A Pseudomonas stutzeri gene cluster encoding the biosynthesis of the CCl4-dechlorination agent pyridine-2,6-bis(thiocarboxylic acid)

Biosynthesis of thiocarboxylic acid-containing natural products

Thiocarboxylic acid-containing natural products are rare and their biosynthesis and biological significance remain unknown. Thioplatensimycin (thioPTM) and thioplatencin (thioPTN), thiocarboxylic acid congeners of the antibacterial natural products platensimycin (PTM) and platencin (PTN), were recently discovered. Here we report the biosynthetic origin of the thiocarboxylic acid moiety in thioPTM and thioPTN. We identify a thioacid cassette encoding two proteins, PtmA3 and PtmU4, responsible for carboxylate activation by coenzyme A and sulfur transfer, respectively. ThioPTM and thioPTN bind tightly to β-ketoacyl-ACP synthase II (FabF) and retain strong antibacterial activities. Density functional theory calculations of binding and solvation free energies suggest thioPTM and thioPTN bind to FabF more favorably than PTM and PTN. Additionally, thioacid cassettes are prevalent in the genomes of bacteria, implicating that thiocarboxylic acid-containing natural products are underappreciated. These results suggest that thiocarboxylic acid, as an alternative pharmacophore, and thiocarboxylic acid-containing natural products may be considered for future drug discovery.

Thioplatensimycin (thioPTM) and thioplatencin (thioPTN) are recently discovered thiocarboxylic acid congeners of the antibacterial compounds PTM and PTN. Here, the authors identify a thioacid cassette encoding PtmA3 and PtmU4 that are responsible for carboxylate activation and sulfur transfer, respectively.

Optimization of physicochemical parameters influencing the production of prodigiosin from Serratia nematodiphila RL2 and exploring its antibacterial activity

In the present study, role of various physicochemical parameters influencing the production of antimicrobial pigment prodigiosin from Serratia nematodiphila RL2 was determined and optimized. The pigment-producing strain was isolated and based on molecular characterization (16S rRNA sequencing), was identified as S. nematodiphila RL2. The pigment produced by S. nematodiphila RL2 was characterized by thin layer chromatography (Rf 0.94), spectrophotometrically (λ_max 535 nm) and identified as prodigiosin. Optimization of production parameters of prodigiosin revealed, nutrient broth medium supplemented with lactose and yeast extract at 1% concentration each, have a positive effect on the bacterial growth (10.25-4.6 mg/ml DCW) as well as pigment production (0.46-0.6 mg/ml). Prodigiosin production (0.64 mg/ml) increases optimally after 46-48 h of incubation, at 35 °C at pH between 6 and 7 with addition of metal ions such as Uranyl acetate. An increase of 65% in prodigiosin production (0.46-0.76 mg/ml) was observed after optimizing the various production parameters than unoptimized conditions. Antimicrobial activity of the prodigiosin was also evaluated and found to be effective antimicrobial agent against bacterial pathogens including Listeria sp., Pseudomonas sp., Yersinia sp. and Shigella sp. Present study indicate that S. nematodiphila RL2 is a potent source of pigment prodigiosin which can be further explored for production of prodigiosin.

Enzymatic Carbon-Sulfur Bond Formation in Natural Product Biosynthesis

Sulfur plays a critical role for the development and maintenance of life on earth, which is reflected by the wealth of primary metabolites, macromolecules, and cofactors bearing this element. Whereas a large body of knowledge has existed for sulfur trafficking in primary metabolism, the secondary metabolism involving sulfur has long been neglected. Yet, diverse sulfur functionalities have a major impact on the biological activities of natural products. Recent research at the genetic, biochemical, and chemical levels has unearthed a broad range of enzymes, sulfur shuttles, and chemical mechanisms for generating carbon-sulfur bonds. This Review will give the first systematic overview on enzymes catalyzing the formation of organosulfur natural products.

An overview of the biological metal uptake pathways in Pseudomonas aeruginosa

Biological metal ions, including Co, Cu, Fe, Mg, Mn, Mo, Ni and Zn ions, are necessary for the survival and the growth of all microorganisms. Their biological functions are linked to their particular chemical properties: they play a role in structuring macromolecules and/or act as co-factors catalyzing diverse biochemical reactions. These metal ions are also essential for microbial pathogens during infection: they are involved in bacterial metabolism and various virulence factor functions. Therefore, during infection, bacteria need to acquire biological metal ions from the host such that there is competition for these ions between the bacterium and the host. Evidence is increasingly emerging of "nutritional immunity" against pathogens in the hosts; this includes strategies making access to metals difficult for infecting bacteria. It is clear that biological metals play key roles during infection and in the battle between the pathogens and the host. Here, we summarize current knowledge about the strategies used by Pseudomonas aeruginosa to access the various biological metals it requires. P. aeruginosa is a medically significant Gram-negative bacterial opportunistic pathogen that can cause severe chronic lung infections in cystic fibrosis patients and that is responsible for nosocomial infections worldwide.

