Cyanide-degrading nitrilases in nature

Benedik, Michael J.; Sewell, B. Trevor

doi:10.2323/jgam.2017.06.002

Cited by 6 publications

(10 citation statements)

References 15 publications

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“…We did not find any experimentally confirmed nitrile-degrading enzyme for this genus in literature. However, predictions for putative nitrilase-encoding genes and closely related cyanide dihydratases exist (Benedik and Sewell, 2018). This would explain the observed phenomenon.…”

Section: Discussionmentioning

confidence: 94%

Impact of Nitriles on Bacterial Communities

Egelkamp

Zimmermann

Schneider

et al. 2019

Front. Environ. Sci.

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Nitriles are organic molecules with-C≡N as functional group and often toxic for living organisms. Detoxification can occur via nitrilases that degrade nitriles directly to carboxylic acids and ammonia, or with nitrile hydratases and amidases that convert nitriles to amides and subsequently to carboxylic acids and ammonia. Despite the knowledge of enzymatic degradation pathways, the influence of these compounds on the composition of bacterial communities is unknown. The tolerances of four phylogenetically different bacterial strains without known nitrile detoxification systems (Agrobacterium tumefaciens, Bacillus subtilis, Corynebacterium glutamicum, and Escherichia coli) to the toxic effects of nine nitriles and the corresponding carboxylic acids were determined. Based on these results, the effect of nitriles on diversity and composition of compost-derived bacterial communities was monitored over time by 16S rRNA gene amplicon-based and metagenome analyses. Acetone cyanohydrin, 2-phenylpropionitrile, and pyruvonitrile exhibited a lethal, phenylacetonitrile, 4-hydroxybenzonitrile, and cyclohexanecarbonitrile a growth-suppressing and succinonitrile, acetonitrile, and crotononitrile a growth-promoting effect on the studied communities. Furthermore, each nitrile had a specific community-shaping effect, e.g., communities showing growth-suppression exhibited high relative abundance of Paenibacillus. In general, analysis of all data indicated a higher resistance of Gram-positive than Gram-negative bacterial community members and test organisms to growth-suppressing nitriles. More than 70 putative nitrilase-encoding and over 20 potential nitrile hydratase-encoding genes were identified during analysis of metagenomes derived from nitrile-enrichments, underlining the high yet often unexplored abundance of nitrile-degrading enzymes.

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Section: Discussionmentioning

confidence: 94%

Impact of Nitriles on Bacterial Communities

Egelkamp

Zimmermann

Schneider

et al. 2019

Front. Environ. Sci.

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“…The most variable region in the nitrilase protein family is the C-terminal region ( 8 , 32 ). Thus, we mapped a phylogenetic tree obtained from the full-length sequences of identified CynDs homologs to an alignment of the C-terminal region (residues 296 to 330) ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Genomic Characterization ofBacillus safensisIsolated from Mine Tailings in Peru and Evaluation of Its Cyanide-Degrading Enzyme CynD

Arévalo

Sifuentes

Portocarrero

et al. 2022

Appl Environ Microbiol

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“…The most variable region in the nitrilase protein family is the C-terminal (Benedik & Sewell, 2018; Thuku et al, 2009). Thus, we associated a phylogenetic tree obtained from the full-length sequences of identified CynDs homologs to an alignment of the C-terminal region (residues 296 to 330) (Fig.…”

Section: Resultsmentioning

confidence: 99%

Isolation of a Bacillus safensis from mine tailings in Peru, genomic characterization and characterization of its cyanide-degrading enzyme CynD

Arevalo

Sifuentes

Portocarrero

et al. 2021

Preprint

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Cyanide is widely used in industry as a potent lixiviant due to its capacity to tightly bind metals. This property imparts cyanide enormous toxicity to all known organisms. Thus, industries that utilize this compound must reduce its concentration in recycled or waste waters. Physical, chemical, and biological treatments have been used for cyanide remediation; however, none of them meet all the desired characteristics: efficiency, low cost and low environmental impact. A better understanding of metabolic pathways and biochemistry of enzymes involved in cyanide degradation is a necessary step to improve cyanide bioremediation efficacy to satisfy the industry requirements. Here, we used several approaches to explore this topic. We have isolated three cyanide-degrading Bacillus strains from water in contact with mine tailings from Lima, Peru, and classified them as Bacillus safensis PER-URP-08, Bacillus licheniformis PER-URP-12, and Bacillus subtilis PER-URP-17 based on 16S rRNA gene sequencing and core genome analyses. Additionally, core genome analyses of 132 publicly available genomes of Bacillus pumilus group including B. safensis and B. altitudinis allowed us to reclassify some strains and identify two strains that did not match with any known species of the Bacillus pumilus group. We searched for possible routes of cyanide-degradation in the genomes of these three strains and identified putative B. licheniformis PER-URP-12 and B. subtilis PER-URP-17 rhodaneses and B. safensis PER-URP-08 cyanide dihydratase (CynD) sequences possibly involved cyanide degradation. We identified characteristic C-terminal residues that differentiate CynD from B. pumilus and B. safensis, and showed that, differently from CynD from B. pumilus C1, recombinant CynD from the Bacillus safensis PER-URP-08 strain remains active up to pH 9 and presents a distinct oligomerization pattern at pH 8 and 9. Moreover, transcripts of B. safensis PER-URP-08 CynD (CynDPER-URP-08) are strongly induced in the presence of cyanide. Our results warrant further investigation of B. safensis PER-URP-08 and CynDPER-URP-08 as potential tools for cyanide-bioremediation.

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Cyanide-degrading nitrilases in nature

Cited by 6 publications

References 15 publications

Impact of Nitriles on Bacterial Communities

Impact of Nitriles on Bacterial Communities

Genomic Characterization ofBacillus safensisIsolated from Mine Tailings in Peru and Evaluation of Its Cyanide-Degrading Enzyme CynD

Isolation of a Bacillus safensis from mine tailings in Peru, genomic characterization and characterization of its cyanide-degrading enzyme CynD

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