S, 3S) configuration of β-OHAsp (Table 1 and Fig.…”

Section: Stereochemistry Of β-Ohaspmentioning

confidence: 99%

“…Based on homology to SyrP and OrbG, the existence of a number of β-OHAsp residues in siderophores has been rationalized (7,11,(24)(25)(26)(27)(28) or predicted (29)(30)(31)(32)(33). Recently, Kurth et al (33) used cucF, a β-hydroxylase domain from the cupriachelin (Fig. 2) gene cluster, as a handle to scan genomes for photoactive Fe(III)-siderophores, leading to the discovery of variochelin (SI Appendix, Fig.…”

Section: Significancementioning

confidence: 99%

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Genomic analysis of siderophore β-hydroxylases reveals divergent stereocontrol and expands the condensation domain family

Reitz

Hardy

Suk

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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Genome mining of biosynthetic pathways streamlines discovery of secondary metabolites but can leave ambiguities in the predicted structures, which must be rectified experimentally. Through coupling the reactivity predicted by biosynthetic gene clusters with verified structures, the origin of the β-hydroxyaspartic acid diastereomers in siderophores is reported herein. Two functional subtypes of nonheme Fe(II)/α-ketoglutarate–dependent aspartyl β-hydroxylases are identified in siderophore biosynthetic gene clusters, which differ in genomic organization—existing either as fused domains (IβHAsp) at the carboxyl terminus of a nonribosomal peptide synthetase (NRPS) or as stand-alone enzymes (TβHAsp)—and each directs opposite stereoselectivity of Asp β-hydroxylation. The predictive power of this subtype delineation is confirmed by the stereochemical characterization of β-OHAsp residues in pyoverdine GB-1, delftibactin, histicorrugatin, and cupriachelin. The l-threo (2S, 3S) β-OHAsp residues of alterobactin arise from hydroxylation by the β-hydroxylase domain integrated into NRPS AltH, while l-erythro (2S, 3R) β-OHAsp in delftibactin arises from the stand-alone β-hydroxylase DelD. Cupriachelin contains both l-threo and l-erythro β-OHAsp, consistent with the presence of both types of β-hydroxylases in the biosynthetic gene cluster. A third subtype of nonheme Fe(II)/α-ketoglutarate–dependent enzymes (IβHHis) hydroxylates histidyl residues with l-threo stereospecificity. A previously undescribed, noncanonical member of the NRPS condensation domain superfamily is identified, named the interface domain, which is proposed to position the β-hydroxylase and the NRPS-bound amino acid prior to hydroxylation. Through mapping characterized β-OHAsp diastereomers to the phylogenetic tree of siderophore β-hydroxylases, methods to predict β-OHAsp stereochemistry in silico are realized.

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Section: Stereochemistry Of β-Ohaspmentioning

confidence: 99%

Section: Significancementioning

confidence: 99%

Genomic analysis of siderophore β-hydroxylases reveals divergent stereocontrol and expands the condensation domain family

Reitz

Hardy

Suk

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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“…Genome miningh as becomeapowerful method for searching for new bioactive secondary metabolites by using the genome data of bacteria. [7][8][9][10][11][12][13][14][15][16][17] Ah igh percentageo fh alogenase-gene-possessing actinobacteria has been reported to contain polyketide synthase genes and/orN RPS genes, thus indicating the genetica nd physiological potentialo fh alogenases for the productiono fs econdary metabolites, possibly halometabolites. [18] So far,m ore than 4000 halometabolites have been discovered, [19] including commercially important antibiotics, such as chloramphenicol, [20] vancomycin, [21] and teicoplanin.…”

Section: Introductionmentioning

confidence: 99%

“…C, DEPT-135, DQF-COSY,T OCSY,N OESY,H MBC, HSQC, and 1 H-15 NHSQC. In the 1 HNMR spectrum, a-protons of amino acid residues (d = 3.72,3.90, 4.18, 4.38, 4.66, and 4.69 ppm) and amide protons (d = 7.24, 7.29, 7.58, 7.69, 7.77, and 8.33 ppm) were observed.…”

mentioning

confidence: 99%

Isolation and Structure Determination of New Antibacterial Peptide Curacomycin Based on Genome Mining