Role for ferredoxin:NAD(P)H oxidoreductase (FprA) in sulfate assimilation and siderophore biosynthesis in Pseudomonads

Pyridine-2,6-bis(thiocarboxylate) (PDTC), produced by certain pseudomonads, is a sulfur-containing siderophore that binds iron, as well as a wide range of transition metals, and it affects the net hydrolysis of the environmental contaminant carbon tetrachloride. The pathway of PDTC biosynthesis has not been defined. Here, we performed a transposon screen of Pseudomonas putida DSM 3601 to identify genes necessary for PDTC production (Pdt phenotype). Transposon insertions within genes for sulfate assimilation (cysD, cysNC, and cysG [cobA2]) dominated the collection of Pdt mutations. In addition, two insertions were within the gene for the LysR-type transcriptional activator FinR (PP1637). Phenotypic characterization indicated that finR mutants were cysteine bradytrophs. The Pdt phenotype of finR mutants could be complemented by the known target of FinR regulation, fprA (encoding ferredoxin:NADP(+) oxidoreductase), or by Escherichia coli cysJI (encoding sulfite reductase). These data indicate that fprA is necessary for effective sulfate assimilation by P. putida and that the effect of finR mutation on PDTC production was due to deficient expression of fprA and sulfite reduction. fprA expression in both P. putida and P. aeruginosa was found to be regulated by FinR, but in a manner dependent upon reduced sulfur sources, implicating FinR in sulfur regulatory physiology. The genes and phenotypes identified in this study indicated a strong dependence upon intracellular reduced sulfur/cysteine for PDTC biosynthesis and that pseudomonads utilize sulfite reduction enzymology distinct from that of E. coli and possibly similar to that of chloroplasts and other proteobacteria.

Natural transformation with synthetic gene cassettes: new tools for integron research and biotechnology

Integrons are genetic elements that can capture and express genes packaged as gene cassettes. Here we report new methods that allow integrons to be studied and manipulated in their native bacterial hosts. Synthetic gene cassettes encoding gentamicin resistance (aadB) and green fluorescence (gfp), or lactose metabolism (lacZY), were made by PCR and self-ligation, converted to large tandem arrays by multiple displacement amplification, and introduced into Escherichia coli or Pseudomonas stutzeri strains via electroporation or natural transformation. Recombinants (GmR or Lac+) were obtained at frequencies ranging from 101 to 106 c.f.u. (µg DNA)−1. Cassettes were integrated by site-specific recombination at the integron attI site in nearly all cases examined (370/384), including both promoterless and promoter-containing cassettes. Fluorometric analysis of gfp-containing recombinants revealed that expression levels from the integron-associated promoter PC were five- to 10-fold higher in the plasmid-borne integron In3 compared with the P. stutzeri chromosomal integrons. Integration of lacZY cassettes into P. stutzeri integrons allowed the bacteria to grow on lactose, and the lacZY gene cassette was stably maintained in the absence of selection. This study is believed to be the first to show natural transformation by gene cassettes, and integron-mediated capture of catabolic gene cassettes.

Natural history of the E1-like superfamily: implication for adenylation, sulfur transfer, and ubiquitin conjugation

