The cyanotrophic bacterium Pseudomonas pseudoalcaligenes CECT5344 responds to cyanide by defence mechanisms against iron deprivation, oxidative damage and nitrogen stress

Role of the Dihydrodipicolinate Synthase DapA1 on Iron Homeostasis During Cyanide Assimilation by the Alkaliphilic Bacterium Pseudomonas pseudoalcaligenes CECT5344

Cyanide is a toxic compound widely used in mining and jewelry industries, as well as in the synthesis of many different chemicals. Cyanide toxicity derives from its high affinity for metals, which causes inhibition of relevant metalloenzymes. However, some cyanide-degrading microorganisms like the alkaliphilic bacterium Pseudomonas pseudoalcaligenes CECT5344 may detoxify hazardous industrial wastewaters that contain elevated cyanide and metal concentrations. Considering that iron availability is strongly reduced in the presence of cyanide, mechanisms for iron homeostasis should be required for cyanide biodegradation. Previous omic studies revealed that in the presence of a cyanide-containing jewelry residue the strain CECT5344 overproduced the dihydrodipicolinate synthase DapA1, a protein involved in lysine metabolism that also participates in the synthesis of dipicolinates, which are excellent metal chelators. In this work, a dapA1 ^- mutant of P. pseudoalcaligenes CECT5344 has been generated and characterized. This mutant showed reduced growth and cyanide consumption in media with the cyanide-containing wastewater. Intracellular levels of metals like iron, copper and zinc were increased in the dapA1 ^- mutant, especially in cells grown with the jewelry residue. In addition, a differential quantitative proteomic analysis by LC-MS/MS was carried out between the wild-type and the dapA1 ^- mutant strains in media with jewelry residue. The mutation in the dapA1 gene altered the expression of several proteins related to urea cycle and metabolism of arginine and other amino acids. Additionally, the dapA1 ^- mutant showed increased levels of the global nitrogen regulator PII and the glutamine synthetase. This proteomic study has also highlighted that the DapA1 protein is relevant for cyanide resistance, oxidative stress and iron homeostasis response, which is mediated by the ferric uptake regulator Fur. DapA1 is required to produce dipicolinates that could act as iron chelators, conferring protection against oxidative stress and allowing the regeneration of Fe-S centers to reactivate cyanide-damaged metalloproteins.

Assimilation of cyanide and cyano-derivatives by Pseudomonas pseudoalcaligenes CECT5344: from omic approaches to biotechnological applications

Mining, jewellery and metal-processing industries use cyanide for extracting gold and other valuable metals, generating large amounts of highly toxic wastewater. Biological treatments may be a clean alternative under the environmental point of view to the conventional physical or chemical processes used to remove cyanide and related compounds from these industrial effluents. Pseudomonas pseudoalcaligenes CECT5344 can grow under alkaline conditions using cyanide, cyanate or different nitriles as the sole nitrogen source, and is able to remove up to 12 mM total cyanide from a jewellery industry wastewater that contains cyanide free and complexed to metals. Complete genome sequencing of this bacterium has allowed the application of transcriptomic and proteomic techniques, providing a holistic view of the cyanide biodegradation process. The complex response to cyanide by the cyanotrophic bacterium P. pseudoalcaligenes CECT5344 and the potential biotechnological applications of this model organism in the bioremediation of cyanide-containing industrial residues are reviewed.

Detoxification of ferrocyanide in asoil-plant system

The detoxification of iron cyanide in a soil-plant system was investigated to assess the total cyanide extracted from contaminated soil and allocated in the leaf tissue of willow trees (Salix caprea). They were grown in soil containing up to 1000 mg/kg dry weight (dw) of cyanide (CN), added as ¹⁵N-labeled potassium ferrocyanide and prepared with a new method for synthesis of labeled iron cyanides. CN content and ¹⁵N enrichment were monitored weekly over the exposure in leaf tissue of different age. The ¹⁵N enrichment in the young and old leaf tissue reached up to 15.197‰ and 9063‰, respectively; it increased significantly over the exposure and with increasing exposure concentrations (p < 0.05). Although the CN accumulation in the old leaf tissue was higher, compared to the young leaf tissue (p < 0.05), the ¹⁵N enrichment in the two tissue types did not differ statistically. This indicates a non-uniform CN accumulation but a uniform ¹⁵N allocation throughout the leaf mass. Significant differences were detected between the measured CN content and the C¹⁵N content, calculated from the ¹⁵N enrichment (p < 0.05), revealing a significant CN fraction within the leaf tissue, which could not be detected as ionic CN. The application of labeled iron CN clearly shows that CN is detoxified during uptake by the willows. However, these results do not exclude other detoxification pathways, not related to the trees. Still, they are strongly indicative of the central role the trees played in CN removal and detoxification under the experimental conditions.

