The LysR-type regulator SftR is involved in soil survival and sulphate ester metabolism in Pseudomonas putida

Arbuscular Mycorrhiza Support Plant Sulfur Supply through Organosulfur Mobilizing Bacteria in the Hypho- and Rhizosphere

This study aimed to elucidate the role of bacteria colonising mycorrhizal hyphae in organically bound sulfur mobilisation, the dominant soil sulfur source that is not directly plant available. The effect of an intact mycorrhizal symbiosis with access to stable isotope organo-³⁴S enriched soils encased in 35 µm mesh cores was tested in microcosms with Agrostis stolonifera and Plantago lanceolata. Hyphae and associated soil were sampled from static mesh cores with mycorrhizal ingrowth and rotating mesh cores that exclude mycorrhizal ingrowth as well as corresponding rhizosphere soil, while plant shoots were analysed for ³⁴S uptake. Static cores increased uptake of ³⁴S at early stages of plant growth when sulfur demand appeared to be high and harboured significantly larger populations of sulfonate mobilising bacteria. Bacterial and fungal communities were significantly different in the hyphospheres of static cores when compared to rotating cores, not associated with plant hosts. Shifts in bacterial and fungal communities occurred not only in rotated cores but also in the rhizosphere. Arylsulfatase activity was significantly higher in the rhizosphere when cores stayed static, while atsA and asfA gene diversity was distinct in the microcosms with static and rotating cores. This study demonstrated that AM symbioses can promote organo-S mobilization and plant uptake through interactions with hyphospheric bacteria, enabling AM fungal ingrowth into static cores creating a positive feedback-loop, detectable in the microbial rhizosphere communities.

Comparison of bacterial diversity, root exudates and soil enzymatic activities in the rhizosphere of AVP1-transgenic and non-transgenic wheat (Triticum aestivum L.)

AIMS

Soil microbial communities are among the most diverse communities that might be affected due to transgenic crops. Therefore, risk assessment studies on transgenes are essentially required as any adverse effects may depend not only on the specific gene and crop involved but also on soil conditions.

METHODS AND RESULTS

The present study deals with the comparison of bacterial populations, root exudates, and activities of soil enzymes in non-transgenic and AVP1-transgenic wheat rhizosphere, overexpressing vacuolar H+pyrophosphatase for salinity and drought stress tolerance. Amounts of organic acids and sugars produced as root exudates and activities of dehydrogenase, phosphatase, and protease enzymes in soil solution showed no significant differences in AVP1-transgenic and non-transgenic wheat rhizosphere, except for urease and phenol oxidase activities. The higher copy number of nifH gene showed the abundance of nitrogen-fixing bacteria in the rhizosphere of AVP1-transgenic wheat compared with non-transgenic wheat. nifH gene sequence analysis indicated the common diazotrophic genera Azospirillum, Bradyrhizobium, Rhizobium, and Pseudomonas in AVP1-transgenic and non-transgenic wheat except for Zoogloea detected only in non-transgenic wheat. Using 454-pyrosequencing of 16S rRNA gene from soil DNA, a total of 156, 282 sequences of 18 phyla were obtained, which represented bacterial (128,006), Archeal (7,928), and unclassified (21,568) sequences. Proteobacteria, Crenarchaeota, and Firmicutes were the most abundant phyla in transgenic and non-transgenic wheat rhizosphere. Further comparison of different taxonomic units at the genus level showed similar distribution in transgenic and non-transgenic wheat rhizosphere.

CONCLUSION

We conclude that AVP1 gene in transgenic wheat has no apparent adverse effects on the soil environment and different bacterial communities. However, bacterial community depends on several other factors not only genetic composition of the host plants.

SIGNIFICANCE OF THE STUDY

The present research supports introduction and cultivation of transgenic plants in agricultural systems without any adverse effects on indigenous bacterial communities and soil ecosystem.