The E1-like superfamily is central to ubiquitin (Ub) conjugation, biosynthesis of cysteine, thiamine, and MoCo, and several secondary metabolites. Yet, its functional diversity and evolutionary history is not well understood. We develop a natural classification of this superfamily and use it to decipher the major adaptive trends occurring in the evolution of the E1-like superfamily. Within the Rossmann fold, E1-like proteins are closest to NAD(P)/FAD-dependent dehydrogenases and S-AdoMet-dependent methyltransferases. Hence, their phosphotransfer activity is an independent catalytic "invention" with respect to such activities seen in other Rossmannoid folds. Sequence and structure analysis reveals a striking diversity of residues and structures involved in adenylation, sulfotransfer, and substrate binding between different E1-like families, allowing us to predict previously uncharacterized functional adaptations. E1-like proteins are fused to several previously undetected domains, such as a predicted sulfur transfer domain containing a novel superfamily of the TATA-binding protein fold, different types of catalytic domains, a novel winged helix-turn-helix domain and potential adaptor domains related to Ub conjugation. On the basis of these fusions, we develop a generalized model for the linking of E1 catalyzed adenylation/thiolation with further downstream reactions. This is likely to involve a dynamic interplay between the E1 active sites and diverse fused C-terminal domains. We also predict participation of E1-like domains in previously uncharacterized bacterial secondary metabolism pathways, new cysteine biosynthesis systems, such as those associated with archaeal O-phosphoseryl tRNA, metal-sulfur cluster assembly (e.g., in nitrogen fixation) and Ub-conjugation. Evolutionary reconstructions suggest that the last universal common ancestor contained a single E1-like domain possessing both phosphotransfer and thiolating activities and participating in multiple sulfotransfer reactions. The E1-like superfamily subsequently expanded to include 26 families clustering into three major radiations. These are broadly involved in Ub activation, cofactor and cysteine biosynthesis, and biosynthesis of secondary metabolites. In light of this, we present evidence that in eukaryotes other E1-like enzymes such as Urm1 were independently recruited for Ubl conjugation, probably functioning without conventional E2-like enzymes.

Common thiolation mechanism in the biosynthesis of tRNA thiouridine and sulphur-containing cofactors

2-Thioribothymidine (s(2)T), a modified uridine, is found at position 54 in transfer RNAs (tRNAs) from several thermophiles; s(2)T stabilizes the L-shaped structure of tRNA and is essential for growth at higher temperatures. Here, we identified an ATPase (tRNA-two-thiouridine C, TtuC) required for the 2-thiolation of s(2)T in Thermus thermophilus and examined in vitro s(2)T formation by TtuC and previously identified s(2)T-biosynthetic proteins (TtuA, TtuB, and cysteine desulphurases). The C-terminal glycine of TtuB is first activated as an acyl-adenylate by TtuC and then thiocarboxylated by cysteine desulphurases. The sulphur atom of thiocarboxylated TtuB is transferred to tRNA by TtuA. In a ttuC mutant of T. thermophilus, not only s(2)T, but also molybdenum cofactor and thiamin were not synthesized, suggesting that TtuC is shared among these biosynthetic pathways. Furthermore, we found that a TtuB-TtuC thioester was formed in vitro, which was similar to the ubiquitin-E1 thioester, a key intermediate in the ubiquitin system. The results are discussed in relation to the mechanism and evolution of the eukaryotic ubiquitin system.

Post-translational modifications in the active site region of methyl-coenzyme M reductase from methanogenic and methanotrophic archaea

Methyl-coenzyme M reductase (MCR) catalyzes the methane-forming step in methanogenic archaea. Isoenzyme I from Methanothermobacter marburgensiswas shown to contain a thioxo peptide bond and four methylated amino acids in the active site region. We report here that MCRs from all methanogens investigated contain the thioxo peptide bond, but that the enzymes differ in their post-translational methylations. The MS analysis included MCR I and MCR II from Methanothermobacter marburgensis, MCR I from Methanocaldococcus jannaschii and Methanoculleus thermophilus, and MCR from Methanococcus voltae, Methanopyrus kandleri and Methanosarcina barkeri. Two MCRs isolated from Black Sea mats containing mainly methanotrophic archaea of the ANME-1 cluster were also analyzed.

Siderophores in fluorescent pseudomonads: new tricks from an old dog

Iron is an essential nutrient for almost all bacteria; however, at neutral pH its bioavailability is limited. Siderophores are iron-binding compounds of low molecular weight that enable the microorganisms that produce them to obtain the necessary iron from the environment. Fluorescent pseudomonads include those that are plant growth promoting, human and plant pathogens, as well as bacteria involved in the biodegradation of xenobiotics. Although pyoverdine is the main siderophore produced by different fluorescent pseudomonads, other siderophores produced by fluorescent pseudomonads include pyochelin, (thio)quinolobactin and pyridine-2, 6-bis thiocarboxylic acid. Research on siderophores continues to reveal new information on their regulation, biosynthesis, function and properties. In this review, we focus on recent advances in the field, particularly on newly characterized siderophores produced by fluorescent pseudomonads and their biotechnological potential.

