A conserved mechanism for nitrile metabolism in bacteria and plants

Mitigating drought stress in fenugreek through synergistic effects of alanine and potassium-enriched biochar

Drought stress adversely affects plant growth, development, and yield. It can decrease seed germination, biomass accumulation, root proliferation, chlorophyll contents, and stomatal conductance. To overcome this critical issue, researchers suggest employing environmentally friendly approaches. The exogenous application of alanine (AL) acts as an osmolyte, which helps balance the cellular water under drought stress. It can also improve root architecture, biomass accumulation, and plant fertilizer use efficiency. Applying biochar can improve soil structure, water, and nutrient retention in soil, which are allied factors in enhancing plant growth under drought stress. Furthermore, the enrichment of potassium (K) in biochar also increases its availability to plants, directly regulating the stomatal conductance to alleviate drought stress. That's why the current study aims to explore the combined effect of AL and potassium-enriched biochar (KBC) on fenugreek cultivated under drought stress. Four levels of AL (control, 2mM, 4mM, and 6mM) were applied with 0%, 1%, and 2% KBC in three replicates. Results showed that 2mM AL + 2%KBC showed significant improvement in plant length (5.24%), plant fresh weight (25.36%), plant dry weight (16.23%), chlorophyll a (7.80%), chlorophyll b (15.83%), total chlorophyll (10.65%) over the control under drought stress. A significant increase in shoot N, P, and K concentration compared to control under drought stress also validated the effectiveness of 2mM AL + 2%KBC. In conclusion, 2mM AL + 2%KBC is an effective amendment for alleviating drought stress in fenugreeks. Under drought stress, growers are recommended to apply 2mM AL + 2%KBC to achieve better fenugreek growth.

Comprehensive insight into recent algal enzymes production and purification advances: Toward effective commercial applications: A review

Algal enzymes are essential catalysts in numerous biological reactions and industrial processes owing to their adaptability and potency. The marketing of algal enzymes has recently risen due to various reasons, including the cost-efficient manner of their cultivation in photobioreactors, the eco-friendly production of high biomass contents, sources of novel enzymes that used in many sectors (biofuel and bioremediation applications), sustainability, and more renewability. Oxidoreductases and hydrolytic enzymes are among the important applied algal enzymes in industrial applications, with annually growing demand. These algal enzymes have opened up new avenues for significant health advantages in reducing and treating oxidative stress, cardiovascular illness, tumors, microbial infections, and viral outbreaks. Despite their promising uses, commercial applications of algal enzymes face many difficulties, such as stability, toxicity, and lower data availability on specific and adequate catalytic mechanisms. Therefore, this review focuses on the algal enzyme types, their uses and advantages over other microbial enzymes, downstream and upstream processing, their commercial and marketing, and their challenges. With the constant development of novel enzymes and their uses, enzyme technology provides exciting options for several industrial sectors.

Pseudomonas fluorescens Inoculation Enhances Salix matsudana Growth by Modifying Phyllosphere Microbiomes, Surpassing Nitrogen Fertilization

The enhancement of plant growth by soil fertilization and microbial inoculation involves different mechanisms, particularly by altering the phyllosphere microbiome. This study investigated how nitrogen (N) fertilization, Pseudomonas fluorescens strain R124 inoculation and their combined effects influence the growth of different-aged Salix matsudana cuttings by modulating N dynamics within the phyllosphere microbiome. Results showed that P. fluorescens inoculation was significantly more effective than N fertilization alone, enhancing biomass, plant nutrient uptake, soil nutrient content and root development by 90.51%, 18.18%, 72.74% and 126.20%, respectively. Crucially, the inoculation notably shifted the beta-diversity of the phyllosphere microbial community, with K-strategy fungi enhancing plant N fixation and subsequent plant growth. Cuttings from middle-aged forests displayed more robust growth than those from young-aged, associated with a varied impact on phyllosphere fungi, notably increasing the relative abundance of Myriangiales in young (76.37%) and Capnodiales in middle-aged cuttings (42.37%), which improve phyllosphere stability and plant health. These findings highlight the effectiveness of microbial inoculation over N fertilization in promoting plant growth and provide valuable insights for the sustainable management of willow plantations at different stages of development.

Phylogenetic and Structural Analysis of Bacterial Nitrilases for the Biodegradation of Nitrile Compounds

BACKGROUND

Microbial nitrilases play a vital role in the biodegradation of nitrilecontaining pollutants, effluent treatments in chemical and textile industries, and the biosynthesis of Indole-3-acetic acid (IAA) from tryptophan in plants. However, the lack of structural information limits the correlation between its activity and substrate specificity.

METHODS

The present study involves the genome mining of bacteria for the distribution and diversity of nitrilases, their phylogenetic analysis and structural characterization for motifs/ domains, followed by interaction with substrates.

RESULTS

Here, we mined the bacterial genomes for nitrilases and correlated their functions to hypothetical, uncharacterized, or putative ones. The comparative genomics revealed four AcNit, As7Nit, Cn5Nit and Cn9Nit predicted nitrilases encoding genes as uncharacterized subgroups of the nitrilase superfamily. The annotation of these nitrilases encoding genes revealed relatedness with nitrilase hydratases and cyanoalanine hydratases. At the proteomics level, the motif analysis of these protein sequences predicted a single motif of 20-28 aa, with glutamate (E), lysine (K) and cysteine (C) residues as a part of catalytic triad along with several other residues at the active site. The structural analysis of the nitrilases revealed geometrical and close conformation in the form of α-helices and β-sheets arranged in a sandwich structure. The catalytic residues constituted the substrate binding pocket and exhibited the broad nitrile substrate spectra for aromatic and aliphatic nitriles-containing compounds. The aromatic amino acid residues Y159 in the active site were predicted to be responsible for substrate specificity. The substitution of non-aromatic alanine residue in place of Y159 completely disrupted the catalytic activity for indole-3-acetonitrile (IAN).

