Nonribosomal peptides for iron acquisition: pyochelin biosynthesis as a case study
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Section snippets
Iron uptake: siderophores
Iron is an essential nutrient that is needed by microbes to perform critical biological processes necessary for survival [1]. Due to the paucity of free iron in aerobic environments, microbes have developed intricate systems to acquire iron from their surroundings [1]. One such system is the biosynthesis of small molecules known as siderophores that have a high affinity for ferric iron [2]. When iron availability is low, microbes synthesize and secrete siderophores, and selectively reimport the
Nonribosomal peptide synthetases (NRPS): chemical logic of peptide chain formation
NRPS enzymes are large multidomain and multifunctional enzymes that display a chemical logic in which each module is responsible for the addition of a single amino acid to a growing peptide chain, including non-proteinogenic amino acids and hydroxy acids. An NRPS module consists of a condensation (C) domain, an adenylation (A) domain, and a peptidyl carrier protein (P) domain, except for the first initiation module, which lacks a condensation domain. The P-domain acts as a tethering system for
Nonribosomal peptide synthetases (NRPS): structural biology of an assembly line
The C-domain, A-domain, and P-domain have been well-studied, with both structural and kinetic characterizations [9, 10, 11, 12, 13]. The first structure elucidating the organization of a full NRPS module was the termination module (C-A-P-T) of surfactin biosynthesis, SrfA-C, from Bacillus subtilis (Figure 1b) [14]. Crystals of the full module were obtained after mutating the serine of the P-domain that is post-translationally modified with Ppant to alanine. The A-domain contains two subdomains,
Pyochelin from Pseudomonas aeruginosa
The chemical logic and structural biology of NRPS modules is key for understanding how the peptide bonds are made by these nanomachines. However, the bioactive peptides produced by these enzymes are far more diverse than the 20 amino acids found in proteins. The diversity is incorporated by accessory enzymes that produce unusual amino and hydroxy acid substrates for adenylation enzymes or by tailoring enzymes that alter amino acids already incorporated into the growing chain. Here, we use the
Accessory enzymes in pyochelin biosynthesis: PchA and PchB
PchA, isochorismate synthase. PchA catalyzes the first step in pyochelin biosynthesis, isomerizing chorismate to isochorismate (Figure 3a) [29, 30]. PchA is part of the menaquinone, siderophore, and tryptophan (MST) family of enzymes that are Mg2+-dependent chorismate utilizing enzymes [34, 35, 36]. Although the structure of PchA remains unsolved, the structure is hypothesized to be homologous to the isochorismate synthases, EntC [37, 38] and MenF [35] (both E. coli enzymes) and the salicylate
Stuffed tailoring domains in pyochelin biosynthesis: PchE and PchF
Most commonly, tailoring domains are incorporated into an NRPS module as an independent domain following the P-domain. However, in some cases tailoring domains are inserted within the A-domain, considered ‘interrupted’ adenylation domains [52]. The tailoring domains of both PchE and PchF are stuffed into interrupted adenylation domains between the core sequence motifs, A8 and A9, of the Asub-domain (Figure 4a) [33, 52]. The adenylation-tailoring didomains lack structural characterization and
Stand-alone tailoring domain: PchG
The terminal cyclized cysteine must be reduced to a thiazolidine while tethered to the Ppant tail on PchF, prior to final methylation and release of the mature pyochelin by the thioesterase domain (Figure 4f) [27]. PchG, a stand-alone tailoring enzyme, is proposed to perform the reduction by proton donation from a general acid and subsequent hydride transfer from NADPH. Structures of a functionally homologous enzyme of yersiniabactin biosynthesis [67], Irp3, have been determined: an apo-form,
Conclusion
Siderophores are small, iron-chelating molecules generated by NRPS systems. NRPS structures have provided insight into how these nanomachines form peptide bonds outside of the ribosome. Recently, several full-module structures have elucidated the different domain interactions and domain alternations that occur during peptide assembly. Additional full-module and cross-module structures are necessary to understand domain interactions between modules. While NRPS enzymes generate peptide assembly,
References and recommended reading
Papers of particular interest, published within the period of review, have been highlighted as:
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Acknowledgements
This publication was made possible by funds from The National Science Foundation (CHE-1403293). T.A.R. was supported by the National Institutes of Health Graduate Training Program in the Dynamic Aspects of Chemical Biology (T32 GM008545). Special thanks to Dr. Catherine Shelton and Jeffrey McFarlane for critically reading the manuscript.