Identification and characterization of Pseudomonas membrane transporters necessary for utilization of the siderophore pyridine-2,6-bis(thiocarboxylic acid) (PDTC)

The compound pyridine-2,6-bis(thiocarboxylic acid) (PDTC) is known to be produced and excreted by three strains of Pseudomonas. Its reactivity includes the complete dechlorination of the environmental contaminant carbon tetrachloride. PDTC functions as a siderophore; however, roles as a ferric reductant and antimicrobial agent have also been proposed. PDTC function and regulation were further explored by characterizing the phenotypes of mutants in predicted membrane transporter genes. The functions of a predicted outer-membrane transporter (PdtK) and a predicted inner-membrane permease (PdtE) were examined in Pseudomonas putida DSM 3601. Uptake of iron from (55)Fe(III):PDTC, and bioutilization of PDTC in a chelated medium, were dependent upon PdtK and PdtE. Another strain of P. putida (KT2440), which lacks pdt orthologues, showed growth inhibition by PDTC that could be relieved by introducing a plasmid containing pdtKCPE. Transcriptional activation in response to exogenously added PDTC (25 muM) was unaltered by the pdtK or pdtE mutations; each mutant showed activation of a pdt transcriptional reporter, indistinguishable from an isogenic PDTC utilization-proficient strain. The data demonstrate that PdtK and PdtE constitute a bipartite outer-membrane/inner-membrane transport system for iron acquisition from Fe(III):PDTC. Disruptions in this portion of the P. putida DSM 3601 pdt gene cluster do not abolish PDTC-dependent transcriptional signalling.

Identification of siderophores ofPseudomonas stutzeri

We have identified two types of siderophores produced by Pseudomonas, one of which has never before been found in the genus. Twelve strains of Pseudomonas stutzeri belonging to genomovars 1, 2, 3, 4, 5, and 9 produced proferrioxamines, the hydroxamate-type siderophores. Pseudomonas stutzeri JM 300 (genomovar 7) and DSM 50238 (genomovar 8) and Pseudomonas balearica DSM 6082 produced amonabactins, catecholate-type siderophores. The major proferrioxamines detected were the cyclic proferrioxamines E and D2. Pseudomonas stutzeri KC also produced cyclic (X1and X2) and linear (G1and G2a-c) proferrioxamines. Our data indicate that the catecholate-type siderophores belong to amonabactins P 750, P 693, T 789, and T 732. A mutant of P. stutzeri KC (strain CTN1) that no longer produced the secondary siderophore pyridine-2,6-dithiocarboxylic acid continued to produce all other siderophores in its normal spectrum. Siderophore profiles suggest that strain KC (genomovar 9) belongs to the proferrioxamine-producing P. stuzeri. Moreover, a putative ferrioxamine outer membrane receptor gene foxA was identified in strain KC, and colony hybridization showed the presence of homologous receptor genes in all P. stutzeri and P. balearica strains tested.Key words: siderophore, Pseudomonas stutzeri, ferrioxamine, amonabactin.

Enzymatic activation of sulfur for incorporation into biomolecules in prokaryotes

Sulfur is a functionally important element of living matter. Incorporation into biomolecules occurs by two basic strategies. Sulfide is added to an activated acceptor in the biosynthesis of cysteine, from which methionine, coenzyme A and a number of biologically important thiols can be constructed. By contrast, the biosyntheses of iron sulfur clusters, cofactors such as thiamin, molybdopterin, biotin and lipoic acid, and the thio modification of tRNA require an activated sulfur species termed persulfidic sulfur (R-S-SH) instead of sulfide. Persulfidic sulfur is produced enzymatically with the IscS protein, the SufS protein and rhodanese being the most prominent biocatalysts. This review gives an overview of sulfur incorporation into biomolecules in prokaryotes with a special emphasis on the properties and the enzymatic generation of persulfidic sulfur as well as its use in biosynthetic pathways.

The role of the siderophore pyridine-2,6-bis (thiocarboxylic acid) (PDTC) in zinc utilization by Pseudomonas putida DSM 3601

Previous work had suggested that in addition to serving the function of a siderophore, pyridine-2,6-bis(thiocarboxylic acid) (PDTC) may also provide producing organisms with the ability to assimilate other divalent transition metals. This was tested further by examining regulation of siderophore production, expression of pdt genes, and growth in response to added zinc. In media containing 10-50 microM ZnCl2, the production of PDTC was found to be differentially repressed, as compared with the production of pyoverdine. The expression of PdtK, the outer membrane receptor involved in PDTC transport, was also reduced in response to added zinc whereas other iron-regulated outer membrane proteins were not. Expression of a chromosomal pdtI: xylE fusion was repressed to a similar extent in response to zinc or iron. Mutants that cannot produce PDTC did not show a growth enhancement with micromolar concentrations of zinc as seen in the wild type strain. The phenotype of the mutant strains was suppressed by the addition of PDTC. The outer membrane receptor and inner membrane permease components of PDTC utilization were necessary for relief of chelator (1,10-phenanthroline)-induced growth inhibition by Zn:PDTC. Iron uptake from 55Fe:PDTC was not affected by a 32-fold molar excess of Zn:PDTC. The data indicate that zinc present as Zn:PDTC can be utilized by strains possessing PDTC utilization functions but that transport is much less efficient than for Fe:PDTC.