CONCLUSION

The present study reports genome mining and simulation of structure-function relationship for uncharacterized bacterial nitrilases and their role in the biodegradation of pollutants and xenobiotics, which could be of applications in different industrial sectors.

Effect of Cyanide-Utilizing Bacteria and Sulfur Supplementation on Reducing Cyanide Concentration and In Vitro Degradability Using In Vitro Gas Production Technique

The objective of this research was to supplement the cyanide-utilizing bacteria and sulfur in the HCN-rich diet, affecting the gas production and fermentation of rumen in vitro, and lowering the HCN content and the digestion of nutrients. A 2 × 2 × 3 factorial experiment in a completely randomized design was applied during the test. In the experiments, three factors were used. Factor A was the level of CUB at 0 and 108 CFU/mL. Factor B was the level of sulfur in the diet at 0% and 3% of dry matter (DM). Factor C was the three levels of potassium cyanide (KCN) at 0, 300, and 600 ppm. The interaction of CUB × sulfur × KCN affected gas production from the immediately soluble fraction (a) (p < 0.05). However, the greatest ruminal cyanide concentration was found when CUB (with and without), sulfur (3%), and KCN (600 ppm) were introduced at 0 h (p < 0.05). It revealed that the addition of CUB and sulfur had a significant impact on gas accumulation at 96 h (p < 0.05). The addition of CUB with sulfur had an effect on pH at 2 h and ruminal cyanide levels at 6 h (p < 0.05). At 2 h, sulfur supplementation with KCN had an effect on NH3-N (p < 0.01). The addition of sulfur (3%) and KCN (300 ppm) produced the highest ammonia nitrogen. However, the combination of sulfur (3%) and KCN (600 ppm) produced the lowest level of ammonia nitrogen (p < 0.01). CUB supplementation increased the in vitro dry matter digestibility (IVDMD) by 11.16% compared to the without-CUB supplemented group (p < 0.05). Supplementation with 3% sulfur increased the in vitro neutral detergent fiber (IVNDFD) by 16.87% but had no effect on IVDMD or in vitro acid detergent fiber (IVADFD) (p < 0.05). The volatile fatty acid (VFA) such as acetate, propionate, and butyrate were not different when CUB, sulfur, and KCN were added. Doses above 600 ppm had the lowest concentrations of TVFA and propionate (p < 0.01). Based on the results of this investigation, supplementing with CUB and sulfur (3%) may improve cumulative gas, digestibility, and TVAF. Supplementing with CUB, on the other hand, reduced HCN the most, by 54.6%.

Extending the benefits of PGPR to bioremediation of nitrile pollution in crop lands for enhancing crop productivity

Incessant release of nitrile group of compounds such as cyanides into agricultural land through industrial effluents and excessive use of nitrile pesticides has resulted in increased nitrile pollution. Release of nitrile compounds (NCs) as plant root exudates is also contributing to the problem. The released NCs interact with soil elements and persists for a long time. Persistent higher concentration of NCs in soil cause toxicity to beneficial microflora and affect crop productivity. The NCs can cause more problems to human health if they reach groundwater and enter the food chain. Nitrile degradation by soil bacteria can be a solution to the problem if thoroughly exploited. However, the impact of such bacteria in plant and soil environments is still not properly explored. Plant growth-promoting rhizobacteria (PGPR) with nitrilase activity has recently gained attention as potential solution to address the problem. This paper reviews the core issue of nitrile pollution in soil and the prospects of application of nitrile degrading bacteria for soil remediation, soil health improvement and plant growth promotion in nitrile-polluted soils. The possible mechanisms of PGPR that can be exploited to degrade NCs, converting them into plant useful compounds and synthesis of the phytohormone IAA from degraded NCs are also discussed at length.

Characterization of nitrilases from Variovorax boronicumulans that functions in insecticide flonicamid degradation and β-cyano-L-alanine detoxification

AIMS

To characterize the functions of nitrilases of Variovorax boronicumulans CGMCC 4969 and evaluate flonicamid (FLO) degradation and β-cyano-L-alanine (Ala(CN)) detoxification by this bacterium.

METHODS AND RESULTS

V. boronicumulans CGMCC 4969 nitrilases (NitA and NitB) were purified and substrate specificity assay indicated that both of them degraded insecticide FLO to N-(4-trifluoromethylnicotinoyl)glycinamide (TFNG-AM) and 4-(trifluoromethyl)nicotinol glycine (TFNG). Ala(CN), a plant detoxification intermediate, was hydrolyzed by NitB. Escherichia coli overexpressing NitA and NitB degraded 41.2 and 93.8% of FLO (0.87 mmol·L^-1 ) within 1 h, with half-lives of 1.30 and 0.25 h, respectively. NitB exhibited the highest nitrilase activity toward FLO. FLO was used as a substrate to compare their enzymatic properties. NitB was more tolerant to acidic conditions and organic solvents than NitA. Conversely, NitA was more tolerant to metal ions than NitB. CGMCC 4969 facilitated FLO degradation in soil and surface water and utilized Ala(CN) as a sole nitrogen source for growth.

