In vivo and in vitro formation of 2,3-dihydroxybenzoylserine by Escherichia coli K12

An Engineered Synthetic Pathway for Discovering Nonnatural Nonribosomal Peptides in Escherichia coli

Peptides that are synthesized independently of the ribosome in plants, fungi, and bacteria can have clinically relevant anticancer, antihemochromatosis, and antiviral activities, among many other. Despite their natural origin, discovering new natural products is challenging, and there is a need to expand the chemical diversity that is accessible. In this work, we created a novel, compressed synthetic pathway for the heterologous expression and diversification of nonribosomal peptides (NRPs) based on homologs of siderophore pathways from Escherichia coli and Vibrio cholerae To enhance the likelihood of successful molecule production, we established a selective pressure via the iron-chelating properties of siderophores. By supplementing cells containing our synthetic pathway with different precursors that are incorporated into the pathway independently of NRP enzymes, we generated over 20 predesigned, novel, and structurally diverse NRPs. This engineering approach, where phylogenetically related genes from different organisms are integrated and supplemented with novel precursors, should enable heterologous expression and molecular diversification of NRPs.IMPORTANCE Nonribosomal peptides (NRPs) constitute a source of bioactive molecules with potential therapeutic applications. However, discovering novel NRPs by rational engineering of biosynthetic pathways remains challenging. Here, we show that a synthetic compressed pathway in which we replaced biosynthetic genes with their ancestral homologs and orthologs enabled successful heterologous NRP expression. Polyamines added exogenously were incorporated into nascent NRPs, and molecular production was pressured by growing the host under conditions that make such NRPs beneficial for survival. This multilayered approach resulted in the assembly of over 20 distinct and novel molecules. We envision this strategy being used to enable the production of NRPs from heterologous pathways.

Biodegradable siderophores: survey on their production, chelating and complexing properties

The academic and industrial research on the interactions of complexing agents with the environment has received more attention for more than half a century ago and has always been concerned with the applications of chelating agents in the environment. In contrast, in recent years, an increasing scholarly interest has been demonstrated in the chemical and biological degradation of chelating agents. This is reflected by the increasing number of chelating agents-related publications between 1950 and middle of 2016. Consequently, the discovery of new green biodegradable chelating agents is of great importance and has an impact in the non-biodegradable chelating agent’s replacement with their green chemistry analogs. To acquire iron, many bacteria growing aerobically, including marine species, produce siderophores, which are low-molecular-weight compounds produced to facilitate acquisition of iron. To date and to the best of our knowledge, this is a concise and complete review article of the current and previous relevant studies conducted in the field of production, purification of siderophore compounds and their metal complexes, and their roles in biology and medicine.

Interactions of a periplasmic binding protein with a tetradentate siderophore mimic

Iron-bound structure: The ferric complex of a tetradentate siderophore mimic was synthesized and co-crystallized with the periplasmic binding protein CeuE of Campylobacter jejuni. In addition to electrostatic and hydrogen-bonding interactions between the binding pocket and the substrate, the structure showed direct coordination of two amino acid side chains to the Fe(III) center (orange, see figure).

Chemistry and biology of siderophores

Siderophores are compounds produced by bacteria, fungi and graminaceous plants for scavenging iron from the environment. They are low-molecular-weight compounds (500-1500 daltons) possessing a high affinity for iron(III) (Kf > 1030), the biosynthesis of which is regulated by iron levels and the function of which is to supply iron to the cell. This article briefly describes the classification and chemical properties of siderophores, before outlining research on siderophore biosynthesis and transport. Clinically important siderophores and the therapeutic potential of siderophore design are described. Appendix 1 provides a comprehensive list of siderophore structures.