Transcriptional regulation of the pdt gene cluster of Pseudomonas stutzeri KC involves an AraC/XylS family transcriptional activator (PdtC) and the cognate siderophore pyridine-2,6-bis(thiocarboxylic acid)

In order to gain an understanding of the molecular mechanisms dictating production of the siderophore and dechlorination agent pyridine-2,6-bis(thiocarboxylic acid) (PDTC), we have begun characterization of a gene found in the pdt gene cluster of Pseudomonas stutzeri KC predicted to have a regulatory role. That gene product is an AraC family transcriptional activator, PdtC. Quantitative reverse transcription-PCR and expression of transcriptional reporter fusions were used to assess a role for pdtC in the transcription of pdt genes. PdtC and an upstream, promoter-proximal DNA segment were required for wild-type levels of expression from the promoter of a predicted biosynthesis operon (P(pdtF)). At least two other transcriptional units within the pdt cluster were also dependent upon pdtC for expression at wild-type levels. The use of a heterologous, Pseudomonas putida host demonstrated that pdtC and an exogenously added siderophore were necessary and sufficient for expression from the pdtF promoter, i.e., none of the PDTC utilization genes within the pdt cluster were required for transcriptional signaling. Tests using the promoter of the pdtC gene in transcriptional reporter fusions indicated siderophore-dependent negative autoregulation similar to that seen with other AraC-type regulators of siderophore biosynthesis and utilization genes. The data increase the repertoire of siderophore systems known to be regulated by this type of transcriptional activator and have implications for PDTC signaling.

Pyridine-2,6-bis(thiocarboxylic acid) Produced by Pseudomonas stutzeri KC Reduces Chromium(VI) and Precipitates Mercury, Cadmium, Lead and Arsenic

Interactions of the Pseudomonas stutzeri KC siderophore pyridine-2,6-bis(thiocarboxylic acid) (pdtc) with chromium(VI), mercury(II), cadmium(II), lead(II), and arsenic(III) are described. Pdtc was found to reduce Cr(VI) to Cr(III) in both bacterial cultures and in abiotic reactions with chemically synthesized pdtc. Cr(III) subsequently formed complexes with pdtc and pdtc hydrolysis products, and their presence was confirmed using electrospray ionization-mass spectrometry (ESI-MS). Cr(III):pdtc complexes were found to slowly release Cr(III) as chromium sulfide and possibly Cr(III) oxides. Pdtc also formed poorly soluble complexes with Hg, Cd, Pb, and As(III). Hydrolysis of those complexes led to the formation of their respective metal sulfides as confirmed by energy dispersive X-ray spectroscopy (EDS) elemental analysis. The pdtc-producing strain P. stutzeri KC showed higher tolerance to most of these metals as compared to a pdtc-negative mutant. A novel role of pdtc is postulated as its involvement in providing an extracellular pool of thiols that are used for redox processes in detoxification of the bacterial extracellular environment. These redox processes can be mediated by transition metal:pdtc complexes.

Pyridine-2,6-bis(thiocarboxylic acid) produced by Pseudomonas stutzeri KC reduces and precipitates selenium and tellurium oxyanions

The siderophore of Pseudomonas stutzeri KC, pyridine-2,6-bis(thiocarboxylic acid) (pdtc), is shown to detoxify selenium and tellurium oxyanions in bacterial cultures. A mechanism for pdtc's detoxification of tellurite and selenite is proposed. The mechanism is based upon determination using mass spectrometry and energy-dispersive X-ray spectrometry of the chemical structures of compounds formed during initial reactions of tellurite and selenite with pdtc. Selenite and tellurite are reduced by pdtc or its hydrolysis product H(2)S, forming zero-valent pdtc selenides and pdtc tellurides that precipitate from solution. These insoluble compounds then hydrolyze, releasing nanometer-sized particles of elemental selenium or tellurium. Electron microscopy studies showed both extracellular precipitation and internal deposition of these metalloids by bacterial cells. The precipitates formed with synthetic pdtc were similar to those formed in pdtc-producing cultures of P. stutzeri KC. Culture filtrates of P. stutzeri KC containing pdtc were also active in removing selenite and precipitating elemental selenium and tellurium. The pdtc-producing wild-type strain KC conferred higher tolerance against selenite and tellurite toxicity than a pdtc-negative mutant strain, CTN1. These observations support the hypothesis that pdtc not only functions as a siderophore but also is involved in an initial line of defense against toxicity from various metals and metalloids.