CONCLUSIONS

CGMCC 4969 efficiently degraded FLO mediated by NitA and NitB; NitB was involved in Ala(CN) detoxification.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study promotes our understanding of versatile functions of nitrilases from CGMCC 4969 that is promising for environmental remediation.

Metabolism of Aldoximes and Nitriles in Plant-Associated Bacteria and Its Potential in Plant-Bacteria Interactions

In plants, aldoximes per se act as defense compounds and are precursors of complex defense compounds such as cyanogenic glucosides and glucosinolates. Bacteria rarely produce aldoximes, but some are able to transform them by aldoxime dehydratase (Oxd), followed by nitrilase (NLase) or nitrile hydratase (NHase) catalyzed transformations. Oxds are often encoded together with NLases or NHases in a single operon, forming the aldoxime-nitrile pathway. Previous reviews have largely focused on the use of Oxds and NLases or NHases in organic synthesis. In contrast, the focus of this review is on the contribution of these enzymes to plant-bacteria interactions. Therefore, we summarize the substrate specificities of the enzymes for plant compounds. We also analyze the taxonomic and ecological distribution of the enzymes. In addition, we discuss their importance in selected plant symbionts. The data show that Oxds, NLases, and NHases are abundant in Actinobacteria and Proteobacteria. The enzymes seem to be important for breaking through plant defenses and utilizing oximes or nitriles as nutrients. They may also contribute, e.g., to the synthesis of the phytohormone indole-3-acetic acid. We conclude that the bacterial and plant metabolism of aldoximes and nitriles may interfere in several ways. However, further in vitro and in vivo studies are needed to better understand this underexplored aspect of plant-bacteria interactions.

Alternative Pathway for 3-Cyanoalanine Assimilation in Pseudomonas pseudoalcaligenes CECT5344 under Noncyanotrophic Conditions

3-Cyanoalanine and cyanohydrins are intermediate nitriles produced in cyanide degradation pathways in plants and bacteria. 3-Cyanoalanine is generated from cyanide by the 3-cyanoalanine synthase, an enzyme mainly characterized in cyanogenic plants. NIT4-type nitrilases use 3-cyanoalanine as a substrate, forming ammonium and aspartate. In some organisms, this enzyme also generates asparagine through an additional nitrile hydratase activity. The alkaliphilic bacterium Pseudomonas pseudoalcaligenes CECT5344 assimilates cyanide through an intermediate cyanohydrin, which is further converted into ammonium by the nitrilase NitC. This bacterium also contains three additional nitrilases, including Nit4. In this work, a proteomic analysis of P. pseudoalcaligenes CECT5344 cells grown with 3-cyanoalanine as the sole nitrogen source has revealed the overproduction of different proteins involved in nitrogen metabolism, including the nitrilase NitC. In contrast, the nitrilase Nit4 was not induced by 3-cyanoalanine, and it was only overproduced in cells grown with a cyanide-containing jewelry-manufacturing residue. Phenotypes of single and double mutant strains defective in nit4 or/and nitC revealed the implication of the nitrilase NitC in the assimilation of 3-cyanoalanine and suggest that the 3-cyanoalanine assimilation pathway in P. pseudoalcaligenes CECT5344 depends on the presence or absence of cyanide. When cyanide is present, 3-cyanoalanine is assimilated via Nit4, but in the absence of cyanide, a novel pathway for 3-cyanoalanine assimilation, in which the nitrilase NitC uses the nitrile generated after deamination of the α-amino group from 3-cyanoalanine, is proposed. IMPORTANCE Nitriles are organic cyanides with important industrial applications, but they are also found in nature. 3-Cyanoalanine is synthesized by plants and some bacteria to detoxify cyanide from endogenous or exogenous sources, but this nitrile may be also involved in other processes such as stress tolerance, nitrogen and sulfur metabolism, and signaling. The cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344 grows with 3-cyanoalanine as the sole nitrogen source, but it does not use this nitrile as an intermediate in the cyanide assimilation pathway. In this work, a quantitative proteomic analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS) was performed to study, for the first time, the response to 3-cyanoalanine at the proteomic level. Proteomic data, together with phenotypes of different nitrilase-defective mutants of P. pseudoalcaligenes CECT5344, provide evidence that in the absence of cyanide, the nitrilase Nit4 is not involved in 3-cyanoalanine assimilation, and instead, the nitrilase NitC participates in a novel alternative 3-cyanoalanine assimilation pathway.

Roseomonas hellenica sp. nov., isolated from roots of wild-growing Alkanna tinctoria

Two Gram-negative, aerobic, rod-shaped and yellow-orange pigmented bacterial strains (LMG 31523^T and LMG 31524) were isolated from roots of wild-growing Alkanna tinctoria plants collected near Thessaloniki, Greece. Analysis of their 16S rRNA gene sequences revealed that they form a separate cluster related to the genus Roseomonas. A comparative whole genome analysis of the two strains and the type strains of related Roseomonas species revealed average nucleotide identity values from 78.84 and 80.32%. The G + C contents of the genomic DNA of strains LMG 31523^T and LMG 31524 were 69.69% and 69.74%, respectively. Combined data from phenotypic, phylogenetic and chemotaxonomic studies indicated that the strains LMG 31523^T and LMG 31524 represent a novel species of the genus Roseomonas. Genome analysis of the new strains showed a number of genes involved in survival in the rhizosphere environment and in plant colonization and confirmed the endophytic characteristics of LMG 31523^T and LMG 31524. Since the strains LMG 31523^T and LMG 31524 were isolated from a plant collected in Greece the name Roseomonas hellenica sp. nov. is proposed. The type strain is LMG 31523^T (=CECT 30032^T).

