Genetics and Assembly Line Enzymology of Siderophore Biosynthesis in Bacteria

Abstract

The regulatory logic of siderophore biosynthetic genes in bacteria involves the universal repressor Fur, which acts together with iron as a negative regulator. However in other bacteria, in addition to the Fur-mediated mechanism of regulation, there is a concurrent positive regulation of iron transport and siderophore biosynthetic genes that occurs under conditions of iron deprivation. Despite these regulatory differences the mechanisms of siderophore biosynthesis follow the same fundamental enzymatic logic, which involves a series of elongating acyl-S-enzyme intermediates on multimodular protein assembly lines: nonribosomal peptide synthetases (NRPS). A substantial variety of siderophore structures are produced from similar NRPS assembly lines, and variation can come in the choice of the phenolic acid selected as the N-cap, the tailoring of amino acid residues during chain elongation, the mode of chain termination, and the nature of the capturing nucleophile of the siderophore acyl chain being released. Of course the specific parts that get assembled in a given bacterium may reflect a combination of the inventory of biosynthetic and tailoring gene clusters available. This modular assembly logic can account for all known siderophores. The ability to mix and match domains within modules and to swap modules themselves is likely to be an ongoing process in combinatorial biosynthesis. NRPS evolution will try out new combinations of chain initiation, elongation and tailoring, and termination steps, possibly by genetic exchange with other microorganisms and/or within the same bacterium, to create new variants of iron-chelating siderophores that can fit a particular niche for the producer bacterium

Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72

“…Two genes (azo2156, azo3836) are not even present in the P. fluorescens Pf5 genome, a plant-associated bacterium known for its capacity to produce and take up a wide range of siderophores 20 , which contains 45 such genes. Although putative receptors for hydroxamate-and catechol-type siderophores, ferricitrate, vitamin B12, colicins and unknown substances are present, there was no evidence for biosynthetic pathways for known hydroxamate or catecholate siderophores 21 . Moreover, production of siderophores was not detected experimentally ( Supplementary Fig.…”

Identification and analysis of a siderophore biosynthetic gene cluster from Agrobacterium tumefaciens C58

“…Siderophores are small molecules that bind iron with high affinity, and are typically produced by prokaryotes, fungi and some plants in response to iron deprivation (reviewed by Crosa & Walsh, 2002;Neilands, 1995;Winkelmann, 2002). Siderophores are generally categorized by the main functional group involved in chelating iron; this may be a catecholate, hydroxamate or hydroxycarboxylate group (Crosa & Walsh, 2002;Winkelmann, 2002).…”

“…Siderophores are generally categorized by the main functional group involved in chelating iron; this may be a catecholate, hydroxamate or hydroxycarboxylate group (Crosa & Walsh, 2002;Winkelmann, 2002). In Gramnegative bacteria, siderophores are secreted by the cell, bind iron extracellularly, and then are taken up by the cell by means of a dedicated TonB-dependent membrane transport system (reviewed by Faraldo-Gomez & Sansom, 2003;Visca et al, 2002).…”

Identification, isolation, and analysis of a gene cluster involved in iron acquisition by Pseudomonas mendocina ymp

“…The target size of each PCR product was between 350 and 1000 bp. Primers to detect NRPS-encoding genes were designed to amplify highly conserved adenylation and thiolation domains (Crosa and Walsh 2002;Mootz and Marahiel 1997). Primers for amplification of ornithine monooxygenase genes (pvdA homologs) targeted highly conserved and functionally essential NAD(H)-binding and FATGY domains (Yamada et al 2003).…”

“…Identifying and localizing siderophore-associated genes in an unsequenced strain is often complicated as simple PCR or hybridization-based strategies are ineffective. Especially problematic are non-ribosomal peptide synthetases (NRPSs): large, single-polymer, multi-domain and multi-functional enzymes often exceeding 250 kDa (Crosa and Walsh 2002;Schwarzer et al 2003;Weber and Marahiel 2001). Though NRPSs and related polyketide synthetases are of great interest due to their roles in the biosynthesis of siderophores and other natural products, PCR or hybridization-based approaches to their isolation can be non-trivial (Mootz and Marahiel 1997;Schwarzer et al 2003;Weber and Marahiel 2001).…”