et al. 2017

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An ew antibacterial cyclic peptide, named curacomycin (1), and its analogue dechlorocuracomycin (2)w ere isolated from Streptomyces curacoi (NBRC 12761 T )a nd Streptomyces noursei (NBRC 15452 T ), respectively,b yu sing genome mining. The chemical structures of these two peptides were determined by using ac ombination of MS (ESI) and NMR spectroscopy.T he structure of compound 1 was determinedt ob eac yclic peptide that consisted of six amino acids, including: valine (Val), leucine (Leu), isoleucine (Ile), ornithine (Orn), b-hydroxyasparagine (OHAsn), and 5chlorotryptophan (ClTrp). The NMR data of compound 2were very similar to that of compound 1,w hich indicated that the structure of compound 2 was ad echlorinated analogue of compound 1.Acomparison of the antimicrobiala ctivitieso ft hese two peptidesi ndicated that the presenceo f chlorine in compound 1 was critical for its antimicrobial activity.T he proposed biosynthetic gene clusters for compounds 1 and 2 were found in the genome data of S. curacoi and S. noursei,r espectively.T he functions of the biosynthetic genes werec onsidered by comparison of the two gene clusters.[a] I.

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“…Halomonas, Marinobacter, Ochrobactrum, Synechococcus, and Vibrio [175][176][177][178]. Using a genome mining strategy, Variovorax boronicumulans BAM-48, a plant-associated terrestrial bacterium wasalso found to produce variochelins [151]. These siderophores support the growth of the producing organism by making important nutrients such as iron biologically available to them and also play a crucial role in determining the microbial community structure [179,180].…”

Section: Lipopeptides As Siderophoresmentioning

confidence: 99%

Lesson from Ecotoxicity: Revisiting the Microbial Lipopeptides for the Management of Emerging Diseases for Crop Protection

Malviya

Sahu

Singh

et al. 2020

IJERPH

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Microorganisms area treasure in terms of theproduction of various bioactive compounds which are being explored in different arenas of applied sciences. In agriculture, microbes and their bioactive compounds are being utilized in growth promotion and health promotion withnutrient fortification and its acquisition. Exhaustive explorations are unraveling the vast diversity of microbialcompounds with their potential usage in solving multiferous problems incrop production. Lipopeptides are one of such microbial compounds which havestrong antimicrobial properties against different plant pathogens. These compounds are reported to be produced by bacteria, cyanobacteria, fungi, and few other microorganisms; however, genus Bacillus alone produces a majority of diverse lipopeptides. Lipopeptides are low molecular weight compounds which havemultiple industrial roles apart from being usedas biosurfactants and antimicrobials. In plant protection, lipopeptides have wide prospects owing totheirpore-forming ability in pathogens, siderophore activity, biofilm inhibition, and dislodging activity, preventing colonization bypathogens, antiviral activity, etc. Microbes with lipopeptides that haveall these actions are good biocontrol agents. Exploring these antimicrobial compounds could widen the vistasof biological pest control for existing and emerging plant pathogens. The broader diversity and strong antimicrobial behavior of lipopeptides could be a boon for dealing withcomplex pathosystems and controlling diseases of greater economic importance. Understanding which and how these compounds modulate the synthesis and production of defense-related biomolecules in the plants is a key question—the answer of whichneeds in-depth investigation. The present reviewprovides a comprehensive picture of important lipopeptides produced by plant microbiome, their isolation, characterization, mechanisms of disease control, behavior against phytopathogens to understand different aspects of antagonism, and potential prospects for future explorations as antimicrobial agents. Understanding and exploring the antimicrobial lipopeptides from bacteria and fungi could also open upan entire new arena of biopesticides for effective control of devastating plant diseases.

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Variochelins, Lipopeptide Siderophores from Variovorax boronicumulans Discovered by Genome Mining

Cited by 22 publications

References 62 publications

Genomic analysis of siderophore β-hydroxylases reveals divergent stereocontrol and expands the condensation domain family

Genomic analysis of siderophore β-hydroxylases reveals divergent stereocontrol and expands the condensation domain family

Isolation and Structure Determination of New Antibacterial Peptide Curacomycin Based on Genome Mining

Lesson from Ecotoxicity: Revisiting the Microbial Lipopeptides for the Management of Emerging Diseases for Crop Protection

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