Plant Nitrilase Homologues in Fungi: Phylogenetic and Functional Analysis with Focus on Nitrilases in Trametes versicolor and Agaricus bisporus

Fungi contain many plant-nitrilase (NLase) homologues according to database searches. In this study, enzymes NitTv1 from Trametes versicolor and NitAb from Agaricus bisporus were purified and characterized as the representatives of this type of fungal NLase. Both enzymes were slightly more similar to NIT4 type than to NIT1/NIT2/NIT3 type of plant NLases in terms of their amino acid sequences. Expression of the synthetic genes in Escherichia coli Origami B (DE3) was induced with 0.02 mM isopropyl β-D-1-thiogalactopyranoside at 20 °C. Purification of NitTv1 and NitAb by cobalt affinity chromatography gave ca. 6.6 mg and 9.6 mg of protein per 100 mL of culture medium, respectively. Their activities were determined with 25 mM of nitriles in 50 mM Tris/HCl buffer, pH 8.0, at 30 °C. NitTv1 and NitAb transformed β-cyano-L-alanine (β-CA) with the highest specific activities (ca. 132 and 40 U mg⁻¹, respectively) similar to plant NLase NIT4. β-CA was transformed into Asn and Asp as in NIT4 but at lower Asn:Asp ratios. The fungal NLases also exhibited significant activities for (aryl)aliphatic nitriles such as 3-phenylpropionitrile, cinnamonitrile and fumaronitrile (substrates of NLase NIT1). NitTv1 was more stable than NitAb (at pH 5–9 vs. pH 5–7). These NLases may participate in plant–fungus interactions by detoxifying plant nitriles and/or producing plant hormones. Their homology models elucidated the molecular interactions with various nitriles in their active sites.

From sequence to function: a new workflow for nitrilase identification

Abstract

Nitrilases are industrially important biocatalysts due to their ability to degrade nitriles to carboxylic acids and ammonia. In this study, a workflow for simple and fast recovery of nitrilase candidates from metagenomes is presented. For identification of active enzymes, a NADH-coupled high-throughput assay was established. Purification of enzymes could be omitted as the assay is based on crude extract containing the expressed putative nitrilases. In addition, long incubation times were avoided by combining nitrile and NADH conversion in a single reaction. This allowed the direct measurement of nitrile degradation and provided not only insights into substrate spectrum and specificity but also in degradation efficiency. The novel assay was used for investigation of candidate nitrilase-encoding genes. Seventy putative nitrilase-encoding gene and the corresponding deduced protein sequences identified during sequence-based screens of metagenomes derived from nitrile-treated microbial communities were analyzed. Subsequently, the assay was applied to 13 selected candidate genes and proteins. Six of the generated corresponding Escherichia coli clones produced nitrilases that showed activity and one unusual nitrilase was purified and analyzed. The activity of the novel arylacetonitrilase Nit09 exhibited a broad pH range and a high long-term stability. The enzyme showed high activity for arylacetonitriles with a K_M of 1.29 mM and a V_max of 13.85 U/mg protein for phenylacetonitrile. In conclusion, we provided a setup for simple and rapid analysis of putative nitrilase-encoding genes from sequence to function. The suitability was demonstrated by identification, isolation, and characterization of the arylacetonitrilase.

Key points

• A simple and fast high-throughput nitrilase screening was developed.

• A set of putative nitrilases was successfully screened with the assay.

• A novel arylacetonitrilase was identified, purified, and characterized in detail.

Electronic supplementary material

The online version of this article (10.1007/s00253-020-10544-9) contains supplementary material, which is available to authorized users.

New molecular insights on the response of the green alga Tetraselmis suecica to nitrogen starvation

Microalgae are currently considered one of the most promising resources for biofuel production, aquaculture feedstock and new pharmaceuticals. Among them, green algae of the genus Tetraselmis are extensively studied for their lipid accumulation in nutrient-starvation conditions. In this paper, we present the full-transcriptome of Tetraselmis suecica and differential expression analysis between nitrogen-starved and -repleted conditions (at stationary phase) focusing not only on lipid metabolism but giving new insights on nutrient starvation responses. Transcripts involved in signal transduction pathways, stress and antioxidant responses and solute transport were strongly up-regulated when T. suecica was cultured under nitrogen starvation. On the contrary, transcripts involved in amino acid synthesis, degradation of sugars, secondary metabolite synthesis, as well as photosynthetic activity were down-regulated under the same conditions. Among differentially expressed transcripts, a polyketide synthase and three lipoxygenases (involved in the synthesis of secondary metabolites with antipredator, anticancer and anti-infective activities) were identified, suggesting the potential synthesis of bioactive compounds by this microalga. In addition, the transcript for a putative nitrilase, enzyme used in nitrile bioremediation, is here reported for the first time for T. suecica. These findings give new insights on T. suecica responses to nutrient starvation and on possible biotechnological applications for green algae.

Interplay of nucleophilic catalysis with proton transfer in the nitrile reductase QueF from Escherichia coli

Proton relay through an active-site network of hydrogen bonds promotes enzymatic nitrile reduction to amine via a covalent thioimidate enzyme intermediate.