Transcriptional and translational adaptation to aerobic nitrate anabolism in the denitrifier Paracoccus denitrificans

Transcriptional adaptation to nitrate-dependent anabolism by Paracoccus denitrificans PD1222 was studied. A total of 74 genes were induced in cells grown with nitrate as N-source compared with ammonium, including nasTSABGHC and ntrBC genes. The nasT and nasS genes were cotranscribed, although nasT was more strongly induced by nitrate than nasS. The nasABGHC genes constituted a transcriptional unit, which is preceded by a non-coding region containing hairpin structures involved in transcription termination. The nasTS and nasABGHC transcripts were detected at similar levels with nitrate or glutamate as N-source, but nasABGHC transcript was undetectable in ammonium-grown cells. The nitrite reductase NasG subunit was detected by two-dimensional polyacrylamide gel electrophoresis in cytoplasmic fractions from nitrate-grown cells, but it was not observed when either ammonium or glutamate was used as the N-source. The nasT mutant lacked both nasABGHC transcript and nicotinamide adenine dinucleotide (NADH)-dependent nitrate reductase activity. On the contrary, the nasS mutant showed similar levels of the nasABGHC transcript to the wild-type strain and displayed NasG protein and NADH–nitrate reductase activity with all N-sources tested, except with ammonium. Ammonium repression of nasABGHC was dependent on the Ntr system. The ntrBC and ntrYX genes were expressed at low levels regardless of the nitrogen source supporting growth. Mutational analysis of the ntrBCYX genes indicated that while ntrBC genes are required for nitrate assimilation, ntrYX genes can only partially restore growth on nitrate in the absence of ntrBC genes. The existence of a regulation mechanism for nitrate assimilation in P. denitrificans, by which nitrate induction operates at both transcriptional and translational levels, is proposed.

Quantitative proteomic analysis of Pseudomonas pseudoalcaligenes CECT5344 in response to industrial cyanide-containing wastewaters using Liquid Chromatography-Mass Spectrometry/Mass Spectrometry (LC-MS/MS)

Biological treatments to degrade cyanide are a powerful technology for cyanide removal from industrial wastewaters. It has been previously demonstrated that the alkaliphilic bacterium Pseudomonas pseudoalcaligenes CECT5344 is able to use free cyanide and several metal−cyanide complexes as the sole nitrogen source. In this work, the strain CECT5344 has been used for detoxification of the different chemical forms of cyanide that are present in alkaline wastewaters from the jewelry industry. This liquid residue also contains large concentrations of metals like iron, copper and zinc, making this wastewater even more toxic. To elucidate the molecular mechanisms involved in the bioremediation process, a quantitative proteomic analysis by LC-MS/MS has been carried out in P. pseudoalcaligenes CECT5344 cells grown with the jewelry residue as sole nitrogen source. Different proteins related to cyanide and cyanate assimilation, as well as other proteins involved in transport and resistance to metals were induced by the cyanide-containing jewelry residue. GntR-like regulatory proteins were also induced by this industrial residue and mutational analysis revealed that GntR-like regulatory proteins may play a role in the regulation of cyanide assimilation in P. pseudoalcaligenes CECT5344. The strain CECT5344 has been used in a batch reactor to remove at pH 9 the different forms of cyanide present in industrial wastewaters from the jewelry industry (0.3 g/L, ca. 12 mM total cyanide, including both free cyanide and metal−cyanide complexes). This is the first report describing the biological removal at alkaline pH of such as elevated concentration of cyanide present in a heterogeneous mixture from an industrial source.

Biodegradation of cyanide wastes from mining and jewellery industries

Cyanide, one of the known most toxic chemicals, is widely used in mining and jewellery industries for gold extraction and recovery from crushed ores or electroplating residues. Cyanide toxicity occurs because this compound strongly binds to metals, inactivating metalloenzymes such as cytochrome c oxidase. Despite the toxicity of cyanide, cyanotrophic microorganisms such as the alkaliphilic bacterium Pseudomonas pseudoalcaligenes CECT5344 may use cyanide and its derivatives as a nitrogen source for growth, making biodegradation of cyanurated industrial waste possible. Genomic, transcriptomic and proteomic techniques applied to cyanide biodegradation ('cyan-omics') provide a holistic view that increases the global insights into the genetic background of cyanotrophic microorganisms that could be used for biodegradation of industrial cyanurated wastes and other biotechnological applications.