Complete Genome Sequence and Function Gene Identify of Prometryne-Degrading Strain Pseudomonas sp. DY-1

The genus Pseudomonas is widely recognized for its potential for environmental remediation and plant growth promotion. Pseudomonas sp. DY-1 was isolated from the agricultural soil contaminated five years by prometryne, it manifested an outstanding prometryne degradation efficiency and an untapped potential for plant resistance improvement. Thus, it is meaningful to comprehend the genetic background for strain DY-1. The whole genome sequence of this strain revealed a series of environment adaptive and plant beneficial genes which involved in environmental stress response, heavy metal or metalloid resistance, nitrate dissimilatory reduction, riboflavin synthesis, and iron acquisition. Detailed analyses presented the potential of strain DY-1 for degrading various organic compounds via a homogenized pathway or the protocatechuate and catechol branches of the β-ketoadipate pathway. In addition, heterologous expression, and high efficiency liquid chromatography (HPLC) confirmed that prometryne could be oxidized by a Baeyer-Villiger monooxygenase (BVMO) encoded by a gene in the chromosome of strain DY-1. The result of gene knock-out suggested that the sulfate starvation-induced (SSI) genes in this strain might also involve in the process of prometryne degradation. These results would provide the molecular basis for the application of strain DY-1 in various fields and would contribute to the study of prometryne biodegradation mechanism as well.

Genetic factors involved in rhizosphere colonization by phytobeneficial Pseudomonas spp

Plant growth-promoting rhizobacteria (PGPR) actively colonize the soil portion under the influence of plant roots, called the rhizosphere. Many plant-beneficial Pseudomonas spp. have been characterized as PGPR. They are ubiquitous rod-shaped motile Gram-negative bacteria displaying a high metabolic versatility. Their capacity to protect plants from pathogens and improve plant growth closely depends on their rhizosphere colonization abilities. Various molecular and cellular mechanisms are involved in this complex process, such as chemotaxis, biofilm formation, secondary metabolites biosynthesis, metabolic versatility, and evasion of plant immunity. The burst in Pseudomonas spp. genome sequencing in recent years has been crucial to better understand how they colonize the rhizosphere. In this review, we discuss the recent advances regarding these mechanisms and the underlying bacterial genetic factors required for successful rhizosphere colonization.

Linking Comparative Genomics of Nine Potato-Associated Pseudomonas Isolates With Their Differing Biocontrol Potential Against Late Blight

For plants, the advantages of associating with beneficial bacteria include plant growth promotion, reduction of abiotic and biotic stresses and enhanced protection against various pests and diseases. Beneficial bacteria rightly equipped for successful plant colonization and showing antagonistic activity toward plant pathogens seem to be actively recruited by plants. To gain more insights into the genetic determinants responsible for plant colonization and antagonistic activities, we first sequenced and de novo assembled the complete genomes of nine Pseudomonas strains that had exhibited varying antagonistic potential against the notorious oomycete Phytophthora infestans, placed them into the phylogenomic context of known Pseudomonas biocontrol strains and carried out a comparative genomic analysis to define core, accessory (i.e., genes found in two or more, but not all strains) and unique genes. Next, we assessed the colonizing abilities of these strains and used bioassays to characterize their inhibitory effects against different stages of P. infestans' lifecycle. The phenotype data were then correlated with genotype information, assessing over three hundred genes encoding known factors for plant colonization and antimicrobial activity as well as secondary metabolite biosynthesis clusters predicted by antiSMASH. All strains harbored genes required for successful plant colonization but also distinct arsenals of antimicrobial compounds. We identified genes coding for phenazine, hydrogen cyanide, 2-hexyl, 5-propyl resorcinol and pyrrolnitrin synthesis, as well as various siderophores, pyocins and type VI secretion systems. Additionally, the comparative genomic analysis revealed about a hundred accessory genes putatively involved in anti-Phytophthora activity, including a type II secretion system (T2SS), several peptidases and a toxin. Transcriptomic studies and mutagenesis are needed to further investigate the putative involvement of the novel candidate genes and to identify the various mechanisms involved in the inhibition of P. infestans by different Pseudomonas strains.