The Plant Growth-Promoting Rhizobacterium Variovorax boronicumulans CGMCC 4969 Regulates the Level of Indole-3-Acetic Acid Synthesized from Indole-3-Acetonitrile

Variovorax is a metabolically diverse genus of plant growth-promoting rhizobacteria (PGPR) that engages in mutually beneficial interactions between plants and microbes. Unlike most PGPR, Variovorax cannot synthesize the phytohormone indole-3-acetic acid (IAA) via tryptophan. However, we found that Variovorax boronicumulans strain CGMCC 4969 can produce IAA using indole-3-acetonitrile (IAN) as the precursor. Thus, in the present study, the IAA synthesis mechanism of V. boronicumulans CGMCC 4969 was investigated. V. boronicumulans CGMCC 4969 metabolized IAN to IAA through both a nitrilase-dependent pathway and a nitrile hydratase (NHase) and amidase-dependent pathway. Cobalt enhanced the metabolic flux via the NHase/amidase, by which IAN was rapidly converted to indole-3-acetamide (IAM) and in turn to IAA. IAN stimulated metabolic flux via the nitrilase, by which IAN was rapidly converted to IAA. Subsequently, the IAA was degraded. V. boronicumulans CGMCC 4969 can use IAN as the sole carbon and nitrogen source for growth. Genome sequencing confirmed the IAA synthesis pathways. Gene cloning and overexpression in Escherichia coli indicated that NitA has nitrilase activity and IamA has amidase activity to respectively transform IAN and IAM to IAA. Interestingly, NitA showed a close genetic relationship with the nitrilase of the phytopathogen Pseudomonas syringae Quantitative PCR analysis indicated that the NHase/amidase system is constitutively expressed, whereas the nitrilase is inducible. The present study helps our understanding of the versatile functions of Variovorax nitrile-converting enzymes that mediate IAA synthesis and the interactions between plants and these bacteria.IMPORTANCE We demonstrated that Variovorax boronicumulans CGMCC 4969 has two enzymatic systems-nitrilase and nitrile hydratase/amidase-that convert indole-3-acetonitrile (IAN) to the important plant hormone indole-3-acetic acid (IAA). The two IAA synthesis systems have very different regulatory mechanisms, affecting the IAA synthesis rate and duration. The nitrilase was induced by IAN, which was rapidly converted to IAA; subsequently, IAA was rapidly consumed for cell growth. The nitrile hydratase (NHase) and amidase system was constitutively expressed and slowly but continuously synthesized IAA. In addition to synthesizing IAA from IAN, CGMCC 4969 has a rapid IAA degradation system, which would be helpful for a host plant to eliminate redundant IAA. This study indicates that the plant growth-promoting rhizobacterium V. boronicumulans CGMCC 4969 has the potential to be used by host plants to regulate the IAA level.

Exploring anaerobic environments for cyanide and cyano-derivatives microbial degradation

Cyanide is one of the most toxic chemicals for living organisms described so far. Its toxicity is mainly based on the high affinity that cyanide presents toward metals, provoking inhibition of essential metalloenzymes. Cyanide and its cyano-derivatives are produced in a large scale by many industrial activities related to recovering of precious metals in mining and jewelry, coke production, steel hardening, synthesis of organic chemicals, and food processing industries. As consequence, cyanide-containing wastes are accumulated in the environment becoming a risk to human health and ecosystems. Cyanide and related compounds, like nitriles and thiocyanate, are degraded aerobically by numerous bacteria, and therefore, biodegradation has been offered as a clean and cheap strategy to deal with these industrial wastes. Anaerobic biological treatments are often preferred options for wastewater biodegradation. However, at present very little is known about anaerobic degradation of these hazardous compounds. This review is focused on microbial degradation of cyanide and related compounds under anaerobiosis, exploring their potential application in bioremediation of industrial cyanide-containing wastes.

A Cyanide-Induced 3-Cyanoalanine Nitrilase in the Cyanide-Assimilating Bacterium Pseudomonas pseudoalcaligenes Strain CECT 5344

Pseudomonas pseudoalcaligenes CECT 5344 is a bacterium able to assimilate cyanide as a sole nitrogen source. Under this growth condition, a 3-cyanoalanine nitrilase enzymatic activity was induced. This activity was encoded by nit4, one of the four nitrilase genes detected in the genome of this bacterium, and its expression in Escherichia coli enabled the recombinant strain to fully assimilate 3-cyanoalanine. P. pseudoalcaligenes CECT 5344 showed a weak growth level with 3-cyanoalanine as the N source, unless KCN was also added. Moreover, a nit4 knockout mutant of P. pseudoalcaligenes CECT 5344 became severely impaired in its ability to grow with 3-cyanoalanine and cyanide as nitrogen sources. The native enzyme expressed in E. coli was purified up to electrophoretic homogeneity and biochemically characterized. Nit4 seems to be specific for 3-cyanoalanine, and the amount of ammonium derived from the enzymatic activity doubled in the presence of exogenously added asparaginase activity, which demonstrated that the Nit4 enzyme had both 3-cyanoalanine nitrilase and hydratase activities. The nit4 gene is located downstream of the cyanide resistance transcriptional unit containing cio1 genes, whose expression levels are under the positive control of cyanide. Real-time PCR experiments revealed that nit4 expression was also positively regulated by cyanide in both minimal and LB media. These results suggest that this gene cluster including cio1 and nit4 could be involved both in cyanide resistance and in its assimilation by P. pseudoalcaligenes CECT 5344.IMPORTANCE Cyanide is a highly toxic molecule present in some industrial wastes due to its application in several manufacturing processes, such as gold mining and the electroplating industry. The biodegradation of cyanide from contaminated wastes could be an attractive alternative to physicochemical treatment. P. pseudoalcaligenes CECT 5344 is a bacterial strain able to assimilate cyanide under alkaline conditions, thus avoiding its volatilization as HCN. This paper describes and characterizes an enzyme (Nit4) induced by cyanide that is probably involved in cyanide assimilation. The biochemical characterization of Nit4 provides a segment for building a cyanide assimilation pathway in P. pseudoalcaligenes This information could be useful for understanding, and hopefully improving, the mechanisms involved in bacterial cyanide biodegradation and its application in the treatment of cyanide-containing wastes.