Deciphering Cyanide-Degrading Potential of Bacterial Community Associated with the Coking Wastewater Treatment Plant with a Novel Draft Genome

Biotreatment processes fed with coking wastewater often encounter insufficient removal of pollutants, such as ammonia, phenols, and polycyclic aromatic hydrocarbons (PAHs), especially for cyanides. However, only a limited number of bacterial species in pure cultures have been confirmed to metabolize cyanides, which hinders the improvement of these processes. In this study, a microbial community of activated sludge enriched in a coking wastewater treatment plant was analyzed using 454 pyrosequencing and Illumina sequencing to characterize the potential cyanide-degrading bacteria. According to the classification of these pyro-tags, targeting V3/V4 regions of 16S rRNA gene, half of them were assigned to the family Xanthomonadaceae, implying that Xanthomonadaceae bacteria are well-adapted to coking wastewater. A nearly complete draft genome of the dominant bacterium was reconstructed from metagenome of this community to explore cyanide metabolism based on analysis of the genome. The assembled 16S rRNA gene from this draft genome showed that this bacterium was a novel species of Thermomonas within Xanthomonadaceae, which was further verified by comparative genomics. The annotation using KEGG and Pfam identified genes related to cyanide metabolism, including genes responsible for the iron-harvesting system, cyanide-insensitive terminal oxidase, cyanide hydrolase/nitrilase, and thiosulfate:cyanide transferase. Phylogenetic analysis showed that these genes had homologs in previously identified genomes of bacteria within Xanthomonadaceae and even presented similar gene cassettes, thus implying an inherent cyanide-decomposing potential. The findings of this study expand our knowledge about the bacterial degradation of cyanide compounds and will be helpful in the remediation of cyanides contamination.

A dual role of the transcriptional regulator TstR provides insights into cyanide detoxification in Lactobacillus brevis

In this study we uncover two genes in Lactobacillus brevis ATCC 367, tstT and tstR, encoding for a rhodanese and a transcriptional regulator involved in cyanide detoxification. TstT (LVIS_0852) belongs to a new class of thiosulphate:cyanide sulphurtransferases. We found that TstR (LVIS_0853) modulates both the expression and the activity of the downstream-encoded tstT. The TstR binding site was identified at -1 to +33, from tstR transcriptional start site. EMSA revealed that sulphite, a product of the reaction catalysed by TstT, improved the interaction between TstR:P(tstR), while Fe(III) disrupted this interaction. Site-directed mutagenesis in TstR identified M64 as a key residue in sulphite recognition, while residues H136-H139-C167-M171 formed a pocket for ferric iron co-ordination. In addition to its role as a transcriptional repressor, TstR is also involved in regulating the thiosulphate:cyanide sulphurtransferase activity of TstT. A threefold increase in TstT activity was observed in the presence of TstR, which was enhanced by the addition of Fe(III). Overexpression of the tstRT operon was found to increase the cyanide tolerance of L. brevis and Escherichia coli. The protein-protein interaction between TstR and TstT described herein represents a novel mechanism for regulation of enzymatic activity by a transcriptional regulator.

Draft whole genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344

Pseudomonas pseudoalcaligenes CECT5344 is a Gram-negative bacterium able to tolerate cyanide and to use it as the sole nitrogen source. We report here the first draft of the whole genome sequence of a P. pseudoalcaligenes strain that assimilates cyanide. Three aspects are specially emphasized in this manuscript. First, some generalities of the genome are shown and discussed in the context of other Pseudomonadaceae genomes, including genome size, G + C content, core genome and singletons among other features. Second, the genome is analysed in the context of cyanide metabolism, describing genes probably involved in cyanide assimilation, like those encoding nitrilases, and genes related to cyanide resistance, like the cio genes encoding the cyanide insensitive oxidases. Finally, the presence of genes probably involved in other processes with a great biotechnological potential like production of bioplastics and biodegradation of pollutants also is discussed.

