Degradation Pathway and Generation of Monohydroxamic Acids from the Trihydroxamate Siderophore Deferrioxamine B

Siderophores are avid ferric ion-chelating molecules that sequester the metal for microbes. Microbes elicit siderophores in numerous and different environments, but the means by which these molecules reenter the carbon and nitrogen cycles is poorly understood. The metabolism of the trihydroxamic acid siderophore deferrioxamine B by a Mesorhizobium loti isolated from soil was investigated. Specifically, the pathway by which the compound is cleaved into its constituent monohydroxamates was examined. High-performance liquid chromatography and mass-spectroscopy analyses demonstrated that M. loti enzyme preparations degraded deferrioxamine B, yielding a mass-to-charge (m/z) 361 dihydroxamic acid intermediate and an m/z 219 monohydroxamate. The dihydroxamic acid was further degraded to yield a second molecule of the m/z 219 monohydroxamate as well as an m/z 161 monohydroxamate. These studies indicate that the dissimilation of deferrioxamine B by M. loti proceeds by a specific, achiral degradation and likely represents the reversal by which hydroxamate siderophores are thought to be synthesized.     

The catabolism and heterotrophic nitrification of the siderophore deferrioxamine B

Summary Three bacteria, two of which were previously noted as active heterotrophic nitrifiers, were examined for their ability to grow and nitrify with the siderophore deferrioxamine B as the carbon source.Pseudomonas aureofaciens displayed limited growth and nitrification while a heterotrophic nitrifyingAlcaligenes sp. was without action concerning its metabolism of deferrioxamine B. The third bacterium, a unique Gram-negative soil isolate, was unable to nitrify deferrioxamine B but grew well when the siderophore was employed as the sole C source. The Gram-negative bacterium removed deferrioxamine B from the medium and left only residual amounts of the compound in solution at the termination of its growth. The organism was without action when the ferrated analogue of deferrioxamine B, ferrioxamine B, sereved as either the C source for growth, for metabolism by resting cells, or as the substrate for cell-free extracts. Deferrioxamine B, by contrast, was rapidly metabolized by resting cells. Cell-free extracts of the bacterium synthesized a monohydroxamate(s) when deferrioxamine B was the substrate. The catabolism of deferrioxamine B, which is synthesized by soil microbes, suggests that soil microflora have the ability to return deferrioxamine B, and perhaps other, siderophores to the C cycle.Abbreviations DFB deferrioxamine B; - FB ferrioxamine B - PhMeSO₂F phenylmethylsulfonyl fluoride     

Directing the Biosynthesis of Putrebactin or Desferrioxamine B in Shewanella putrefaciens through the Upstream Inhibition of Ornithine Decarboxylase

To manage iron acquisition in an oxic environment, Shewanella putrefaciens produces the macrocyclic dihydroxamic acid putrebactin (PB) as its native siderophore. In this work, we have established the siderophore profile of S. putrefaciens in cultures augmented with the native PB precursor putrescine and in putrescine-depleted cultures. Compared to base medium, PB increased by two-fold in cultures of S. putrefaciens with 10?mM NaCl and 20?mM exogenous putrescine. In cultures augmented with 1,4-diaminobutan-2-one (DAB), PB decreased with only 0.02-fold PB detectable at 10?mM DAB. As an ornithine decarboxylase (ODC) inhibitor, DAB depleted levels of endogenous putrescine which attenuated downstream PB assembly. Under putrescine-depleted conditions, S. putrefaciens produced as its replacement siderophore the cadaverine-based desferrioxamine B (DFO-B), as characterised by ESI-MS of the Fe(III) -loaded form (m/z(obs) 614.13; m/z(calc) 614.27). A third siderophore, independent of DAB, was observed in low levels. LC/MS Analysis of the Fe(III) -loaded extract gave m/z(obs) 440.93, which, formulated as a 1?:?1 Fe(III) complex with a macrocyclic dihydroxamic acid, comprising one putrescine- and one cadaverine-based precursor (m/z(calc) 440.14). These results show that the production of native PB or non-native DFO-B by S. putrefaciens can be directed though upstream inhibition of ODC. This approach could be used to increase the molecular diversity of siderophores produced by S. putrefaciens and to map alternative diamine-dependent metabolites.     