Cyanide bioremediation: the potential of engineered nitrilases

The cyanide-degrading nitrilases are of notable interest for their potential to remediate cyanide contaminated waste streams, especially as generated in the gold mining, pharmaceutical, and electroplating industries. This review provides a brief overview of cyanide remediation in general but with a particular focus on the cyanide-degrading nitrilases. These are of special interest as the hydrolysis reaction does not require secondary substrates or cofactors, making these enzymes particularly good candidates for industrial remediation processes. The genetic approaches that have been used to date for engineering improved enzymes are described; however, recent structural insights provide a promising new approach.

The β-cyanoalanine synthase pathway: beyond cyanide detoxification

Production of cyanide through biological and environmental processes requires the detoxification of this metabolic poison. In the 1960s, discovery of the β-cyanoalanine synthase (β-CAS) pathway in cyanogenic plants provided the first insight on cyanide detoxification in nature. Fifty years of investigations firmly established the protective role of the β-CAS pathway in cyanogenic plants and its role in the removal of cyanide produced from ethylene synthesis in plants, but also revealed the importance of this pathway for plant growth and development and the integration of nitrogen and sulfur metabolism. This review describes the β-CAS pathway, its distribution across and within higher plants, and the diverse biological functions of the pathway in cyanide assimilation, plant growth and development, stress tolerance, regulation of cyanide and sulfide signalling, and nitrogen and sulfur metabolism. The collective roles of the β-CAS pathway highlight its potential evolutionary and ecological importance in plants.

Proteomics and functional analyses of Arabidopsis nitrilases involved in the defense response to microbial pathogens

Proteomics and functional analyses of the Arabidopsis - Pseudomonas syringae pv. tomato interactions reveal that Arabidopsis nitrilases are required for plant defense and R gene-mediated resistant responses to microbial pathogens. A high-throughput in planta proteome screen has identified Arabidopsis nitrilase 2 (AtNIT2), which was de novo-induced by Pseudomonas syringae pv. tomato (Pst) infection. The AtNIT2, AtNIT3, and AtNIT4 genes, but not AtNIT1, were distinctly induced in Arabidopsis leaves by Pst infection. Notably, avirulent Pst DC3000 (avrRpt2) infection led to significant induction of AtNIT2 and AtNIT4 in leaves. Pst DC3000 and Pst DC3000 (avrRpt2) significantly grew well in leaves of nitrilase transgenic (nit2i-2) and mutant (nit1-1 and nit3-1) lines compared to the wild-type leaves. In contrast, NIT2 overexpression in nit2 mutants led to significantly high growth of the two Pst strains in leaves. The nitrilase transgenic and mutant lines exhibited enhanced susceptibility to Hyaloperonospora arabidopsidis infection. The nit2 mutation enhanced Pst DC3000 (avrRpt2) growth in salicylic acid (SA)-deficient NahG transgenic and sid2 and npr1 mutant lines. Infection with Pst DC3000 or Pst DC3000 (avrRpt2) induced lower levels of indole-3-acetic acid (IAA) in nit2i and nit2i NahG plants than in wild-type plants, but did not alter the IAA level in NahG transgenic plants. This suggests that Arabidopsis nitrilase 2 is involved in IAA signaling of defense and R gene-mediated resistance responses to Pst infection. Quantification of SA in these transgenic and mutant plants demonstrates that Arabidopsis nitrilase 2 is not required for SA-mediated defense response to the virulent Pst DC3000 but regulates SA-mediated resistance to the avirulent Pst DC3000 (avrRpt2). These results collectively suggest that Arabidopsis nitrilase genes are involved in plant defense and R gene-mediated resistant responses to microbial pathogens.

Determination of the Michaelis-Menten kinetics and the genes expression involved in phyto-degradation of cyanide and ferri-cyanide

Hydroponic experiments were conducted with different species of plants (rice, maize, soybean and willow) exposed to ferri-cyanide to investigate the half-saturation constant (K M ) and the maximal metabolic capacity (v max ) involved in phyto-assimilation. Three varieties for each testing species were collected from different origins. Measured concentrations show that the uptake rates responded biphasically to ferri-cyanide treatments by showing increases linearly at low and almost constant at high concentrations from all treatments, indicating that phyto-assimilation of ferri-cyanide followed the Michaelis-Menten kinetics. Using non-linear regression, the highest v max was by rice, followed by willows. The lowest v max was found for soybean. All plants, except maize (DY26) and rice (XJ12), had a similar K M value, suggesting the same enzyme was active in phyto-assimilation of ferri-cyanide. Transcript level, by real-time quantitative PCR, of enzymes involved in degradation of cyanides showed that the analyzed genes were differently expressed during different cyanides exposure. The expression of CAS and ST genes responded positively to KCN exposure, suggesting that β-CAS and ST pathways were two possible pathways for cyanide detoxification in rice. The transcript level of NIT and ASPNASE genes also showed a remarkable up-regulation to KCN, implying the contribution to the pool of amino acid aspartate, which is an end product of CN metabolism. Up-regulation of GS genes suggests that acquisition of ammonium released from cyanide degradation may be an additional nitrogen source for plant nutrition. Results also revealed that the expressions of these genes, except for GS, were relatively constant during iron cyanide exposure, suggesting that they are likely metabolized by plants through a non-defined pathway rather than the β-CAS pathway.

Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica

Background

Improved understanding of bacterial-fungal interactions in the rhizosphere should assist in the successful application of bacteria as biological control agents against fungal pathogens of plants, providing alternatives to chemicals in sustainable agriculture. Rhizoctonia solani is an important soil-associated fungal pathogen and its chemical treatment is not feasible or economic. The genomes of the plant-associated bacteria Serratia proteamaculans S4 and Serratia plymuthica AS13 have been sequenced, revealing genetic traits that may explain their diverse plant growth promoting activities and antagonistic interactions with R. solani. To understand the functional response of this pathogen to different bacteria and to elucidate whether the molecular mechanisms that the fungus exploits involve general stress or more specific responses, we performed a global transcriptome profiling of R. solani Rhs1AP anastomosis group 3 (AG-3) during interaction with the S4 and AS13 species of Serratia using RNA-seq.

Results

Approximately 104,504 million clean 75-100 bp paired-end reads were obtained from three libraries, each in triplicate (AG3-Control, AG3-S4 and AG3-AS13). Transcriptome analysis revealed that approximately 10 % of the fungal transcriptome was differentially expressed during challenge with Serratia. The numbers of S4- and AS13-specific differentially expressed genes (DEG) were 866 and 292 respectively, while there were 1035 common DEGs in the two treatment groups. Four hundred and sixty and 242 genes respectively had values of log₂ fold-change > 3 and for further analyses this cut-off value was used. Functional classification of DEGs based on Gene Ontology enrichment analysis and on KEGG pathway annotations revealed a general shift in fungal gene expression in which genes related to xenobiotic degradation, toxin and antioxidant production, energy, carbohydrate and lipid metabolism and hyphal rearrangements were subjected to transcriptional regulation.

Conclusions

This RNA-seq profiling generated a novel dataset describing the functional response of the phytopathogen R. solani AG3 to the plant-associated Serratia bacteria S4 and AS13. Most genes were regulated in the same way in the presence of both bacterial isolates, but there were also some strain-specific responses. The findings in this study will be beneficial for further research on biological control and in depth exploration of bacterial-fungal interactions in the rhizosphere.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1758-z) contains supplementary material, which is available to authorized users.

Proteome reference maps of the Lotus japonicus nodule and root

Legume symbiosis with rhizobia results in the formation of a specialized organ, the root nodule, where atmospheric dinitrogen is reduced to ammonia. In Lotus japonicus (Lotus), several genes involved in nodule development or nodule function have been defined using biochemistry, genetic approaches, and high-throughput transcriptomics. We have employed proteomics to further understand nodule development. Two developmental stages representing nodules prior to nitrogen fixation (white) and mature nitrogen fixing nodules (red) were compared with roots. In addition, the proteome of a spontaneous nodule formation mutant (snf1) was determined. From nodules and roots, 780 and 790 protein spots from 2D gels were identified and approximately 45% of the corresponding unique gene accessions were common. Including a previous proteomics set from Lotus pod and seed, the common gene accessions were decreased to 7%. Interestingly, an indication of more pronounced PTMs in nodules than in roots was determined. Between the two nodule developmental stages, higher levels of pathogen-related 10 proteins, HSPs, and proteins involved in redox processes were found in white nodules, suggesting a higher stress level at this developmental stage. In contrast, protein spots corresponding to nodulins such as leghemoglobin, asparagine synthetase, sucrose synthase, and glutamine synthetase were prevalent in red nodules. The distinct biochemical state of nodules was further highlighted by the conspicuous presence of several nitrilases, ascorbate metabolic enzymes, and putative rhizobial effectors.

Increased β-cyanoalanine nitrilase activity improves cyanide tolerance and assimilation in Arabidopsis

Plants naturally produce cyanide (CN) which is maintained at low levels in their cells by a process of rapid assimilation. However, high concentrations of environmental CN associated with activities such as industrial pollution are toxic to plants. There is thus an interest in increasing the CN detoxification capacity of plants as a potential route to phytoremediation. Here, Arabidopsis seedlings overexpressing the Pseudomonas fluorescens β-cyanoalanine nitrilase pinA were compared with wild-type and a β-cyanoalanine nitrilase knockout line (ΔAtnit4) for growth in the presence of exogenous CN. After incubation with CN, +PfpinA seedlings had increased root length, increased fresh weight, and decreased leaf bleaching compared with wild-type, indicating increased CN tolerance. The increased tolerance was achieved without an increase in β-cyanoalanine synthase activity, the other enzyme in the cyanide assimilation pathway, suggesting that nitrilase activity is the limiting factor for cyanide detoxification. Labeling experiments with [¹³C]KCN demonstrated that the altered CN tolerance could be explained by differences in flux from CN to Asn caused by altered β-cyanoalanine nitrilase activity. Metabolite profiling after CN treatment provided new insight into downstream metabolism, revealing onward metabolism of Asn by the photorespiratory nitrogen cycle and accumulation of aromatic amino acids.