The nit1C gene cluster of Pseudomonas pseudoalcaligenes CECT5344 involved in assimilation of nitriles is essential for growth on cyanide

A proteomic approach was used to identify several proteins induced by cyanide in the alkaliphilic bacterium Pseudomonas pseudoalcaligenes CECT5344, two of them, NitB and NitG, encoded by genes that belong to the nit1C gene cluster. The predicted products of the nit1C gene cluster are a Fis-like σ(54) -dependent transcriptional activator (NitA), a nitrilase (NitC), an S-adenosylmethionine superfamily member (NitD), an N-acyltransferase superfamily member (NitE), a trifunctional polypeptide of the AIRS/GARS family (NitF), an NADH-dependent oxidoreductase (NitH) and two hypothetical proteins of unknown function (NitB and NitG). RT-PCR analysis suggested that nitBCDEFGH genes were co-transcribed, whereas the regulatory nitA gene was divergently transcribed. Real-time RT-PCR revealed that expression of the nitBCDEFGH genes was induced by cyanide and repressed by ammonium. The P. pseudoalcaligenes CECT5344 nit1C gene cluster was found to be involved in assimilation of free and organic cyanides (nitriles) as deduced for the inability to grow with cyanides showed by the NitA, NitB and NitC mutant strains. The wild-type strain CECT5344 showed a nitrilase activity that allows growth on cyanide or hydroxynitriles. The NitB and NitC mutants only presented low basal levels of nitrilase activity that were not enough to support growth on either free cyanide or aliphatic nitriles, suggesting that nitrilase NitC is specific and essential for cyanide and aliphatic nitriles assimilation.

Metabolic adaptation of Pseudomonas pseudoalcaligenes CECT5344 to cyanide: role of malate-quinone oxidoreductases, aconitase and fumarase isoenzymes

In general, the biodegradation of a toxic compound by a micro-organism requires the concurrence of, at least, two features in the biological system: first, the capability of the micro-organism to metabolize the toxic compound, and secondly, the capacity to resist its toxic effect. Pseudomonas pseudoalcaligenes CECT5344 is a bacterium used in the biodegradation of cyanide because it is capable to use it as a nitrogen source. The present review is mainly focused on the putative role of iron-containing enzymes of the tricarboxylic acid cycle in cyanide resistance by P. pseudoalcaligenes CECT5344.

A composite biochemical system for bacterial nitrate and nitrite assimilation as exemplified by Paracoccus denitrificans

The denitrifying bacterium Paracoccus denitrificans can grow aerobically or anaerobically using nitrate or nitrite as the sole nitrogen source. The biochemical pathway responsible is expressed from a gene cluster comprising a nitrate/nitrite transporter (NasA), nitrite transporter (NasH), nitrite reductase (NasB), ferredoxin (NasG) and nitrate reductase (NasC). NasB and NasG are essential for growth with nitrate or nitrite as the nitrogen source. NADH serves as the electron donor for nitrate and nitrite reduction, but only NasB has a NADH-oxidizing domain. Nitrate and nitrite reductase activities show the same Km for NADH and can be separated by anion-exchange chromatography, but only fractions containing NasB retain the ability to oxidize NADH. This implies that NasG mediates electron flux from the NADH-oxidizing site in NasB to the sites of nitrate and nitrite reduction in NasC and NasB respectively. Delivery of extracellular nitrate to NasBGC is mediated by NasA, but both NasA and NasH contribute to nitrite uptake. The roles of NasA and NasC can be substituted during anaerobic growth by the biochemically distinct membrane-bound respiratory nitrate reductase (Nar), demonstrating functional overlap. nasG is highly conserved in nitrate/nitrite assimilation gene clusters, which is consistent with a key role for the NasG ferredoxin, as part of a phylogenetically widespread composite nitrate and nitrite reductase system.

Bacterial cyanide degradation is under review: Pseudomonas pseudoalcaligenes CECT5344, a case of an alkaliphilic cyanotroph

There are thousands of areas in the U.S.A. and Europe contaminated with cyanide-containing wastes as a consequence of a large number of industrial activities such as gold mining, steel and aluminium manufacturing, electroplating and nitrile pesticides used in agriculture. Chemical treatments to remove cyanide are expensive and generate other toxic products. By contrast, cyanide biodegradation constitutes an appropriate alternative treatment. In the present review we provide an overview of how cells deal in the presence of the poison cyanide that irreversible binds to metals causing, among other things, iron-deprivation conditions outside the cell and metalloenzymes inhibition inside the cell. In this sense, several systems must be present in a cyanotrophic organism, including a siderophore-based acquisition mechanism, a cyanide-insensitive respiratory system and a cyanide degradation/assimilation pathway. The alkaliphilic autochthonous bacterium Pseudomonas pseudocaligenes CECT5344 presents all these requirements with the production of siderophores, a cyanide-insensitive bd-related cytochrome [Cio (cyanide-insensitive oxidase)] and a cyanide assimilation pathway that generates ammonium, which is further incorporated into organic nitrogen.