Biology of Pseudomonas stutzeri

Pseudomonas stutzeri is a nonfluorescent denitrifying bacterium widely distributed in the environment, and it has also been isolated as an opportunistic pathogen from humans. Over the past 15 years, much progress has been made in elucidating the taxonomy of this diverse taxonomical group, demonstrating the clonality of its populations. The species has received much attention because of its particular metabolic properties: it has been proposed as a model organism for denitrification studies; many strains have natural transformation properties, making it relevant for study of the transfer of genes in the environment; several strains are able to fix dinitrogen; and others participate in the degradation of pollutants or interact with toxic metals. This review considers the history of the discovery, nomenclatural changes, and early studies, together with the relevant biological and ecological properties, of P. stutzeri.

Reconstitution of a new cysteine biosynthetic pathway in Mycobacterium tuberculosis

A new pathway for cysteine biosynthesis has been elucidated in Mycobacterium tuberculosis. This pathway involves a protein-bound thiocarboxylate (CysO-SH) as the sulfide donor, similar to thiamin biosynthesis. Cysteine synthase M (CysM) catalyzes the addition of cysteine to the carboxy terminus of the protein-bound thiocarboxylate to generate a CysO-cysteine adduct. A protease, Mec+, hydrolyzes the CysO-cysteine adduct to release cysteine and regenerate CysO. Mec+ contains a JAMM motif, and this work provides the first functional characterization of the JAMM motif in prokaryotes. MoeZ, a paralogue of ThiF, has been shown to transfer sulfur onto CysO.

The Serratia gene cluster encoding biosynthesis of the red antibiotic, prodigiosin, shows species- and strain-dependent genome context variation

The prodigiosin biosynthesis gene cluster (pig cluster) from two strains of Serratia (S. marcescens ATCC 274 and Serratia sp. ATCC 39006) has been cloned, sequenced and expressed in heterologous hosts. Sequence analysis of the respective pig clusters revealed 14 ORFs in S. marcescens ATCC 274 and 15 ORFs in Serratia sp. ATCC 39006. In each Serratia species, predicted gene products showed similarity to polyketide synthases (PKSs), non-ribosomal peptide synthases (NRPSs) and the Red proteins of Streptomyces coelicolor A3(2). Comparisons between the two Serratia pig clusters and the red cluster from Str. coelicolor A3(2) revealed some important differences. A modified scheme for the biosynthesis of prodigiosin, based on the pathway recently suggested for the synthesis of undecylprodigiosin, is proposed. The distribution of the pig cluster within several Serratia sp. isolates is demonstrated and the presence of cryptic clusters in some strains shown. The pig cluster of Serratia marcescens ATCC 274 is flanked by cueR and copA homologues and this configuration is demonstrated in several S. marcescens strains, whilst these genes are contiguous in strains lacking the pig cluster.

The Pseudomonas siderophore quinolobactin is synthesized from xanthurenic acid, an intermediate of the kynurenine pathway

To cope with iron deficiency fluorescent pseudomonads produce pyoverdines which are complex peptidic siderophores that very efficiently scavenge iron. In addition to pyoverdine some species also produce other siderophores. Recently, it was shown that Pseudomonas fluorescens ATCC 17400 produces the siderophore quinolobactin, an 8-hydroxy-4-methoxy-2-quinoline carboxylic acid (Mossialos, D., Meyer, J.M., Budzikiewicz, H., Wolff, U., Koedam, N., Baysse, C., Anjaiah, V., and Cornelis, P. (2000) Appl Environ Microbiol 66: 487-492). The entire quinolobactin biosynthetic, transport and uptake gene cluster, consisting out of two operons comprising 12 open reading frames, was cloned and sequenced. Based on the genes present and physiological complementation assays a biosynthetic pathway for quinolobactin is proposed. Surprisingly, this pathway turned out to combine genes derived from the eukaryotic tryptophan-xanthurenic acid branch of the kynurenine pathway and from the pathway for the biosynthesis of pyridine-2,6-bis(thiocarboxylic acid) from P. stutzeri, PDTC. These results clearly show the involvement of the tryptophan-kynurenine-xanthurenic acid pathway in the synthesis of an authentic quinoline siderophore.