Further characterization and proposed pathway of deferrioxamine B catabolism

Most siderophores are catabolism resistant because of their non-peptidic or cyclic peptide chemical structures. Siderophore degradation is thus a rare event, and one which has received little attention. Based on literature precedence and the generation of monohydroxamic acid(s) by cell-free extracts of a deferrioxamine B degrading bacterium, a catabolic scheme of the siderophore is proposed. Data are also presented concerning parameters such as the pH profile, inducible nature of the siderophore-degrading metabolism and the ability of the deferrioxamine B degrading bacterium to metabolize some of the hypothesized products of deferrioxamine B dissimilation.     

Identification of siderophores and siderophore-mediated uptake of iron in Stemphylium botryosum

Under iron-deficient conditions Stemphylium botryosum f. sp. lycopersici produces three major siderophores; dimerum acid, coprogen B and an unidentified monohydroxamate siderophore designated as A. The system of siderophores mediating uptake of iron was characterized. It exhibits active transport, saturation kinetics and an optimum at pH 6 and 30°. The rate of iron uptake via dimerum acid and coprogen B was four times higher than siderophore A. S. botryosum was capable of taking up iron from hydroxamate siderophores produced by other fungi, e.g. ferrichrome, fusigen, rhodotorulic acid but not ferrioxamine B. Double labelling experiments suggest that ferric coprogen B accumulates in mycelial cells as an intact chelate.     

Degradation of desferrioxamines by Azospirillum irakense: Assignment of metabolites by HPLC/electrospray mass spectrometry

Based on a recent finding that an Azospirillum isolate ASP-1 possessing high 16S rDNA similarity to Azospirillum irakense was able to degrade desferrioxamine type siderophores (Winkelmann et al. BioMetals 9, 78-83, 1996), various members of the genus Azospirillum were analyzed for their ability to degrade desferrioxamines. While the desferrioxamine-degrading activity was absent or scarcely detectable in strains of A. lipoferum, A. brasilense, A. amazonense, degradation activity seemed to be confined to the species A. irakense (KBC-1, KA3). Also the identity of strain ASP-1 as A. irakense could be confirmed by species-specific oligonucleotide hybridization, InterLINE PCR fingerprinting and carbon source utilization pattern (BIOLOG) analysis. Products of desferrioxamine B degradation were analyzed by analytical HPLC and HPLC/electrospray mass spectrometry. Using whole cells and purified enzyme it was shown that the trihydroxamate desferrioxamine B (561 amu) is split at the N-terminal amide bond yielding a monohydroxamate (MH₁, 219 amu) and a dihydroxamate (DH₁, 361 amu) metabolite. A second monohydroxamate (MH₂, 319 amu) resulted from DH₁ after splitting the acetylhydroxamate bond. Minor amounts of a further dihydroxamate (DH₂, 419 amu) originated from splitting the second amide bond in desferrioxamine B. In addition to desferrioxamine B, several other linear and cyclic desferrioxamines and derivatives were degraded, whereas desferricoprogen and desferri-ferrichrome were not degraded, indicating high substrate specificity of the desferrioxamine hydrolase in A. irakense species. A simple microtiter plate assay was developed which can be used to phenotypically discriminate and identify species of A. irakense from other Azospirillum species by their characteristic feature of desferrioxamine degradation.     