Chromosome-mediated 2,3-dihydroxybenzoic acid is a precursor in the biosynthesis of the plasmid-mediated siderophore anguibactin in Vibrio anguillarum

We have isolated a recombinant clone harboring the chromosomal aroC gene, encoding chorismate synthase, from Vibrio anguillarum 775 by complementation of the Escherichia coli aroC mutant AB2849 which was transfected with a cosmid gene bank of the plasmidless V. anguillarum H775-3. The nucleotide sequence was determined, and an open reading frame that corresponds to a protein of 372 amino acids was found. The calculated mass of 40,417 Da was correlated with the size of the V. anguillarum aroC product detected in vitro. The homology of the V. anguillarum aroC gene to the aroC genes of E. coli and Salmonella typhi is 68% at the nucleotide level and 78% at the protein level. The expression of the aroC transcript is not regulated by iron, as determined by Northern (RNA) blot hybridization analysis. After insertion of an antibiotic resistance gene cassette within the cloned aroC gene, an aroC mutant of V. anguillarum was generated by allelic exchange. This mutant is deficient in the production of 2,3-dihydroxybenzoic acid (2,3-DHBA). Our bioassay and complementation experiments with this mutant demonstrate that the chromosome-mediated 2,3-DHBA is a precursor of the pJM1 plasmid-mediated siderophore anguibactin.

Biosynthesis of the Escherichia coli siderophore enterobactin: sequence of the entF gene, expression and purification of EntF, and analysis of covalent phosphopantetheine

The sequence of the entF gene which codes for the serine activating enzyme in enterobactin biosynthesis is reported. The gene encodes a protein with a calculated molecular weight of 142,006 and shares homologies with the small subunits of gramicidin S synthetase and tyrocidine synthetase. We have subcloned and overexpressed entF in a multicopy plasmid and attempted to demonstrate L-serine-dependent ATP-[32P]PPi exchange activity and its participation in enterobactin biosynthesis, but the overexpressed enzyme appears to be essentially inactive in crude extract. A partial purification of active EntF from wild-type Escherichia coli, however, has confirmed the expected activities of EntF. In a search for possible causes for the low level of activity of the overexpressed enzyme, we have discovered that EntF contains a covalently bound phosphopantetheine cofactor.

Expression of iron-regulated proteins in Yersinia species and their relation to virulence

Under iron-starvation conditions, the different Yersinia species expressed various iron-regulated proteins. Among them, two high-molecular-weight outer membrane proteins were synthesized in high-virulence-phenotype Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica serovars O:8 and O:Tacoma but were present neither in low-virulence phenotype Y. enterocolitica serovars O:3 and O:9 nor in avirulent Y. frederiksenii, Y. kristensenii, Y. intermedia, and Y. enterocolitica serovar O:39. Thus, the degree of virulence correlates with the presence of the two high-molecular-weight proteins in Yersinia species.

Influence of iron on growth, morphology, outer membrane protein composition, and synthesis of siderophores in Campylobacter jejuni

Three human isolates of Campylobacter jejuni were grown in a biphasic culture medium with and without the addition of a synthetic chelator to induce iron limitation. Cells grown in low-iron medium exhibited slower growth rates and altered cellular morphology. Increased numbers of longer, more filamentous forms were seen in Gram-stained smears. Three proteins, with apparent Mrs of 82,000, 76,000, and 74,000, were consistently present in the outer membrane of cells grown in low-iron medium. At least one of these proteins (76,000 to 74,000) was exposed on the cell surface. A bioassay was used to look for the production of siderophores by these and other strains of C. jejuni. Seven of 26 strains tested produced detectable amounts of siderophores. Growing strains at 42 degrees C failed to suppress siderophore synthesis or to alter the outer membrane protein profiles of iron-starved cells. The ability of three strains to utilize exogenously supplied siderophores for growth in low-iron medium was also examined. All three strains were able to utilize enterochelin and ferrichrome, but none utilized aerobactin, rhodotorulic acid, or desferrioxamine B. The effect of iron on the virulence of C. jejuni for 11-day-old chicken embryos inoculated via the chorioallantoic membrane was also determined.

Iron-vibriobactin transport system is not required for virulence of Vibrio cholerae

The possible requirement of a functional siderophore (vibriobactin)-mediated iron transport system in the pathogenicity of Vibrio cholerae was determined. Two mutants of V. cholerae defective in the iron-vibriobactin transport system were examined for their ability to multiply and elicit diarrhea in infant mice. One mutant, 40130, was unable to synthesize vibriobactin. The second mutant, 1510, was able to synthesize, but not transport, the siderophore. Both mutants retained the ability to multiply and produce disease in the infant mouse, and virulence was indistinguishable from the parent strains. This indicates that a functional iron-vibriobactin transport system is not essential for cholera pathogenesis. These mutants, like the wild-type strains, were found to have a ferric citrate iron uptake system and could utilize citrate or asparagine for growth in low-iron medium. Compounds of this type may increase the availability of iron to V. cholerae in the host.