Physiological and molecular genetic evaluation of the dechlorination agent, pyridine-2,6-bis(monothiocarboxylic acid) (PDTC) as a secondary siderophore of Pseudomonas

The bacterial metabolite and transition metal chelator pyridine-2,6-dithiocarboxylic acid (PDTC), promotes a novel and effective means of dechlorination of the toxic and carcinogenic pollutant, carbon tetrachloride. Pyridine-2,6-dithiocarboxylic acid has been presumed to act as a siderophore in the Pseudomonas strains known to produce it. To explore further the physiological function of PDTC production, we have examined its regulation, the phenotype of PDTC-negative (pdt) mutants, and envelope proteins associated with PDTC in P. putida strain DSM 3601. Aspects of the regulation of PDTC production and outer membrane protein composition were consistent with siderophore function. Pyridine-2,6-dithiocarboxylic acid production was coordinated with production of the well-characterized siderophore pyoverdine; exogenously added pyoverdine led to decreased PDTC production, and added PDTC led to decreased pyoverdine production. Positive regulation of a chromosomal pdtI-xylE transcriptional fusion, and of a 66 kDa outer membrane protein (IROMP), was seen in response to exogenous PDTC. Tests with transition metal chelators indicated that PDTC could provide a benefit under conditions of metal limitation; the loss of PDTC biosynthetic capacity caused by a pdtI transposon insertion resulted in increased sensitivity to 1,10-phenanthroline, a chelator that has high affinity for a range of divalent transition metals (e.g. Fe(2+), Cu(2+), Zn(2+)). Exogenously added PDTC could also suppress a phenotype of pyoverdine-negative (Pvd-) mutants, that of sensitivity to EDDHA, a chelator with higher affinity and specificity for Fe(3+). Measurement of 59Fe incorporation showed uptake from 59Fe:PDTC by DSM 3601 grown in low-iron medium, but not by cells grown in high iron medium, or by the pdtI mutant, which did not show expression of the 66 kDa envelope protein. These data verified a siderophore function for PDTC, and have implicated it in the uptake of transition metals in addition to iron.

Customized cDNA microarray for expression profiling of environmentally important genes of Pseudomonas stutzeri strain KC

DNA microarray is a powerful tool for parallel detection of multiple target genes in biological systems. In this study, a low-density DNA microarray has been custom designed by using Pseudomonas stutzeri strain KC ORFs that are implicated in carbon tetrachloride degradation. PCR amplified strain KC probes of varying lengths were obtained using ORF-specific primers. Purified short probes (80-120 bp) and full-length amplicons were directly immobilized on gamma-aminosilane coated and superaldehyde trade mark glass substrates without any chemical modification. The full-length amplicons exhibited a much higher signal compared to the shorter probes upon hybridization with the Cy5/Cy3-labeled unfragmented cDNA targets. The meager signal with the shorter probes limits the advantage of using the multiple probes of the same genes for enhancing the specificity of hybridization with environmental samples. Nevertheless, expression analysis of strain KC genome, under controlled laboratory conditions, revealed the constitutive expression of at least 11 putative ORFs of the pdt operon. Comparatively weaker hybridization signals with the cDNA from mutant cells suggested a low abundance of mRNA transcripts in the KC 1896 mutant. Similar expression levels of the pdt ORFs I, J, K, M, N, O, P, and fur gene both under iron-limiting conditions and in presence of iron (20 micro M Fe(3+)) suggested metal ion-independent regulation of the pdt operon. The tailor-made array with strain KC gene-specific probes served as a model for demonstrating the utility of cDNA microarray technology in monitoring the expression of environmentally important genes in bacteria.

Diversity of siderophore-mediated iron uptake systems in fluorescent pseudomonads: not only pyoverdines

Fluorescent pseudomonads are gamma-proteobacteria known for their capacity to colonize various ecological niches. This adaptability is reflected by their sophisticated and diverse iron uptake systems. The majority of fluorescent pseudomonads produce complex peptidic siderophores called pyoverdines or pseudobactins, which are very efficient iron scavengers. A tremendous variety of pyoverdines has been observed, each species producing a different pyoverdine. This variety can be used as an interesting tool to study the diversity and taxonomy of fluorescent pseudomonads. Other siderophores, including newly described ones, are also produced by pseudomonads, sometimes endowed with interesting properties in addition to iron scavenging, such as formation of complexes with other metals or antimicrobial activity. Factors other than iron limitation, and different regulatory proteins also seem to influence the production of siderophores in pseudomonads and are reviewed here as well. Another peculiarity of pseudomonads is their ability to use a large number of heterologous siderophores via different TonB-dependent receptors. A first genomic analysis of receptors in four different fluorescent pseudomonads suggests that their siderophore ligand repertoire is likely to overlap, and that not all receptors recognize siderophores as ligands.