Degradation of sulfonated azo dyes by the purified lignin peroxidase from <Emphasis Type="Italic">Brevibacillus laterosporus</Emphasis> MTCC 2298

Lignin peroxidase (EC 1.11.1.14) was purified from the Brevibacillus laterosporus MTCC 2298 by ion exchange chromatography. The K_m value of the purified lignin peroxidase (using n-propanol as substrate) was 1.6 mM. The MW of purified enzyme determined with the help of MW-standard markers was approximately 205 kDa. Purity of the enzyme was confirmed by native polyacrylamide gel electrophoresis (PAGE) and the activity staining using a substrate L-DOPA. Sulfonated azo dyes such as Methyl orange and Blue-2B were degraded by the purified lignin peroxidase. Degradation of the dyes was confirmed by HPLC, GC-MS, and FTIR spectroscopy. The mainly elected products of Methyl orange were 4-substituted hexanoic acid (m/z = 207), 4-cyclohexenone lactone cation (m/z = 191), and 4-isopropanal-2, 5-cyclohexa-dienone (m/z = 149) and for Blue-2B were 4-(2-hexenoic acid)-2, 5-cyclohexa-diene-one (m/z = 207; M − 1 = 206) and dehydro-acetic acid derivative (m/z = 223).     

利用重组大肠杆菌合成几丁寡糖的研究

提取根瘤菌Mesorhizobium.loti基因组,克隆编码N-乙酰氨基葡萄糖转移酶nodC基因,插入质粒pUC19的lac启动子的下游,构建并筛选出能够合成几丁寡糖的重组大肠杆菌DCL-3。利用优化的MMYNG培养基,重组大肠杆菌DCL-3在10L发酵罐中培养26h后,培养液菌体浓度测定OD560=10.8,几丁寡糖得率达到526mg/L。收集重组细菌的细胞并煮沸破碎,利用活性炭的吸附和P4凝胶层析对几丁寡糖产物进行分离纯化。纯化产物的液质分析(LC-ESI-MS)结果表明主要寡糖产物为几丁四糖(m/z,831[M H] )和几丁五糖(m/z,1034[M H] )。     

The nutritional selectivity of a siderophore-catabolizing bacterium

The ability of a siderophore-catabolizing bacterium to assimilate ferric ion was examined. While the bacterium utilizes the siderophore deferrioxamine B (DFB) as a carbon source, it was incapable of using the ferricion analogue (ferrioxamine B) as an iron source. It did, however, assimilate the ferric ion of the chelator ferric nitrilotriacetic acid and of the siderophore ferrirhodotorulic acid (ferriRA). Neither ferriRA nor its deferrated analog (RA), however, were capable of functioning as carbon sources for the bacterium. The microbe thus employs a nutritional selectivity with respect to these two siderophores. That is, it does not use the siderophore it employs as a carbon source (DFB) as an iron source nor does the siderophore utilized as an iron source, i.e. ferriRA, nor its deferrated analog (RA), serve as carbon sources for the organism.This paper is dedicated to the memory of Professor Thomas Emery. Professor Emery was instrumental in giving support and advice at a time when such mentorship greatly aided the corresponding author in developing a program concerning the catabolism of siderophores by microbes.     

Detection and differentiation of microbial siderophores by isoelectric focusing and chrome azurol S overlay

Siderophores are microbial, low molecular weight iron-chelating compounds. Fluorescent Pseudomonads produce different, strain-specific fluorescent siderophores (pyoverdines) as well as non-fluorescent siderophores in response to low iron conditions. We present an isoelectric focusing method applicable to unpurified as well as to purified pyoverdine samples where the fluorescent siderophores are visualized under UV illumination. Siderophores from different Pseudomonas sp., amongst which are P. aeruginosa, P. fluorescens and P. putida, including egg yolk, rhizospheric and clinical isolates as well as some derived Tn5 mutants were separated by this technique. Different patterns could be observed for strains known to produce different siderophores. The application of the chrome azurol S assay as a gel overlay further allows immediate detection of non-fluorescent siderophores or possibly degradation products with residual siderophore activity. The method was also applied to other microbial siderophores such as deferrioxamine B.     