A proteome analysis of the tetracyanonickelate (II) responses in Klebsiella oxytoca

Tetracyanonickelate (II) (TCN) has been proved to be degraded by Klebsiella oxytoca. In order to examine the physiological responses of TCN degradation by this bacterium, two-dimensional (2-DE) electrophoresis approach and Matrix-assisted laser desorption/ionization-time of flight-mass spectrometry allow us to identify 91 proteins spots that were significantly altered in the presence of 1 mM TCN in relative to that in 1 mM ammonia when K. oxytoca grown at the late-log phase. Among them, 43 proteins were successfully identified. Fractions enriched in hydrophobic proteins were obtained with a specific extraction method based on temperature-dependent phase partitioning with Triton X-114, with the successful identification of 26 proteins out of 41 differential proteins. Some proteins were related with TCN metabolism. OsmC-like protein, molecular chaperone DnaK, glutathione S-transferase, alkyl hydroperoxide reductase, DNA protection during starvation conditions and DNA binding ferritin-like protein can counteract the oxidative stress from TCN biodegradation. The nitrogenase had been suggested to participate in TCN degradation by K. oxytoca, and was upregulated in TCN-treated cells as expected. The induction of glutamine synthetase could enhance the assimilation of limited nitrogen source produced from the bioconversion of TCN into ammonia as the alternate nitrogen source for bacteria growth. These findings could provide new insights into the inducible mechanisms underlying the capacity of K. oxytoca to tolerate TCN stress.

Cyanide degradation by Pseudomonas pseudoalcaligenes CECT5344 involves a malate:quinone oxidoreductase and an associated cyanide-insensitive electron transfer chain

The alkaliphilic bacterium Pseudomonas pseudoalcaligenes CECT5344 is able to grow with cyanide as the sole nitrogen source. Membrane fractions from cells grown under cyanotrophic conditions catalysed the production of oxaloacetate from L-malate. Several enzymic activities of the tricarboxylic acid and glyoxylate cycles in association with the cyanide-insensitive respiratory pathway seem to be responsible for the oxaloacetate formation in vivo. Thus, in cyanide-grown cells, citrate synthase and isocitrate lyase activities were significantly higher than those observed with other nitrogen sources. Malate dehydrogenase activity was undetectable, but a malate:quinone oxidoreductase activity coupled to the cyanide-insensitive alternative oxidase was found in membrane fractions from cyanide-grown cells. Therefore, oxaloacetate production was linked to the cyanide-insensitive respiration in P. pseudoalcaligenes CECT5344. Cyanide and oxaloacetate reacted chemically inside the cells to produce a cyanohydrin (2-hydroxynitrile), which was further converted to ammonium. In addition to cyanide, strain CECT5344 was able to grow with several cyano derivatives, such as 2- and 3-hydroxynitriles. The specific system required for uptake and metabolization of cyanohydrins was induced by cyanide and by 2-hydroxynitriles, such as the cyanohydrins of oxaloacetate and 2-oxoglutarate.

Characterization of the Pseudomonas pseudoalcaligenes CECT5344 Cyanase, an enzyme that is not essential for cyanide assimilation

Cyanase catalyzes the decomposition of cyanate into CO(2) and ammonium, with carbamate as an unstable intermediate. The cyanase of Pseudomonas pseudoalcaligenes CECT5344 was negatively regulated by ammonium and positively regulated by cyanate, cyanide, and some cyanometallic complexes. Cyanase activity was not detected in cell extracts from cells grown with ammonium, even in the presence of cyanate. Nevertheless, a low level of cyanase activity was detected in nitrogen-starved cells. The cyn gene cluster of P. pseudoalcaligenes CECT5344 was cloned and analyzed. The cynA, cynB, and cynD genes encode an ABC-type transporter, the cynS gene codes for the cyanase, and the cynF gene encodes a novel sigma(54)-dependent transcriptional regulator which is not present in other bacterial cyn gene clusters. The CynS protein was expressed in Escherichia coli and purified by following a simple and rapid protocol. The P. pseudoalcaligenes cyanase showed an optimal pH of 8.5 degrees C and a temperature of 65 degrees C. An insertion mutation was generated in the cynS gene. The resulting mutant was unable to use cyanate as the sole nitrogen source but showed the same resistance to cyanate as the wild-type strain. These results, in conjunction with the induction pattern of the enzymatic activity, suggest that the enzyme has an assimilatory function. Although the induction of cyanase activity in cyanide-degrading cells suggests that some cyanate may be generated from cyanide, the cynS mutant was not affected in its ability to degrade cyanide, which unambiguously indicates that cyanate is not a central metabolite in cyanide assimilation.