Genome-wide mining of potential virulence-associated genes in Riemerella anatipestifer using random transposon mutagenesis

Riemerella anatipestifer infection is a severe disease confronting the duck industry worldwide. However, little is known about the molecular basis of R. anatipestifer pathogenesis. In this study, we screened 3580 transposon Tn4351 insertion mutagenesis mutants of the highly virulent strain YZb1 in a duckling infection experiment and found 29 of them to be attenuated and 28 potential virulence-associated genes were identified. Molecular characterization of transposon insertion sites showed that of the 28 screened genes, two were predicted to encode TonB-dependent outer membrane receptor (plugs), sixteen encoded enzymes, and seven encoded hypothetical proteins. In addition, of the 28 affected genes, 19 were only found in bacteria belonging to the phylum Bacteroidetes and 10 were only found in the family Flavobacteriaceae. The median lethal dose of the mutants M11 and M29, which was affected in Riean_0060 and Riean_1537 respectively, were about 1700-fold and 210-fold higher than that of the wild-type strain YZb1, and those of the complemented strains M11(pRES-Riean_0060) and M29(pRES-Riean_1537) were decreased by 25- and 3-fold respectively compared to those of the mutants M11 and M29. Additional analysis indicated that the blood bacterial loading of ducklings infected with M11 or M29 was decreased significantly, as compared with that in ducklings infected with the wild-type strain YZb1. Thus, our results indicate that Riean_0060 and Riean_1537 were involved in R. anatipestifer pathogenesis.

Comparative proteomic analysis reveals mechanistic insights into Pseudomonas putida F1 growth on benzoate and citrate

Pseudomonas species are capable to proliferate under diverse environmental conditions and thus have a significant bioremediation potential. To enhance our understanding of their metabolic versatility, this study explores the changes in the proteome and physiology of Pseudomonas putida F1 resulting from its growth on benzoate, a moderate toxic compound that can be catabolized, and citrate, a carbon source that is assimilated through central metabolic pathways. A series of repetitive batch cultivations were performed to ensure a complete adaptation of the bacteria to each of these contrasting carbon sources. After several growth cycles, cell growth stabilized at the maximum level and exhibited a reproducible growth profile. The specific growth rates measured for benzoate (1.01 ± 0.11 h-1) and citrate (1.11 ± 0.12 h-1) were similar, while a higher yield was observed for benzoate (0.6 and 0.3 g cell mass per g of benzoate and citrate, respectively), reflecting the different degrees of carbon reduction in the two substrates. Comparative proteomic analysis revealed an enrichment of several oxygenases/dehydrogenases in benzoate-grown cells, indicative of the higher carbon reduction of benzoate. Moreover, the upregulation of all 14 proteins implicated in benzoate degradation via the catechol ortho-cleavage pathway was observed, while several stress-response proteins were increased to aid cells to cope with benzoate toxicity. Unexpectedly, citrate posed more challenges than benzoate in the maintenance of pH homeostasis, as indicated by the enhancement of the Na+/H+ antiporter and carbonic anhydrase. The study provides important mechanistic insights into Pseudomonas adaptation to varying carbon sources that are of great relevance to bioremediation efforts.