The nitrogen-fixing symbiotic bacterium Mesorhizobium loti has and expresses the gene encoding pyridoxine 4-oxidase involved in the degradation of vitamin B6

The gene product of mll6785 of a nitrogen-fixing symbiotic bacterium Mesorhizobium loti MAFF303099 was identified as pyridoxine 4-oxidase, the first enzyme in the vitamin B6-degradation pathway. The gene was cloned and ligated into pET-21a+. Escherichia coli BL21(DE3) was co-transformed with the constructed plasmid plus pKY206 containing groESL genes encoding chaperonins. The overexpressed protein was purified to homogeneity by the ammonium sulfate fractionation and three chromatography steps. The enzymatic properties of the purified protein, such as K(m) values for pyridoxine (213+/-19 microM) and oxygen (78+/-10 microM), were compared to those of pyridoxine 4-oxidase from two bacteria with known vitamin B6-degradation pathway. M. loti grown in a Rhizobium medium showed the enzyme activity. The results suggest that M. loti also contains the degradation pathway of vitamin B6.     

Chemical nature, ligand denticity and quantification of fungal siderophores

Thirtyfive siderophore producing fungi were categorized for their hydroxamate, catecholate or carboxylate nature by chemical and bioassays. Out of 35 fungi, 30 were hydroxamates and 5 showed carboxylate nature. However, none of the fungi produced catecholate type of siderophores. Eighteen out of 29 fungi were trihydroxamate and the rest 11 fungi were dihydroxamates. Twenty-three fungi were hexadentate and 6 were tetradentate in nature. Quantification of siderophores using standard compounds deferrioxamine mesylate and rhizoferrin revealed that Phanerochaete chrysosporium produced maximum among the hydroxamate producing fungi and Mycotypha africana resulted maximum among the carboxylate producing fungi.     

A spectrophotometric assay for the degradation of the siderophore deferrioxamine B

A spectrophotometric assay using ferric perchlorate in a perchloric acid solution has been developed to monitor the degradation of the trihydroxamate siderophore deferrioxamine B to monohydroxamates. Using the ferric perchlorate solution and employing various concentrations of acetohydroxamic acid (as the model monohydroxamic acid) while maintaining a constant amount of deferrioxamine B resulted in the shifting of the absorption maximum from that of ferrioxamine B to longer wavelengths and toward that of a pure ferri-acetomonohydroxamic acid solution. A similar result was noted when a cell-free extract, from a bacterium capable of using deferrioxamine B as its sole carbon source, was given the siderophore in a phosphate buffer and aliquots of the enzyme-deferrioxamine B solution were removed for analysis. The assay may thus be used to monitor the formation of the monohydroxamic acid degradation products of the siderophore by the enzyme(s) in the cell-free extract.     

Studies on siderophore exchange properties between staphylococci and various species of gram-positive and gram-negative bacteria

The ability of iron utilizing by means of staphylococcal siderophores by bacteria belonging to genera: Acinetobacter, Corynebacterium, Curtobacterium, Clavibacter, Bacillus and Mycobacterium was investigated. The staphylococcal donor strains (18 species) used in these experiments were characterized by the ability to utilize siderophores produced by various strains belonging to aforenamed genera. The utilization of staphylococcal siderophores was studied on agar media in which minimally effective concentrations of ethylenediaminedi-ortho-hydroxyphenylacetic acid (EDDA) were used to inhibit indicator strains. Test colonies (staphylococcal) were applied to the surface of the media to determine whether the indicator organisms could obtain the required iron for growth by utilizing chelators from the test colony. The growth inhibition by EDDA of most strains from the Acinetobacter rods and from the coryneform-organisms (plant pathogen) genera, and strains from the species: B. subtilis, M. phlei, M. smegmatis, M. fortuitum was reversed by staphylococcal siderophores. None of the staphylococcal strains investigated, had the ability to exchange siderophores with strains from the species: C. pseudodiphtheriticum, Corynebacterium ANF group, B. megaterium, M. vaccae, M. chitae and M. parafortuitum.     