Structural, functional, and evolutionary analysis of moeZ, a gene encoding an enzyme required for the synthesis of the Pseudomonas metabolite, pyridine-2,6-bis(thiocarboxylic acid)

BACKGROUND

Pyridine-2,6-bis(thiocarboxylic acid) (pdtc) is a small secreted metabolite that has a high affinity for transition metals, increases iron uptake efficiency by 20% in Pseudomonas stutzeri, has the ability to reduce both soluble and mineral forms of iron, and has antimicrobial activity towards several species of bacteria. Six GenBank sequences code for proteins similar in structure to MoeZ, a P. stutzeri protein necessary for the synthesis of pdtc.

RESULTS

Analysis of sequences similar to P. stutzeri MoeZ revealed that it is a member of a superfamily consisting of related but structurally distinct proteins that are members of pathways involved in the transfer of sulfur-containing moieties to metabolites. Members of this family of enzymes are referred to here as MoeB, MoeBR, MoeZ, and MoeZdR. MoeB, the molybdopterin synthase activating enzyme in the molybdopterin cofactor biosynthesis pathway, is the most characterized protein from this family. Remarkably, lengths of greater than 73% nucleic acid homology ranging from 35 to 486 bp exist between Pseudomonas stutzeri moeZ and genomic sequences found in some Mycobacterium, Mesorhizobium, Pseudomonas, Streptomyces, and cyanobacteria species.

CONCLUSIONS

The phylogenetic relationship among moeZ sequences suggests that P. stutzeri may have acquired moeZ through lateral gene transfer from a donor more closely related to mycobacteria and cyanobacteria than to proteobacteria. The importance of this relationship lies in the fact that pdtc, the product of the P. stutzeri pathway that includes moeZ, has an impressive set of capabilities, some of which could make it a potent pathogenicity factor.

Antimicrobial properties of pyridine-2,6-dithiocarboxylic acid, a metal chelator produced by Pseudomonas spp

Pyridine-2,6-dithiocarboxylic acid (pdtc) is a metal chelator produced by Pseudomonas spp. It has been shown to be involved in the biodegradation of carbon tetrachloride; however, little is known about its biological function. In this study, we examined the antimicrobial properties of pdtc and the mechanism of its antibiotic activity. The growth of Pseudomonas stutzeri strain KC, a pdtc-producing strain, was significantly enhanced by 32 microM pdtc. All nonpseudomonads and two strains of P. stutzeri were sensitive to 16 to 32 microM pdtc. In general, fluorescent pseudomonads were resistant to all concentrations tested. In competition experiments, strain KC demonstrated antagonism toward Escherichia coli. This effect was partially alleviated by 100 microM FeCl3. Less antagonism was observed in mutant derivatives of strain KC (CTN1 and KC657) which lack the ability to produce pdtc. A competitive advantage was restored to strain CTN1 by cosmid pT31, which restores pdtc production. pT31 also enhanced the pdtc resistance of all pdtc-sensitive strains, indicating that this plasmid contains elements responsible for resistance to pdtc. The antimicrobial effect of pdtc was reduced by the addition of Fe(III), Co(III), and Cu(II) and enhanced by Zn(II). Analyses by mass spectrometry determined that Cu(I):pdtc and Co(III):pdtc2 form immediately under our experimental conditions. Our results suggest that pdtc is an antagonist and that metal sequestration is the primary mechanism of its antimicrobial activity. It is also possible that Zn(II), if present, may play a role in pdtc toxicity.

Carbon tetrachloride dechlorination by the bacterial transition metal chelator pyridine-2,6-bis(thiocarboxylic acid)

A reaction pathway is proposed to explain the formation of end products during defined chemical reactions between carbon tetrachloride (CCl4) and either metal complexes of pyridine-2,6-bis(thiocarboxylic acid) (PDTC) or pure cultures of Pseudomonas stutzeri KC. The pathway includes one-electron reduction of CCl4 by the Cu(II):PDTC complex, condensation of trichloromethyl and thiyl radicals, and hydrolysis of a labile thioester intermediate. Products detected were carbon dioxide, chloride, carbonyl sulfide, carbon disulfide, and dipicolinic acid. Spin-trapping and electrospray MS/MS experiments gave evidence of trichloromethyl and thiyl radicals generated by reaction of CCl4 with PDTC and copper. Experiments testing the effects of transition metals showed that dechlorination by PDTC requires copper and is inhibited by cobalt but not by iron or nickel. PDTC was shown to react stoichiometrically rather than catalytically without added reducing equivalents. With added reductants, an increased turnover was seen along with increased chloroform production.