TonB-dependent outer-membrane proteins and siderophore utilization in Pseudomonas fluorescens Pf-5

The soil bacterium Pseudomonas fluorescens Pf-5 produces two siderophores, a pyoverdine and enantio-pyochelin, and its proteome includes 45 TonB-dependent outer-membrane proteins, which commonly function in uptake of siderophores and other substrates from the environment. The 45 proteins share the conserved β-barrel and plug domains of TonB-dependent proteins but only 18 of them have an N-terminal signaling domain characteristic of TonB-dependent transducers (TBDTs), which participate in cell-surface signaling systems. Phylogenetic analyses of the 18 TBDTs and 27 TonB-dependent receptors (TBDRs), which lack the N-terminal signaling domain, suggest a complex evolutionary history including horizontal transfer among different microbial lineages. Putative functions were assigned to certain TBDRs and TBDTs in clades including well-characterized orthologs from other Pseudomonas spp. A mutant of Pf-5 with deletions in pyoverdine and enantio-pyochelin biosynthesis genes was constructed and characterized for iron-limited growth and utilization of a spectrum of siderophores. The mutant could utilize as iron sources a large number of pyoverdines with diverse structures as well as ferric citrate, heme, and the siderophores ferrichrome, ferrioxamine B, enterobactin, and aerobactin. The diversity and complexity of the TBDTs and TBDRs with roles in iron uptake clearly indicate the importance of iron in the fitness and survival of Pf-5 in the environment.

Transcription factors CysB and SfnR constitute the hierarchical regulatory system for the sulfate starvation response in Pseudomonas putida

Pseudomonas putida DS1 is able to utilize dimethyl sulfone as a sulfur source. Expression of the sfnFG operon responsible for dimethyl sulfone oxygenation is directly regulated by a sigma(54)-dependent transcriptional activator, SfnR, which is encoded within the sfnECR operon. We investigated the transcription mechanism for the sulfate starvation-induced expression of these sfn operons. Using an in vivo transcription assay and in vitro DNA-binding experiments, we revealed that SfnR negatively regulates the expression of sfnECR by binding to the downstream region of the transcription start point. Additionally, we demonstrated that a LysR-type transcriptional regulator, CysB, directly activates the expression of sfnECR by binding to its upstream region. CysB is a master regulator that controls the sulfate starvation response of the sfn operons, as is the case for the sulfonate utilization genes of Escherichia coli, although CysB(DS1) appeared to differ from that of E. coli CysB in terms of the effect of O-acetylserine on DNA-binding ability. Furthermore, we investigated what effector molecules repress the expression of sfnFG and sfnECR in vivo by using the disruptants of the sulfate assimilatory genes cysNC and cysI. The measurements of mRNA levels of the sfn operons in these gene disruptants suggested that the expression of sfnFG is repressed by sulfate itself while the expression of sfnECR is repressed by the downstream metabolites in the sulfate assimilatory pathway, such as sulfide and cysteine. These results indicate that SfnR plays a role independent of CysB in the sulfate starvation-induced expression of the sfn operons.

Transcriptional regulation of the sulfate-starvation-induced gene sfnA by a sigma54-dependent activator of Pseudomonas putida

The sigma(54)-dependent transcriptional regulator SfnR is essential for the use of dimethyl sulfone (DMSO(2)) as a sulfur source by Pseudomonas putida DS1. SfnR binds three SfnR-binding sites (sites 1, 2 and 3) within an intergenic region of the divergently transcribed sfnAB and sfnFG gene clusters. The site 1 region, proximal to the sfnF gene, is indispensable for the expression of the sfnFG operon, which encodes components of DMSO(2) monooxygenase. We investigated the transcriptional regulation of the sfnAB operon and possible functions of the sfnA gene. RT-PCR analysis revealed that the sfnAB gene cluster, which is similar to homologues of the acyl-CoA dehydrogenase family, was transcribed as an operon, and its expression was regulated by SfnR under conditions of sulfate starvation. Deletion analyses using lacZ as a reporter demonstrated that the region up to at least -138 bp from the transcription start point of sfnA (containing sites 2 and 3) was necessary for the expression of the sfnAB operon. A growth test of the sfnA-disrupted mutant revealed the possibility that sfnA may be involved in the use of methanethiol as a sulfur source.

