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Xia Y, Zhao J, Saeed M, Hussain N, Chen X, Guo Z, Yong Y, Chen H. Molecular Modification Strategies of Nitrilase for Its Potential Application in Agriculture. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:15106-15121. [PMID: 38949086 DOI: 10.1021/acs.jafc.4c03388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Some feed source plants will produce secondary metabolites such as cyanogenic glycosides during metabolism, which will produce some poisonous nitrile compounds after hydrolysis and remain in plant tissues. The consumption of feed-source plants without proper treatment affect the health of the animals' bodies. Nitrilases can convert nitriles and have been used in industry as green biocatalysts. However, due to their bottleneck problems, their application in agriculture is still facing challenges. Acid-resistant nitrilase preparations, high-temperature resistance, antiprotease activity, strong activity, and strict reaction specificity urgently need to be developed. In this paper, the application potential of nitrilase in agriculture, especially in feed processing industry was explored, the source properties and catalytic mechanism of nitrilase were reviewed, and modification strategies for nitrilase application in agriculture were proposed to provide references for future research and application of nitrilase in agricultural and especially in the biological feed scene.
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Affiliation(s)
- Yutong Xia
- School of the Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
| | - Jia Zhao
- School of the Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
| | - Muhammad Saeed
- School of the Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
- Department of Poultry Science, Faculty of Animal Production and Technology, The Cholistan University of Veterinary and Animal Sciences, Bahawalpur 63100, Pakistan
| | - Nazar Hussain
- School of the Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
| | - Xihua Chen
- School of the Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
| | - Zhongjian Guo
- School of the Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
| | - Yangchun Yong
- Biofuels Institute, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
| | - Huayou Chen
- School of the Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
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2
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Cederfelt D, Badgujar D, Au Musse A, Lohkamp B, Danielson UH, Dobritzsch D. The Allosteric Regulation of Β-Ureidopropionase Depends on Fine-Tuned Stability of Active-Site Loops and Subunit Interfaces. Biomolecules 2023; 13:1763. [PMID: 38136634 PMCID: PMC10741476 DOI: 10.3390/biom13121763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
The activity of β-ureidopropionase, which catalyses the last step in the degradation of uracil, thymine, and analogous antimetabolites, is cooperatively regulated by the substrate and product of the reaction. This involves shifts in the equilibrium of the oligomeric states of the enzyme, but how these are achieved and result in changes in enzyme catalytic competence has yet to be determined. Here, the regulation of human β-ureidopropionase was further explored via site-directed mutagenesis, inhibition studies, and cryo-electron microscopy. The active-site residue E207, as well as H173 and H307 located at the dimer-dimer interface, are shown to play crucial roles in enzyme activation. Dimer association to larger assemblies requires closure of active-site loops, which positions the catalytically crucial E207 stably in the active site. H173 and H307 likely respond to ligand-induced changes in their environment with changes in their protonation states, which fine-tunes the active-site loop stability and the strength of dimer-dimer interfaces and explains the previously observed pH influence on the oligomer equilibrium. The correlation between substrate analogue structure and effect on enzyme assembly suggests that the ability to favourably interact with F205 may distinguish activators from inhibitors. The cryo-EM structure of human β-ureidopropionase assembly obtained at low pH provides first insights into the architecture of its activated state. and validates our current model of the allosteric regulation mechanism. Closed entrance loop conformations and dimer-dimer interfaces are highly conserved between human and fruit fly enzymes.
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Affiliation(s)
- Daniela Cederfelt
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
| | - Dilip Badgujar
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
- Department of Cell and Molecular Biology, Uppsala University, 751 23 Uppsala, Sweden
| | - Ayan Au Musse
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
- School of Science and Technology, Örebro University, 701 82 Örebro, Sweden
| | - Bernhard Lohkamp
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Stockholm, Sweden;
| | - U. Helena Danielson
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
| | - Doreen Dobritzsch
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
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Park CK, Horton NC. Structures, functions, and mechanisms of filament forming enzymes: a renaissance of enzyme filamentation. Biophys Rev 2019; 11:927-994. [PMID: 31734826 PMCID: PMC6874960 DOI: 10.1007/s12551-019-00602-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/24/2019] [Indexed: 12/19/2022] Open
Abstract
Filament formation by non-cytoskeletal enzymes has been known for decades, yet only relatively recently has its wide-spread role in enzyme regulation and biology come to be appreciated. This comprehensive review summarizes what is known for each enzyme confirmed to form filamentous structures in vitro, and for the many that are known only to form large self-assemblies within cells. For some enzymes, studies describing both the in vitro filamentous structures and cellular self-assembly formation are also known and described. Special attention is paid to the detailed structures of each type of enzyme filament, as well as the roles the structures play in enzyme regulation and in biology. Where it is known or hypothesized, the advantages conferred by enzyme filamentation are reviewed. Finally, the similarities, differences, and comparison to the SgrAI endonuclease system are also highlighted.