Identification and characterization of KpsS, a novel polysaccharide sulphotransferase in Mesorhizobium loti

Plants enter into symbiotic relationships with bacteria that allow survival in nutrient-limiting environments. The bacterium Mesorhizobium loti enters into a symbiosis with the legume host, Lotus japonicus, which results in the formation of novel plant structures called root nodules. The bacteria colonize the nodules, and are internalized into the cytoplasm of the plant cells, where they reduce molecular dinitrogen for the plant. Symbiosis between M. loti and L. japonicus requires bacterial synthesis of secreted and cell-surface polysaccharides. We previously reported the identification of an unusual sulphate-modified form of capsular polysaccharide (KPS) in M. loti. To better understand the physiological function of sulphated KPS, we isolated the sulphotransferase responsible for KPS sulphation from M. loti extracts, determined its amino acid sequence and identified the corresponding M. loti open reading frame, mll7563 (which we have named kpsS). We demonstrated that partially purified KpsS functions as a fucosyl sulphotransferase in vitro. Furthermore, mutants deficient for this gene exhibit a lack of KPS sulphation and a decreased rate of nodule formation on L. japonicus. Interestingly, the kpsS gene product shares no significant amino acid similarity with previously identified sulphotransferases, but exhibited sequence identity to open reading frames of unknown function in diverse bacteria that interact with eukaryotes.     

The mechanism and specificity of iron transport in Rhodotorula pilimanae probed by synthetic analogs of rhodotorulic acid

The yeast Rhodotorula pilimanae produces the dihydroxamate siderophore rhodotorulic acid (RA) in prodigious amounts when starved for iron. Synthetic dihydroxamate analogs of RA have been prepared in which the diketopiperazine ring of RA is replaced by a simple chain of n methylene groups. It is found that R. pilimanae is able to accumulate iron using these achiral complexes, as well as from simple monohydroxamate analogs, at rates comparable to those of RA. While the Fe2RA3 complex does not enter the cell, there is a receptor system whose geometric requirements for siderophore recognition have been probed using analogs. In contrast to mono- or dihydroxamate ligands, the trihydroxamate siderophores such as ferrioxamine B are completely ineffective at delivering iron to R. pilimanae. This is ascribed to the greater stability of these complexes, which blocks release of the Fe(III) in a ligand exchange process that is required for uptake. To explore whether this ligand exchange involves redox catalysis, Ga(III) was substituted for Fe(III). The gallium was taken up at rates near those of iron and were also energy-dependent, as determined by metabolic inhibition with KCN.     

Characterization of astaxanthin esters in Haematococcus pluvialis by liquid chromatography-atmospheric pressure chemical ionization mass spectrometry

After first being analyzed by HPLC, 4 free carotenoids, 15 astaxanthin monoesters, 12 astaxanthin diesters, and 3 astacin monoesters in Haematococcus pluvialis were identified by liquid chromatography-atmospheric pressure chemical ionization mass spectrometry (LC-(APCI)MS). Identification of each compound was based on the characteristic fragment ions of the positive ion mode, negative ion mode, and MS(2). Astaxanthin esters were identified based on the loss of one or two fatty acids. In a positive ion mode, astaxanthin monoesters had characteristic fragment ions at m/z 597 [M+H-fatty acid](+) and m/z 579 and 561 that resulted from a continuous loss of water. The relative intensity of m/z 579 in MS(2) amounted to more than 80% of that of the molecular ion. In astaxanthin diesters, the intensity of m/z 561 occasionally was equal to that of m/z 579, but in general the former, amounting to 50 to 60% or more of the molecular ion, was stronger than the latter, which decreased to 20 to 30% of the molecular ion. In addition, a set of compounds with maximum absorbance at 400 nm, detected by high-performance liquid chromatography-diode array detector (HPLC-DAD), had strong characteristic fragment ions at m/z 871 and 593 in the positive ion mode MS(2). They were presumed to be linolenic acid or an isomer of omega-6-gamma-linolenic acid esters of astacin.     