Effects of azasteroids on growth and development of the free-living stages of Nippostrongylus brasiliensis and Nematospiroides dubius

25-Azasteroids were evaluated for their effects on the growth and development of the free-living stages of Nippostrongylus brasiliensis and Nematospiroides dubius. Increasing the concentration of 25-azasteroids in axenic cultures of either species resulted in a decrease in the percentage and mean length of larvae that developed to the third stage. Morphologic abnormalities of inhibited larvae were similar to those shown by larvae cultured in sterol-deficient medium. Addition of cholesterol to the culture medium reversed the inhibitive effects of azasteroid. Azasteroid completely inhibited growth and development of N. brasiliensis when the only sterol present in the culture medium was sitosterol. These results suggest similar pathways of sterol metabolism and similar mechanisms of action by azasteroids in the nematodes and insects that have been studied.

Expression of hydroxamate and phenolate siderophores by Shigella flexneri

Shigella flexneri strains were assayed for the ability to synthesize and utilize phenolate and hydroxamate siderophores. The hydroxamate aerobactin was synthesized by all isolates tested, whereas phenolates were only rarely produced. Expression of aerobactin was accompanied by production of a single iron-regulated outer membrane protein (Mr = 74,000). This protein was not produced by a mutant defective in aerobactin utilization and may serve as the aerobactin receptor. Phenolate (enterobactin)-producing strains synthesized three additional outer membrane proteins (Mr = 74,000, 81,000, and 83,000) in response to iron starvation. These proteins are the same apparent size as those produced by Escherichia coli K-12 strains. Ent sequences are apparently present in strains which do not synthesize this compound. Although normally silent, ent genes can be activated in Ent- strains to produce Ent+ variants. These laboratory variants are phenotypically indistinguishable from clinical Ent+ isolates.

Effect of iron limitation on growth, siderophore production, and expression of outer membrane proteins of Vibrio cholerae

Vibrio cholerae strains secrete a phenolate-type siderophore when grown in low-iron medium. The siderophore was detected as early as 3.5 h after downshift to iron-poor medium, and it continued to accumulate in the medium as the cells entered stationary phase. Two clinical isolates and an environmental isolate were examined for the amount of siderophore produced. The environmental isolate produced more siderophore and continued to secrete it at concentrations of iron that repressed synthesis in the clinical isolates. Concomitant with production of siderophore, at least six new proteins were seen in the outer membranes of iron starved cells. One of the proteins was large (200,000 Mr [220K]) and appeared to be loosely associated with the outer membrane. The other five proteins had approximate Mr values of 77K, 76K, 75K, 73K, and 62K. The 62K protein, like the 40K major outer membrane protein, was heat modifiable. One or more of these proteins may be a component of the receptor for the iron-siderophore complex.

Synthesis and utilization of siderophores by Shigella flexneri

Strains of Shigella flexneri secrete a hydroxamate-type siderophore when grown in low-iron media. This hydroxamate appears to be identical with aerobactin, a siderophore synthesized by Aerobacter aerogenes. In contrast to other enteric bacteria, S. flexneri did not produce detectable phenolate siderophores, although it could utilize an exogenously supplied phenolate.

Reduction of methionine sulfoxide to methionine by Escherichia coli

L-Methionine-dl-sulfoxide can support the growth of an Escherichia coli methionine auxotroph, suggesting the presence of an enzyme(s) capable of reducing the sulfoxide to methionine. This was verified by showing that a cell-free extract of E. coli catalyzes the conversion of methionine sulfoxide to methionine. This reaction required reduced nicotinamide adenine dinucleotide phosphate and a generating system for this compound. The specific activity of the enzyme increased during logarithmic growth and was maximal when the culture attained a density of about 10(9) cells per ml.