Structure and conservation of a polyethylene glycol-degradative operon in sphingomonads

Sphingopyxis terrae, and Sphingopyxis macrogoltabida strains 103 and 203, can degrade polyethylene glycols (PEGs). They differ in the following respects: (i) different substrate specificities (chain length) of assimilable PEG, (ii) PEG-inducible or constitutive PEG-degradative proteins, and (iii) symbiotic or axenic degradation of PEG. S. terrae was able to incorporate PEG 6000, but strain 103 could not incorporate more than PEG 4000, suggesting that the difference in assimilable PEG chain length depends on the ability to take up substrate. PEG-degradative genes (pegB, C, D, A, E and R) from these strains were cloned. Their primary structures shared a high homology of more than 99 %. The peg genes encode a TonB-dependent receptor (pegB), a PEG-aldehyde dehydrogenase (pegC), a permease (pegD), a PEG dehydrogenase (pegA) and an acyl-CoA ligase (pegE), and in the opposite orientation, an AraC-type transcription regulator (pegR). The peg operon was flanked by two different sets of transposases. These three strains contained large plasmids and the operon was located in one of the large plasmids in S. terrae. The peg genes could be detected in other PEG-degrading sphingomonads. These results suggest that the peg genes have evolved in a plasmid-mediated manner. An insertion of a transposon gene (pegF) between pegD and pegA in strain 203 was found, which caused the constitutive expression of pegA in this strain.

Uncoupling of choline-O-sulphate utilization from osmoprotection in Pseudomonas putida

The genomic context of the recognized bet genes for choline-O-sulphate (COS) utilization in Pseudomonas putida KT2440 is such that betC (choline sulphatase) lies adjacent to an ATP-binding cassette transporter and a LysR type regulator, but well away from betBA, encoding enzymes for transformation of choline into glycine betaine. The consequences of such genetic layout of the functions for COS metabolism have been examined with a suite of genetic and biochemical approaches. An early clue of the utilities of the betencoded products was exposed by the phenotypes of a betC deletion. This mutant still accumulated intact COS but failed to use this compound as carbon or nitrogen source. Furthermore, betC expression was downregulated at high salt concentrations, showing that the principal role of this gene lied in COS metabolism, not in osmoprotection. In contrast, the betBA genes were required for choline transformation into the highly effective compatible solute glycine betaine (and the concomitant endurance to high salt) and also for its utilization as carbon or nitrogen source. Thus, unlike in the cases of Bacillus subtilis and Sinorhizobium meliloti, betC is unrelated to osmoprotection in Pseudomonas putida while the betBA genes are required for both betaine synthesis and tolerance to high osmotic pressure.

The crystal structure of SdsA1, an alkylsulfatase from Pseudomonas aeruginosa, defines a third class of sulfatases

Pseudomonas aeruginosa is both a ubiquitous environmental bacterium and an opportunistic human pathogen. A remarkable metabolic versatility allows it to occupy a multitude of ecological niches, including wastewater treatment plants and such hostile environments as the human respiratory tract. P. aeruginosa is able to degrade and metabolize biocidic SDS, the detergent of most commercial personal hygiene products. We identify SdsA1 of P. aeruginosa as a secreted SDS hydrolase that allows the bacterium to use primary sulfates such as SDS as a sole carbon or sulfur source. Homologues of SdsA1 are found in many pathogenic and some nonpathogenic bacteria. The crystal structure of SdsA1 reveals three distinct domains. The N-terminal catalytic domain with a binuclear Zn2+ cluster is a distinct member of the metallo-beta-lactamase fold family, the central dimerization domain ensures resistance to high concentrations of SDS, whereas the C-terminal domain provides a hydrophobic groove, presumably to recruit long aliphatic substrates. Crystal structures of apo-SdsA1 and complexes with substrate analog and products indicate an enzymatic mechanism involving a water molecule indirectly activated by the Zn2+ cluster. The enzyme SdsA1 thus represents a previously undescribed class of sulfatases that allows P. aeruginosa to survive and thrive under otherwise bacteriocidal conditions.