百脉根根瘤菌群体感应相关基因的克隆与表达

在实验室的纯培养条件下,检测不到百脉根根瘤菌自体诱导物的产生,但是通过基因序列同源性比对分析发现,百脉根根瘤菌基因组中至少含有4种自体诱导物合成酶基因;将其中一个自体诱导物合成酶基因ml4543克隆到大肠杆菌表达载体pET30a,构建得到能异源表达该基因的大肠杆菌重组菌株;对该大肠杆菌重组菌株进行自体诱导物检测发现,该合成酶基因在大肠杆菌中能合成至少3种自体诱导物因子。     

Simultaneous determination of asperosaponin VI and its active metabolite hederagenin in rat plasma by liquid chromatography-tandem mass spectrometry with positive/negative ion-switching electrospray ionization and its application in pharmacokinetic study

A new liquid chromatography-tandem mass spectrometry (LC-MS/MS) method operated in the positive/negative electrospray ionization (ESI) switching mode has been developed and validated for the simultaneous determination of asperosaponin VI and its active metabolite hederagenin in rat plasma. After addition of internal standards diazepam (for asperosaponin VI) and glycyrrhetic acid (for hederagenin), the plasma sample was deproteinized with acetonitrile, and separated on a reversed phase C18 column with a mobile phase of methanol (solvent A)-0.05% glacial acetic acid containing 10 mM ammonium acetate and 30 μM sodium acetate (solvent B) using gradient elution. The detection of target compounds was done in multiple reaction monitoring (MRM) mode using a tandem mass spectrometry equipped with positive/negative ion-switching ESI source. At the first segment, the MRM detection was operated in the positive ESI mode using the transitions of m/z 951.5 ([M+Na](+))→347.1 for asperosaponin VI and m/z 285.1 ([M+H](+))→193.1 for diazepam for 4 min, then switched to the negative ESI mode using the transitions of m/z 471.3 ([M-H](-))→471.3 for hederagenin and m/z 469.4 ([M-H](-))→425.4 for glycyrrhetic acid, respectively. The sodiated molecular ion [M+Na](+) at m/z 951.5 was selected as the precursor ion for asperosaponin VI, since it provided better sensitivity compared to the deprotonated and protonated molecular ions. Sodium acetate was added to the mobile phase to make sure that abundant amount of the sodiated molecular ion of asperosaponin VI could be produced, and more stable and intensive mass response of the product ion could be obtained. For the detection of hederagenin, since all of the mass responses of the fragment ions were very weak, the deprotonated molecular ion [M-H](-)m/z 471.3 was employed as both the precursor ion and the product ion. But the collision energy was still used for the MRM, in order to eliminate the influences induced by the interference substances from the rat plasma. The validated method was successfully applied to study the pharmacokinetics of asperosaponin VI and its active metabolite hederagenin in rat plasma after oral administration of asperosaponin VI at a dose of 90 mg/kg.     

Mass-spectrometric identification of trehalose 6-monomycolate synthesized by the cell-free system of Bacterionema matruchotii

The fluffy layer fraction prepared from Bacterionema matruchotii was found to possess high activity for the biosynthesis of mycolic acids which were bound to an unknown compound by an alkali-labile linkage [T. Shimakata, M. Iwaki, and T. Kusaka (1984) Arch. Biochem. Biophys. 229, 329-339]. To determine the structure of the mycolate-containing compound, it was purified and analyzed by field desorption (FD) and secondary ion mass spectrometry (SI-MS). When non-labelled palmitic acid was used as a precursor in the in vitro biosynthetic system, the underivatized product had a cationized molecular ion, [M + Na]+, at m/z 843 in FD-MS and a protonated ion, [M + H]+, at m/z 821 in SI-MS, corresponding to the quasimolecular ion of trehalose monomycolate (C32:0). In SI-MS, characteristic fragment ions due to cleavage of glycosidic linkages were clearly detected in addition to the molecular ion. If [1-13C]palmitic acid was the precursor, 2 mass unit increases in both the quasimolecular and fragment ions were observed, indicating that two molecules of palmitate were incorporated into the product. alpha-Trehalose was found in the aqueous phase after saponification of the product. By the electron impact mass spectrometry of the trimethylsilylated product, the mycolate was found to be esterified with an hydroxyl group at position 6 of the trehalose molecule. These results clearly demonstrated that the predominant product synthesized by the fluffy layer fraction with palmitate as substrate was 6-monomycolate (C32:0) of alpha-D-trehalose. Because newly synthesized mycolic acid was mainly in the form of trehalose monomycolate instead of free mycolate or trehalose dimycolate, the role of trehalose in the biosynthesis of mycolic acid is discussed.