Electronic and resonance Raman spectra of iron(III) complexes of enterobactin, catechol, and N-methyl-2,3-dihydroxybenzamide

Resonance Raman electronic absorption and circular dichroism spectra and pH titration curves are reported for the trianionic ferric complexes of enterobactin, catechol, and N-methyl-2,3-dihydroxybenzamide (MDHB). The spectral signatures of the enterobactin and MDHB complexes are virtually identical and differ from those of the catechol complex in ways that reflect the influence of the amide group on the electronic structure. Excitation in either the visible charge-transfer bands or the near-ultraviolet pi-pi* bands enhances Raman bands associated with benzene ring modes, although the relative enhancements differ markedly in the two regions. The data stronly support a structural model in which iron is bound exclusively to the phenolate oxygen atoms in all three complexes.

Derepression of certain aromatic amino acid biosynthetic enzymes of Escherichia coli K-12 by growth in Fe3+-deficient medium

3-Deoxy-arabino-heptulosonic acid 7-phosphate synthase, prephenate dehydratase, tryptophan synthase, and 2,3-dihydroxybenzoylserine synthase enzyme activities are derepressed in wild-type Escherichia coli K-12 cells grown on Fe3+-deficient medium. This derepression is reversed when FeSO4 is added to the growth medium. Addition of shikimic acid to the Fe3+-deficient growth medium caused repression of the first three enzyme activities but not of 2,3-dihydroxybenzoylserine synthase activity. Addition of 2,3-dihydroxybenzoic acid to the Fe3+-deficient growth medium has no effect on any of the above-mentioned enzyme activities. The Fe3+ deficiency-mediated derepression of 3-deoxyarabino-heptulosonic acid 7-phosphate synthase activity is due to an elevation of the tyrosine-sensitive isoenzyme; the phenylalanine-sensitive isoenzyme is not derepressed under these conditions.

Effect of helium gas at elevated pressure on iron transport and growth of Escherichia coli

Helium at an ambient pressure of 68 at m with 0.2 atm of O(2) shortened by 1 to 1.5 h the lag phase for growth of Escherichia coli in minimal medium supplemented with 2 muliters of cell-free culture filtrate (CFF) per ml or with 1 muM 2,3-dihydroxybenzoylserine (DHBS), an iron chelator. The lag phase of cultures not exposed to helium could be shortened by use of supplements, but higher concentrations were required-10 to 30 muliters of CFF per ml or 10 to 50 muM DHBS. Strain AN 193 of E. coli, which requires the DHBS precursor 2,3-dihydroxybenzoic acid (DHBA), grew well in media with 10 muM DHBA when exposed to helium at 68 atm, whereas 100 muM DHBA was required for growth in unexposed cultures. In the presence of 100 muM DHBA plus 1.0 muM ethylenediaminetetraactic acid, growth was inhibited at 1 and 68 atm. Growth was restored, however, by the addition of 0.1 muM FeSO(4) at 68 atm and 1.0 muM FeSO(4) at 1 atm, but lag times were invariably shorter in the pressurized cultures. Hydrostatic pressures of 68 atm did not reduce the lag phase in the presence of CFF, DHBS, or DHBA. Our results suggest that 68 atm of helium pressure, but not hydrostatic pressure, elicited a more rapid transport of iron into the cells.

Studies on the enzymes involved in the biosynthesis of cyclo-tris (N-2,3-dihydroxybenzoyl-L-seryl) in Escherichia coli: kinetic properties of the L-serine-activating enzyme

Some kinetic properties of the formation of a thioester-bound l-seryl-enzyme intermediate are described. The rate constant of formation is 3.12 x 10(2) M(-1) s(-1) and the rate constant for spontaneous breakdown is 2.47 x 10(-3) s(-1). These constants yield a value of log K = 5.10 for the overall equilibrium constant which agrees favorably with a value of 5.20 calculated from equilibrium binding data. E(1).serine formation requires a thiol group which is extremely reactive to N-ethylmaleimide; the second-order rate constant for enzyme inactivation by this reagent is 77.1 M(-1) s(-1) at pH 6.6 and 0 C. Excess l-serine does not protect the enzyme against inactivation. In addition to an adenosine triphosphate-[(32)P]-inorganic pyrophosphate exchange, the enzyme also catalyzes an l-serine-dependent adenosine triphosphate-[(3)H]adenosine monophosphate exchange in accordance with the scheme proposed for the activation of serine.