Regulation of the Bacillus subtilis ytmI operon, involved in sulfur metabolism

The YtlI regulator of Bacillus subtilis activates the transcription of the ytmI operon encoding an l-cystine ABC transporter, a riboflavin kinase, and proteins of unknown function. The expression of the ytlI gene and the ytmI operon was high with methionine and reduced with sulfate. Using deletions and site-directed mutagenesis, a cis-acting DNA sequence important for YtlI-dependent regulation was identified upstream from the -35 box of ytmI. Gel mobility shift assays confirmed that YtlI specifically interacted with this sequence. The replacement of the sulfur-regulated ytlI promoter by the xylA promoter led to constitutive expression of a ytmI'-lacZ fusion in a ytlI mutant, suggesting that the repression of ytmI expression by sulfate was mainly at the level of YtlI synthesis. We further showed that the YrzC regulator negatively controlled ytlI expression while this repressor also acted on ytmI expression via YtlI. The cascade of regulation observed in B. subtilis is conserved in Listeria spp. Both a YtlI-like regulator and a ytmI-type operon are present in Listeria spp. Indeed, the Lmo2352 protein from Listeria monocytogenes was able to replace YtlI for the activation of ytmI expression and a lmo2352'-lacZ fusion was repressed in the presence of sulfate via YrzC in B. subtilis. A common motif, AT(A/T)ATTCCTAT, was found in the promoter region of the ytlI and lmo2352 genes. Deletion of part of this motif or the introduction of point mutations in this sequence confirmed its involvement in ytlI regulation.

Importance of organosulfur utilization for survival of Pseudomonas putida in soil and rhizosphere

The sulfur present in both agricultural and uncultivated soils is largely in the form of sulfonates and sulfate esters and not as free, bioavailable inorganic sulfate. Desulfurization of the former compounds in vitro has previously been studied in Pseudomonas putida, a common rhizosphere inhabitant. Survival of P. putida strains was now investigated in three sulfur-deficient Danish soils which were found to contain 60 to 70% of their sulfur in sulfonate or sulfate ester form, as determined by X-ray near-edge spectroscopy. The soil fitness of P. putida S-313 was compared with that of isogenic strains with mutations in the sftR and asfA genes (required for in vitro desulfurization of sulfate esters and arylsulfonates, respectively) and in the ssu locus (required in vitro for the desulfurization of both sulfonates and sulfate esters). asfA or sftR mutants showed significantly reduced survival compared to the parent strain in bulk soil that had been enriched with carbon and nitrogen to mimic rhizosphere conditions, but this reduced survival was not observed in the absence of these additives. In a tomato rhizosphere grown in compost, survival of sftR and ssu mutants was reduced relative to the parent strain. The results demonstrate that the ability to desulfurize sulfonates and sulfate esters is critical for survival of bacteria in the rhizosphere but less so in bulk soils outside the influence of plant roots, where carbon is the limiting nutrient for growth.

The sigma54-dependent transcriptional activator SfnR regulates the expression of the Pseudomonas putida sfnFG operon responsible for dimethyl sulphone utilization

Pseudomonas putida DS1 is able to utilize dimethyl sulphide through dimethyl sulphoxide, dimethyl sulphone (DMSO2), methanesulphonate (MSA) and sulphite as a sulphur source. We previously demonstrated that sfnR encoding a sigma54-dependent transcriptional regulator is essential for DMSO2 utilization by P. putida DS1. To identify the target genes of SfnR, we carried out transposon mutagenesis on an sfnR disruptant (DMSO2-utilization-defective phenotype) using mini-Tn5, which contains two outward-facing constitutively active promoters; as a result, we obtained a mutant that restored the ability to utilize DMSO2. The DMSO2-positive mutant carried a mini-Tn5 insertion in the intergenic region between two opposite-facing operons, sfnAB and sfnFG. Both sfnA and sfnB products were similar to acyl-CoA dehydrogenase family proteins, whereas sfnF and sfnG encoded a putative NADH-dependent FMN reductase (SfnF) and an FMNH2-dependent monooxygenase (SfnG). Disruption and complementation of the sfn genes indicated that the sfnG product is essential for DMSO2 utilization by P. putida DS1. Furthermore, an enzyme assay demonstrated that SfnG is an FMNH2-dependent DMSO2 monooxygenase that converts DMSO2 to MSA. It was revealed that the expression of the sfnFG operon is directly activated by the binding of SfnR at its upstream region. Site-directed mutagenesis of the SfnR binding sequences allowed us to define a potential recognition sequence for SfnR. These results provided insight into regulation of sulphate starvation-induced genes in bacteria.

