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Schwartz SL, Rangel LT, Payette JG, Fournier GP. A Proterozoic microbial origin of extant cyanide-hydrolyzing enzyme diversity. Front Microbiol 2023; 14:1130310. [PMID: 37065136 PMCID: PMC10098168 DOI: 10.3389/fmicb.2023.1130310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/07/2023] [Indexed: 04/03/2023] Open
Abstract
In addition to its role as a toxic environmental contaminant, cyanide has been hypothesized to play a key role in prebiotic chemistry and early biogeochemical evolution. While cyanide-hydrolyzing enzymes have been studied and engineered for bioremediation, the extant diversity of these enzymes remains underexplored. Additionally, the age and evolution of microbial cyanide metabolisms is poorly constrained. Here we provide comprehensive phylogenetic and molecular clock analyses of the distribution and evolution of the Class I nitrilases, thiocyanate hydrolases, and nitrile hydratases. Molecular clock analyses indicate that bacterial cyanide-reducing nitrilases were present by the Paleo- to Mesoproterozoic, and were subsequently horizontally transferred into eukaryotes. These results present a broad diversity of microbial enzymes that could be optimized for cyanide bioremediation.
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Affiliation(s)
- Sarah L. Schwartz
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA, United States
- Graduate Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
- *Correspondence: Sarah L. Schwartz,
| | - L. Thiberio Rangel
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Jack G. Payette
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Gregory P. Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
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2
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Jones LB, Wang X, Gullapalli JS, Kunz DA. Characterization of the Nit6803 nitrilase homolog from the cyanotroph Pseudomonas fluorescens NCIMB 11764. Biochem Biophys Rep 2021; 25:100893. [PMID: 33506113 PMCID: PMC7815647 DOI: 10.1016/j.bbrep.2020.100893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/21/2020] [Accepted: 12/21/2020] [Indexed: 11/01/2022] Open
Abstract
We report the purification and characterization of a nitrilase (E.C. 3.5.5.1) (Nit11764) essential for the assimilation of cyanide as the sole nitrogen source by the cyanotroph, Pseudomonas fluorescens NCIMB 11764. Nit11764, is a member of a family of homologous proteins (nitrile_sll0784) for which the genes typically reside in a conserved seven-gene cluster known as Nit1C. The physical properties and substrate specificity of Nit11764 resemble those of Nit6803, the current reference protein for the family, and the only true nitrilase that has been crystallized. The substrate binding pocket of the two enzymes places the substrate in direct proximity to the active site nucleophile (C160) and conserved catalytic triad (Glu44, Lys126). The two enzymes exhibit a similar substrate profile, however, for Nit11764, cinnamonitrile, was found to be an even better substrate than fumaronitrile the best substrate previously identified for Nit6803. A higher affinity for cinnamonitrile (Km 1.27 mM) compared to fumaronitrile (Km 8.57 mM) is consistent with docking studies predicting a more favorable interaction with hydrophobic residues lining the binding pocket. By comparison, 3,4-dimethoxycinnamonitrile was a poorer substrate the substituted methoxyl groups apparently hindering entry into the binding pocket. in situ 1H NMR studies revealed that only one of the two nitrile substituents in the dinitrile, fumaronitrile, was attacked yielding trans-3-cyanoacrylate (plus ammonia) as a product. The essentiality of Nit11764 for cyanotrophy remains uncertain given that cyanide itself is a poor substrate and the catalytic efficiencies for even the best of nitrile substrates (~5 × 103 M-1 s-1) is less than stellar.
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Affiliation(s)
- Lauren B Jones
- Division of Biochemistry and Molecular Biology, Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Xiaoqiang Wang
- Division of Biochemistry and Molecular Biology, Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA.,BioDiscovery Institute, Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Jaya S Gullapalli
- Division of Biochemistry and Molecular Biology, Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Daniel A Kunz
- Division of Biochemistry and Molecular Biology, Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
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3
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Wang YA, Sun Y, Le Blanc JM, Solomides C, Zhan T, Lu B. Nitrilase 1 modulates lung tumor progression in vitro and in vivo. Oncotarget 2017; 7:21381-92. [PMID: 26967383 PMCID: PMC5008292 DOI: 10.18632/oncotarget.7820] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/23/2016] [Indexed: 12/11/2022] Open
Abstract
Uncovering novel growth modulators for non-small cell lung cancer (NSCLC) may lead to new therapies for these patients. Previous studies suggest Nit1 suppresses chemically induced carcinogenesis of the foregut in a mouse model. In this study we aimed to determine the role of Nit1 in a transgenic mouse lung cancer model driven by a G12D Kras mutation. Nit1 knockout mice (Nit1−/−) were crossed with KrasG12D/+ mice to investigate whether a G12D Kras mutation and Nit1 inactivation interact to promote or inhibit the development of NSCLC. We found that lung tumorigenesis was suppressed in the Nit1-null background (Nit1−/−:KrasG12D/+). Micro-CT scans and gross tumor measurements demonstrated a 5-fold reduction in total tumor volumes compared to Nit1+/+KrasG12D/+ (p<0.01). Furthermore, we found that Nit1 is highly expressed in human lung cancer tissues and cell lines and use of siRNA against Nit1 decreased overall cell survival of lung cancer cells in culture. In addition, cisplatin response was enhanced in human lung cancer cells when Nit1 was knocked down and Nit1−/−:KrasG12D/+ tumors showed increased sensitivity to cisplatin in vivo. Together, our data indicate that Nit1 may play a supportive role in the modulation of lung tumorigenesis and represent a novel target for NSCLCs treatment.