Colicin B: mode of action and inhibition by enterochelin

Adsorption of colicin B to a sensitive strain of Escherichia coli results in rapid cessation of deoxyribonucleic acid, ribonucleic acid, and protein synthesis. Some classes of mutants insensitive to colicin B hyperexcrete a colicin inhibitor into their growth medium. This inhibitor functions by preventing adsorption of colicin B and does not rescue cells to which colicin has already adsorbed. The inhibitor is insensitive to nucleases, proteolytic enzymes, and lysozyme and is not extracted into organic solvents. The inhibitory material has a low molecular weight, which rules out identification as lipopolysaccharide, although purified lipopolysaccharide has some inhibitory activity. Evidence is presented that the inhibitor is enterochelin, an iron chelator which is the cyclic trimer of 2,3-dihydroxybenzoylserine. Enterochelin does not inhibit colicin M, a colicin that is produced by many strains colicinogenic for colicin B.

Excretion of enterochelin by exbA and exbB mutants of Escherichia coli

Escherichia coli mutants that are insensitive to colicins B and I hyperproduce and excrete the iron chelator enterochelin, which is an inhibitor of these colicins. These mutants are classified as exbA and exbB. The exbA mutants are chromium sensitive and require iron for growth, and the mutations are located in the tonB region at min 25 of the E. coli chromosome. tonB mutants in which the genome of phage lambda is inserted into the bacterial chromosome within the tonB gene also exhibit enterochelin excretion. The exbB mutants require methionine and probably result from deletions which are located between min 56 and 58. Colicin insensitivity, enterochelin excretion and methionine auxotrophy are recessive in exbB merodiploids. The methionine requirement of exbB strains is satisfied by cystathionine or homocysteine, and exbB mutants are sensitive to ethionine.

Biosynthesis of the iron-transport compound enterochelin: mutants of Escherichia coli unable to synthesize 2,3-dihydroxybenzoate

Mutants of Escherichia coli K-12 blocked in each of the three enzymatic reactions between chorismate and 2,3-dihydroxybenzoate, in the pathway leading to the iron-sequestering compound enterochelin, have been isolated and biochemically characterized. The three genes concerned (designated entA, entB and entC) have been shown to be clustered on the chromosome between purE and gal and to be located near minute 14 by cotransduction with the purE, lip, and fep genes. entA, entB, and entC were shown to be the structural genes for 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase, 2,3-dihydro-2,3-dihydroxybenzoate synthetase, and isochorismate synthetase, respectively.

Iron transport in Salmonella typhimurium: mutants blocked in the biosynthesis of enterobactin

A number of mutants of Salmonella typhimurium were isolated which are blocked in the biosynthesis of enterobactin, an iron chelator that is secreted by the wild-type bacteria when they are grown on low iron media. One class of these enb mutants accumulates the enterobactin precursor 2,3-dihydroxybenzoic acid, and another class does not accumulate any detectable catechol precursor. The enb mutants grow very well on a glucose-mineral salts medium. Addition of citrate, itself an iron chelator, to the medium drastically inhibits growth unless the medium is supplemented with enterobactin or iron salts. Citrate inhibits iron uptake from the medium by enb mutants; enterobactin counteracts this inhibition and also, by itself, increases iron uptake. Thus, the apparent function of enterobactin is to promote the absorption of iron from the medium by the bacteria. Transduction experiments showed that the genes for enterobactin biosynthesis are closely linked on the S. typhimurium chromosome. It is suggested that they form an operon which is repressed by the presence of iron. S. typhimurium can utilize the iron chelate ferrichrome. (Deferriferrichrome is a cyclic hexapeptide that is produced by some fungi but not by S. typhimurium.) The enb mutants use ferrichrome as an effective growth factor.