References (69)
Nonribosomal peptide synthetase biosynthetic clusters of ESKAPE pathogens
Nat Prod Rep
(2017)Breaking a pathogen's iron will: inhibiting siderophore production as an antimicrobial strategy
Biochim Biophys Acta
(2015)- et al.
The specificity-conferring code of adenylation domains in nonribosomal peptide synthetases
Chem Biol
(1999) - et al.
Structural and functional aspects of the nonribosomal peptide synthetase condensation domain superfamily: discovery, dissection and diversity
Biochim Biophys Acta
(2017) - et al.
X-ray crystallography and electron microscopy of cross- and multi-module nonribosomal peptide synthetase proteins reveal a flexible architecture
Structure
(2017) - et al.
MbtH-like proteins as integral components of bacterial nonribosomal peptide synthetases
Biochemistry
(2010) - et al.
Dihydroaeruginoic acid synthetase and pyochelin synthetase, products of the pchEF genes, are induced by extracellular pyochelin in Pseudomonas aeruginosa
Microbiology
(1998) - et al.
Essential PchG-dependent reduction in pyochelin biosynthesis of Pseudomonas aeruginosa
J Bacteriol
(2001) - et al.
In vitro reconstitution of the Pseudomonas aeruginosa nonribosomal peptide synthesis of pyochelin: characterization of backbone tailoring thiazoline reductase and N-methyltransferase activities
Biochemistry
(2001) - et al.
Structure and mechanism of MbtI, the salicylate synthase from Mycobacterium tuberculosis
Biochemistry
(2007)
Implications of binding mode and active site flexibility for inhibitor potency against the salicylate synthase from Mycobacterium tuberculosis
Biochemistry
Crystal structures of Yersinia enterocolitica salicylate synthase and its complex with the reaction products salicylate and pyruvate
J Mol Biol
KtzJ-dependent serine activation and O-methylation by KtzH for kutznerides biosynthesis
J Antibiot (Tokyo)
The bacitracin biosynthesis operon of ATCC 10716: molecular characterization of three multi-modular peptide synthetases
Chem Biol
Interdomain and intermodule organization in epimerization domain containing nonribosomal peptide synthetases
ACS Chem Biol
Trapping open and closed forms of FitE: a group III periplasmic binding protein
Proteins
Reconstitution of the myxothiazol biosynthetic gene cluster by Red/ET recombination and heterologous expression in Myxococcus xanthus
Appl Environ Microbiol
Yersiniabactin synthetase: a four-protein assembly line producing the nonribosomal peptide/polyketide hybrid siderophore of Yersinia pestis
Chem Biol
Holo structure and steady state kinetics of the thiazolinyl imine reductases for siderophore biosynthesis
Biochemistry
Nutritional immunity: transition metals at the pathogen–host interface
Nat Rev Microbiol
Peptide siderophores
J Pept Sci
The long-overlooked enzymology of a nonribosomal peptide synthetase-independent pathway for virulence-conferring siderophore biosynthesis
Chem Commun (Camb)
Strategic paradigm shifts in the antimicrobial drug discovery process of the 21st century
Infect Disord Drug Targets
Chain termination steps in nonribosomal peptide synthetase assembly lines: directed acyl-S-enzyme breakdown in antibiotic and siderophore biosynthesis
ChemBioChem
Carrier protein structure and recognition in polyketide and nonribosomal peptide biosynthesis
Biochemistry
Structural insights into nonribosomal peptide enzymatic assembly lines
Nat Prod Rep
Structural biology of nonribosomal peptide synthetases
Methods Mol Biol
Conformational dynamics in the Acyl-CoA synthetases, adenylation domains of non-ribosomal peptide synthetases, and firefly luciferase
ACS Chem Biol
Crystal structure of the termination module of a nonribosomal peptide synthetase
Science
Structures of two distinct conformations of holo-non-ribosomal peptide synthetases
Nature
Synthetic cycle of the initiation module of a formylating nonribosomal peptide synthetase
Nature
Structure of the EntB multidomain nonribosomal peptide synthetase and functional analysis of its interaction with the EntE adenylation domain
Chem Biol
Rational manipulation of carrier-domain geometry in nonribosomal peptide synthetases
ChemBioChem
Enzymatic tailoring of ornithine in the biosynthesis of the Rhizobium cyclic trihydroxamate siderophore vicibactin
J Am Chem Soc
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