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Affiliation(s)
- Yong Antican Wang
- Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Yunguang Sun
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA.,Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Justin M Le Blanc
- Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | | | - Tingting Zhan
- Department of Pharmacology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Bo Lu
- Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
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A novel role for the tumour suppressor Nitrilase1 modulating the Wnt/β-catenin signalling pathway. Cell Discov 2016; 2:15039. [PMID: 27462437 PMCID: PMC4860965 DOI: 10.1038/celldisc.2015.39] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/08/2015] [Indexed: 02/07/2023] Open
Abstract
Nitrilase1 was classified as a tumour suppressor in association with the fragile histidine-triad protein Fhit. However, knowledge about nitrilase1 and its tumour suppressor function is still limited. Whereas nitrilase1 and Fhit are discrete proteins in mammals, they are merged in Drosophila melanogaster and Caenorhabditis elegans. According to the Rosetta-Stone hypothesis, proteins encoded as fusion proteins in one organism and as separate proteins in another organism may act in the same signalling pathway. Although a direct interaction of human nitrilase1 and Fhit has not been shown, our previous finding that Fhit interacts with β-catenin and represses its transcriptional activity in the canonical Wnt pathway suggested that human nitrilase1 also modulates Wnt signalling. In fact, human nitrilase1 forms a complex with β-catenin and LEF-1/TCF-4, represses β-catenin-mediated transcription and shows an additive effect together with Fhit. Knockdown of human nitrilase1 enhances Wnt target gene expression. Moreover, our experiments show that β-catenin competes away human nitrilase1 from LEF-1/TCF and thereby contributes to the activation of Wnt-target gene transcription. Inhibitory activity of human nitrilase1 on vertebrate Wnt signalling was confirmed by repression of Wnt-induced double axis formation in Xenopus embryogenesis. In line with this finding, the Drosophila fusion protein Drosophila NitFhit directly binds to Armadillo and represses the Wingless pathway in reporter gene assays. Genetic experiments confirmed the repressive activity of Drosophila NitFhit on Wingless signalling in the Drosophila wing imaginal disc. In addition, colorectal tumour microarray analysis revealed a significantly reduced expression of human nitrilase1 in poorly differentiated tumours. Taken together, repression of the canonical Wnt pathway represents a new mechanism for the human nitrilase1 tumour suppressor function.
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Pourtaji A, Robati RY, Lari P, Hosseinzadeh H, Ramezani M, Abnous K. Proteomics screening of adenosine triphosphate-interacting proteins in the liver of diazinon-treated rats. Hum Exp Toxicol 2015; 35:1084-92. [PMID: 26721910 DOI: 10.1177/0960327115619771] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
AIM Diazinon (DZN) is one of the most important organophosphorus compounds used to control pests in agriculture in many countries. Several studies have shown that exposure to DZN may alter protein expression in the liver. In order to further investigate the mechanism of DZN toxicity, differentially expressed ATP-interacting proteins, following subacute exposure to toxin, were separated and identified in rat liver. MAIN METHODS Male rats were equally divided into four groups: control (corn oil) and DZN (15 mg/kg) by gavage once a day for 4 weeks. After homogenization of liver tissue, lysates were incubated ATP-sepharose beads. After several washes, ATP-interacting proteins were eluted and separated on 2-D polyacrylamide gels. Deferentially expressed proteins were cut and identified using matrix-assisted laser desorption/ionization/time-of-flight and Mascot database. Identified proteins were classified according to their biological process using protein analysis through evolutionary relationships (PANTHER) Web site. KEY FINDING In this work, we showed that several key proteins involved in biological processes such as antioxidant system, oxidative stress, apoptosis, and metabolism were differentially expressed after subacute exposure to DZN.