Mutations affecting iron transport in Escherichia coli

A mutant of Escherichia coli K-12 unable to form an essential component of the enterochelin-dependent iron transport system has been isolated. This strain carries a mutation in a gene designated fep, mapping close to two genes, entA and entD, concerned with enterochelin synthesis. Strain AN102, which carries the fep(-) allele, accumulates large quantities of enterochelin and gives a growth response to sodium citrate. The cytochrome b(1) and total iron content, and the measurement of the uptake of (55)Fe(3+), indicate an impairment of the enterochelin-dependent iron transport system. The growth response to sodium citrate is related to the presence, in strain AN102, of an inducible citrate-dependent iron transport system.

Role of microbial iron transport compounds in bacterial spoilage of eggs

Microbial iron transport compounds, belonging either to the hydroxamate family excreted by pseudomonads, or to the phenolate family excreted by salmonellae, reverse the bacteriostatic effect of conalbumin on the growth of these bacteria in egg white. The presence of microgram quantities of these compounds permits both salmonellae and pseudomonads to reach dense populations in egg white. The role of these iron transport compounds in bacterial egg spoilage is discussed.

Iron transport in Escherichia coli: relationship between chromium sensitivity and high iron requirement in mutants of Escherichia coli

Utilization of iron (Fe(3+)) by Escherichia coli depends upon a system which is determined by at least two genetic loci. Mutants which carry a deletion of the tonB-trp region of the chromosome grow only when very high concentrations of iron are present in the medium. These strains are sensitive to chromic ion (Cr(3+)) and, unlike the parent strain, fail to grow on MnSO(4) when FeSO(4) is not added to the medium. A second type of mutant, Chr2, which was isolated on the basis of its sensitivity to chromic ion, also requires a high concentration of iron for growth. This mutant can be distinguished phenotypically from the deletion mutants since it grows normally on low concentrations of iron, provided citrate is added to the medium. The chromium sensitivity of both types of mutants can be reversed by high concentrations of exogenous iron. The data are interpreted to indicate that the E. coli mutants studied are defective in iron transport and that residual iron transport is in some way inhibited by chromic ion.

Iron transport in Escherichia coli: roles of energy-dependent uptake and 2,3-dihydroxybenzoylserine

Escherichia coli strains B/r and 2276 contain an active transport system for iron. The system is energy-dependent, repressed by excess iron in the growth medium, and capable of accumulating iron inside of the cells at concentrations 2,000-fold higher than those in the medium. Two tonB-trp deletion mutants, strains B/rlt and B/lt7, which are sensitive to chromic ion and require high levels of iron for normal growth, are deficient in this active transport system. A point mutant, strain Chr2, which is also sensitive to chromic ion and requires high levels of iron for growth, has the active uptake system but cannot synthesize a specific chelator for iron, 2,3-dihydroxybenzoylserine (DHBS). Evidence is presented to support the hypothesis that both the active uptake system and chelation of iron by DHBS play a role in iron uptake from iron-deficient medium. The chromium sensitivity of the mutants can be explained by inhibition of uptake of exogenous iron.

Itoic acid synthesis in Bacillus subtilis

Under conditions of iron deficiency, strains of Bacillus subtilis produced 2,3-dihydroxybenzoic acid (DHB), 2,3-dihydroxybenzolyglycine (DHBG), or both of these compounds. DHB(G) production [production of DHB(G) refers to the production of DHB, or DHBG, or both] was proportional to the amount of iron present and occurred logarithmically, paralleling growth. Supplementation of media with more than 150 mug of iron per liter at zero-time inhibited DHB accumulation completely. In the presence of DHB, lower levels of iron inhibited DHB(G) production, so that the actual inhibitor of synthesis may involve the Fe(3+):[DHB(G)](3) complex. The strains producing DHBG also produced coproporphyrin III during iron-deficient growth, whereas a strain producing DHB did not produce coproporphyrin III under these conditions. Accumulation of DHB(G) was influenced by the levels of aromatic amino acids and anthranilic acid in the medium. In vivo experiments with strain B-1471 demonstrated that DHB was coupled to added glycine to form DHBG. Metabolism of DHB(G) was observed in two of the strains studied.