Real-time reverse transcription PCR analysis of expression of atrazine catabolism genes in two bacterial strains isolated from soil

The level of expression of highly conserved, plasmid-borne, and widely dispersed atrazine catabolic genes (atz) was studied by RT-qPCR in two telluric atrazine-degrading microbes. RT-qPCR assays, based on the use of real-time PCR, were developed in order to quantify atzABCDEF mRNAs in Pseudomonas sp. ADP and atzABC mRNAs in Chelatobacter heintzii. atz gene expression was expressed as mRNA copy number per 10(6) 16S rRNA. In Pseudomonas sp. ADP, atz genes were basally expressed. It confirmed atrazine-degrading kinetics indicating that catabolic activity starts immediately after adding the herbicide. atz gene expression increased transitorily in response to atrazine treatment. This increase was only observed while low amount of atrazine remained in the medium. In C. heintzii, only atzA was basally expressed. atzA and atzB expression levels were similarly and significantly increased in response to atrazine treatment. atzC was not expressed even in the presence of high amounts of atrazine. This study showed that atz genes are basally expressed and up-regulated in response to atrazine treatment. atz gene expression patterns are different in Pseudomonas ADP and C. heintzii suggesting that the host may influence the expression of plasmid-borne atrazine-catabolic potential.

A CysB-regulated and sigma54-dependent regulator, SfnR, is essential for dimethyl sulfone metabolism of Pseudomonas putida strain DS1

Pseudomonas putida strain DS1 utilizes dimethyl sulfide (DMS) as a sulfur source, and desulfurizes it via dimethyl sulfoxide (DMSO), dimethyl sulfone (DMSO(2)) and methanesulfonate (MSA). Its Tn5 mutant, Dfi74J, no longer utilized DMS, DMSO and DMSO(2), but could oxidize DMS to DMSO(2), suggesting that the conversion of DMSO(2) to MSA was interrupted in the mutant. Sequencing of the Tn5 flanking region of Dfi74J demonstrated that a gene, sfnR (designated for dimethyl sulfone utilization), encoding a transcriptional regulator containing an ATP-dependent sigma(54)-association domain and a DNA-binding domain, was disrupted. sfnR is part of an operon with two other genes, sfnE and sfnC, located immediately upstream of sfnR and in the same orientation. The genes encode NADH-dependent FMN reductase (SfnE) and FMNH(2)-dependent monooxygenase (SfnC). Complementation of Dfi74J with an sfnR-expressing plasmid led to restoration of its growth on DMS, DMSO and DMSO(2). An rpoN-defective mutant of strain DS1, which lacks the sigma(54) factor, grew on MSA, but not on DMS, DMSO and DMSO(2), indicating that SfnR controls expression of gene(s) involved in DMSO(2) metabolism by interaction with sigma(54)-RNA polymerase. Northern hybridization and a reporter gene assay with an sfn-lacZ transcriptional fusion elucidated that expression of the sfnECR operon was induced under sulfate limitation and was dependent on a LysR-type transcriptional regulator, CysB. This is believed to be the first report that a sigma(54)-dependent transcriptional regulator induced under sulfate limitation is involved in sulfur assimilation.

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.