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Affiliation(s)
- A Pourtaji
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - R Yazdian Robati
- Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - P Lari
- Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - H Hosseinzadeh
- Pharmaceutical Research Center, Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - M Ramezani
- Nanotechnology Research Center, Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - K Abnous
- Pharmaceutical Research Center, Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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Liu H, Gao Y, Zhang M, Qiu X, Cooper AJL, Niu L, Teng M. Structures of enzyme-intermediate complexes of yeast Nit2: insights into its catalytic mechanism and different substrate specificity compared with mammalian Nit2. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1470-81. [PMID: 23897470 DOI: 10.1107/s0907444913009347] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 04/06/2013] [Indexed: 11/11/2022]
Abstract
The Nit (nitrilase-like) protein subfamily constitutes branch 10 of the nitrilase superfamily. Nit proteins are widely distributed in nature. Mammals possess two members of the Nit subfamily, namely Nit1 and Nit2. Based on sequence similarity, yeast Nit2 (yNit2) is a homologue of mouse Nit1, a tumour-suppressor protein whose substrate specificity is not yet known. Previous studies have shown that mammalian Nit2 (also a putative tumour suppressor) is identical to ω-amidase, an enzyme that catalyzes the hydrolysis of α-ketoglutaramate (α-KGM) and α-ketosuccinamate (α-KSM) to α-ketoglutarate (α-KG) and oxaloacetate (OA), respectively. In the present study, crystal structures of wild-type (WT) yNit2 and of WT yNit2 in complex with α-KG and with OA were determined. In addition, the crystal structure of the C169S mutant of yNit2 (yNit2-C169S) in complex with an endogenous molecule of unknown structure was also solved. Analysis of the structures revealed that α-KG and OA are covalently bound to Cys169 by the formation of a thioester bond between the sulfhydryl group of the cysteine residue and the γ-carboxyl group of α-KG or the β-carboxyl group of OA, reflecting the presumed reaction intermediates. However, an enzymatic assay suggests that α-KGM is a relatively poor substrate of yNit2. Finally, a ligand was found in the active site of yNit2-C169S that may be a natural substrate of yNit2 or an endogenous regulator of enzyme activity. These crystallographic analyses provide information on the mode of substrate/ligand binding at the active site of yNit2 and insights into the catalytic mechanism. These findings suggest that yNit2 may have broad biological roles in yeast, especially in regard to nitrogen homeostasis, and provide a framework for the elucidation of the substrate specificity and biological role of mammalian Nit1.
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Affiliation(s)
- Hejun Liu
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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Doskočilová A, Kohoutová L, Volc J, Kourová H, Benada O, Chumová J, Plíhal O, Petrovská B, Halada P, Bögre L, Binarová P. NITRILASE1 regulates the exit from proliferation, genome stability and plant development. THE NEW PHYTOLOGIST 2013; 198:685-698. [PMID: 23437871 DOI: 10.1111/nph.12185] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/09/2013] [Indexed: 05/08/2023]
Abstract
Nitrilases are highly conserved proteins with catabolic activity but much less understood functions in cell division and apoptosis. To elucidate the biological functions of Arabidopsis NITRILASE1, we characterized its molecular forms, cellular localization and involvement in cell proliferation and plant development. We performed biochemical and mass spectrometry analyses of NITRILASE1 complexes, electron microscopy of nitrilase polymers, imaging of developmental and cellular distribution, silencing and overexpression of nitrilases to study their functions. We found that NITRILASE1 has an intrinsic ability to form filaments. GFP-NITRILASE1 was abundant in proliferating cells, distributed in cytoplasm, in the perinuclear area and associated with microtubules. As cells exited proliferation and entered differentiation, GFP-NITRILASE1 became predominantly nuclear. Nitrilase silencing dose-dependently compromised plant growth, led to loss of tissue organization and sustained proliferation. Cytokinesis was frequently aborted, leading to enlarged polyploid cells. In reverse, independently transformed cell lines overexpressing GFP-NITRILASE1 showed slow growth and increased rate of programmed cell death. Altogether, our data suggest that NITRILASE1 homologues regulate the exit from cell cycle and entry into differentiation and simultaneously are required for cytokinesis. These functions are essential to maintain normal ploidy, genome stability and tissue organization.
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Affiliation(s)
- Anna Doskočilová
- Institute of Microbiology AS CR, v. v. i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Lucie Kohoutová
- Institute of Microbiology AS CR, v. v. i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Jindřich Volc
- Institute of Microbiology AS CR, v. v. i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Hana Kourová
- Institute of Microbiology AS CR, v. v. i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Oldřich Benada
- Institute of Microbiology AS CR, v. v. i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Jana Chumová
- Institute of Microbiology AS CR, v. v. i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Ondřej Plíhal
- Institute of Microbiology AS CR, v. v. i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Beáta Petrovská
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany AS CR, v. v. i., Sokolovská 6, 772 00, Olomouc, Czech Republic
| | - Petr Halada
- Institute of Microbiology AS CR, v. v. i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - László Bögre
- Plant Molecular Sciences, Centre for Systems and Synthetic Biology, School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
| | - Pavla Binarová
- Institute of Microbiology AS CR, v. v. i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
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