The β-cyanoalanine pathway is involved in the response to water deficit in Arabidopsis thaliana

The β-cyanoalanine pathway is primarily responsible for detoxification of excess cyanide produced by plants. Recent evidence suggests that cyanide detoxification via this pathway may be involved in the response and tolerance to water deficit in plants. The aim of this study was to explore this role in Arabidopsis thaliana in greater detail. The first objective was to establish responsiveness of the pathway to the magnitude and duration of water deficit. The second objective was to examine how interruption of single genes (AtCysA1, AtCysC1 and AtNIT4) encoding enzymes of the pathway influenced the ability to metabolize cyanide and withstand water deficit. Arabidopsis plants were exposed to conditions which emulated acute and chronic water deficit, followed by measurement of tissue cyanide concentration, activity of enzymes, and physiological parameters. The results for wild-type Arabidopsis demonstrated a transient increase in cyanide concentration and β-cyanoalanine synthase activity, followed by a decrease in both. The increase in enzyme activity was localized to the tissue in direct proximity to the stress. The knockdown AtCysA1 mutant did not differ from wild-type while AtCysC1 mutants were slightly more sensitive to water deficit. The AtNIT4 mutant was the most sensitive showing decreased growth along with altered chlorophyll content under water deficit as compared to wild-type. Collectively, the results indicated that the pathway is responsive to water deficit although the severity of stress did not alter the nature of the response, implying that the capacity to remove cyanide generated during water deficit may contribute to tolerance to this stress in Arabidopsis.

The pathway of auxin biosynthesis in plants

The plant hormone auxin, which is predominantly represented by indole-3-acetic acid (IAA), is involved in the regulation of plant growth and development. Although IAA was the first plant hormone identified, the biosynthetic pathway at the genetic level has remained unclear. Two major pathways for IAA biosynthesis have been proposed: the tryptophan (Trp)-independent and Trp-dependent pathways. In Trp-dependent IAA biosynthesis, four pathways have been postulated in plants: (i) the indole-3-acetamide (IAM) pathway; (ii) the indole-3-pyruvic acid (IPA) pathway; (iii) the tryptamine (TAM) pathway; and (iv) the indole-3-acetaldoxime (IAOX) pathway. Although different plant species may have unique strategies and modifications to optimize their metabolic pathways, plants would be expected to share evolutionarily conserved core mechanisms for auxin biosynthesis because IAA is a fundamental substance in the plant life cycle. In this review, the genes now known to be involved in auxin biosynthesis are summarized and the major IAA biosynthetic pathway distributed widely in the plant kingdom is discussed on the basis of biochemical and molecular biological findings and bioinformatics studies. Based on evolutionarily conserved core mechanisms, it is thought that the pathway via IAM or IPA is the major route(s) to IAA in plants.

Pseudomonas syringae pv. syringae B728a hydrolyses indole-3-acetonitrile to the plant hormone indole-3-acetic acid

Nitrilase enzymes catalyse the hydrolysis of nitrile compounds to the corresponding carboxylic acid and ammonia, and have been identified in plants, bacteria and fungi. There is mounting evidence to support a role for nitrilases in plant-microbe interactions, but the activity of these enzymes in plant pathogenic bacteria remains unexplored. The genomes of the plant pathogenic bacteria Pseudomonas syringae pv. syringae B728a and Pseudomonas syringae pv. tomato DC3000 contain nitrilase genes with high similarity to characterized bacterial arylacetonitrilases. In this study, we show that the nitrilase of P. syringae pv. syringae B728a is an arylacetonitrilase, which is capable of hydrolysing indole-3-acetonitrile to the plant hormone indole-3-acetic acid, and allows P. syringae pv. syringae B728a to use indole-3-acetonitrile as a nitrogen source. This enzyme may represent an additional mechanism for indole-3-acetic acid biosynthesis by P. syringae pv. syringae B728a, or may be used to degrade and assimilate aldoximes and nitriles produced during plant secondary metabolism. Nitrilase activity was not detected in P. syringae pv. tomato DC3000, despite the presence of a homologous nitrilase gene. This raises the interesting question of why nitrilase activity has been retained in P. syringae pv. syringae B728a and not in P. syringae pv. tomato DC3000.

Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens

BACKGROUND

Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species.

RESULTS

Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome.

CONCLUSIONS

P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plant-inducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome.

Nitrilase enzymes and their role in plant-microbe interactions

Nitrilase enzymes (nitrilases) catalyse the hydrolysis of nitrile compounds to the corresponding carboxylic acid and ammonia, and have a wide range of industrial and biotechnological applications, including the synthesis of industrially important carboxylic acids and bioremediation of cyanide and toxic nitriles. Nitrilases are produced by a wide range of organisms, including plants, bacteria and fungi, but despite their biotechnological importance, the role of these enzymes in living organisms is relatively underexplored. Current research suggests that nitrilases play important roles in a range of biological processes. In the context of plant-microbe interactions they may have roles in hormone synthesis, nutrient assimilation and detoxification of exogenous and endogenous nitriles. Nitrilases are produced by both plant pathogenic and plant growth-promoting microorganisms, and their activities may have a significant impact on the outcome of plant-microbe interactions. In this paper we review current knowledge of the role of nitriles and nitrilases in plants and plant-associated microorganisms, and discuss how greater understanding of the natural functions of nitrilases could be applied to benefit both industry and agriculture.