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Affiliation(s)
- Chad K. Park
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721 USA
| | - Nancy C. Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721 USA
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4
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Zhang Q, Lu X, Zhang Y, Tang X, Zheng R, Zheng Y. Development of a robust nitrilase by fragment swapping and semi‐rational design for efficient biosynthesis of pregabalin precursor. Biotechnol Bioeng 2019; 117:318-329. [DOI: 10.1002/bit.27203] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/06/2019] [Accepted: 10/13/2019] [Indexed: 01/20/2023]
Affiliation(s)
- Qin Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and BioengineeringZhejiang University of TechnologyHangzhou China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of EducationZhejiang University of TechnologyHangzhou China
| | - Xia‐Feng Lu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and BioengineeringZhejiang University of TechnologyHangzhou China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of EducationZhejiang University of TechnologyHangzhou China
| | - Yan Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and BioengineeringZhejiang University of TechnologyHangzhou China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of EducationZhejiang University of TechnologyHangzhou China
| | - Xiao‐Ling Tang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and BioengineeringZhejiang University of TechnologyHangzhou China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of EducationZhejiang University of TechnologyHangzhou China
| | - Ren‐Chao Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and BioengineeringZhejiang University of TechnologyHangzhou China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of EducationZhejiang University of TechnologyHangzhou China
| | - Yu‐Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and BioengineeringZhejiang University of TechnologyHangzhou China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of EducationZhejiang University of TechnologyHangzhou China
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5
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Mulelu AE, Kirykowicz AM, Woodward JD. Cryo-EM and directed evolution reveal how Arabidopsis nitrilase specificity is influenced by its quaternary structure. Commun Biol 2019; 2:260. [PMID: 31341959 PMCID: PMC6637149 DOI: 10.1038/s42003-019-0505-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 06/13/2019] [Indexed: 01/17/2023] Open
Abstract
Nitrilases are helical enzymes that convert nitriles to acids and/or amides. All plants have a nitrilase 4 homolog specific for ß-cyanoalanine, while in some plants neofunctionalization has produced nitrilases with altered specificity. Plant nitrilase substrate size and specificity correlate with helical twist, but molecular details of this relationship are lacking. Here we determine, to our knowledge, the first close-to-atomic resolution (3.4 Å) cryo-EM structure of an active helical nitrilase, the nitrilase 4 from Arabidopsis thaliana. We apply site-saturation mutagenesis directed evolution to three residues (R95, S224, and L169) and generate a mutant with an altered helical twist that accepts substrates not catalyzed by known plant nitrilases. We reveal that a loop between α2 and α3 limits the length of the binding pocket and propose that it shifts position as a function of helical twist. These insights will allow us to start designing nitrilases for chemoenzymatic synthesis.
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Affiliation(s)
- Andani E. Mulelu
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925 South Africa
- Structural Biology Research Unit, University of Cape Town, Cape Town, 7925 South Africa
| | - Angela M. Kirykowicz
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925 South Africa
- Structural Biology Research Unit, University of Cape Town, Cape Town, 7925 South Africa
| | - Jeremy D. Woodward
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925 South Africa
- Structural Biology Research Unit, University of Cape Town, Cape Town, 7925 South Africa
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6
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Sharma M, Akhter Y, Chatterjee S. A review on remediation of cyanide containing industrial wastes using biological systems with special reference to enzymatic degradation. World J Microbiol Biotechnol 2019; 35:70. [DOI: 10.1007/s11274-019-2643-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/08/2019] [Indexed: 11/24/2022]
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7
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Woodward JD, Trompetter I, Sewell BT, Piotrowski M. Substrate specificity of plant nitrilase complexes is affected by their helical twist. Commun Biol 2018; 1:186. [PMID: 30417123 PMCID: PMC6214922 DOI: 10.1038/s42003-018-0186-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 10/01/2018] [Indexed: 01/09/2023] Open
Abstract
Nitrilases are oligomeric, helix-forming enzymes from plants, fungi and bacteria that are involved in the metabolism of various natural and artificial nitriles. These biotechnologically important enzymes are often specific for certain substrates, but directed attempts at modifying their substrate specificities by exchanging binding pocket residues have been largely unsuccessful. Thus, the basis for their selectivity is still unknown. Here we show, based on work with two highly similar nitrilases from the plant Capsella rubella, that modifying nitrilase helical twist, either by exchanging an interface residue or by imposing a different twist, without altering any binding pocket residues, changes substrate preference. We reveal that helical twist and substrate size correlate and when binding pocket residues are exchanged between two nitrilases that show the same twist but different specificities, their specificities change. Based on these findings we propose that helical twist influences the overall size of the binding pocket.
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Affiliation(s)
- Jeremy D Woodward
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925, South Africa.,Department of Molecular Genetics and Physiology of Plants, Ruhr-Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Inga Trompetter
- Department of Molecular Genetics and Physiology of Plants, Ruhr-Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - B Trevor Sewell
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925, South Africa
| | - Markus Piotrowski
- Department of Molecular Genetics and Physiology of Plants, Ruhr-Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany.
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8
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Crystal structure and pH-dependent allosteric regulation of human β-ureidopropionase, an enzyme involved in anticancer drug metabolism. Biochem J 2018; 475:2395-2416. [PMID: 29976570 DOI: 10.1042/bcj20180222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
β-Ureidopropionase (βUP) catalyzes the third step of the reductive pyrimidine catabolic pathway responsible for breakdown of uracil-, thymine- and pyrimidine-based antimetabolites such as 5-fluorouracil. Nitrilase-like βUPs use a tetrad of conserved residues (Cys233, Lys196, Glu119 and Glu207) for catalysis and occur in a variety of oligomeric states. Positive co-operativity toward the substrate N-carbamoyl-β-alanine and an oligomerization-dependent mechanism of substrate activation and product inhibition have been reported for the enzymes from some species but not others. Here, the activity of recombinant human βUP is shown to be similarly regulated by substrate and product, but in a pH-dependent manner. Existing as a homodimer at pH 9, the enzyme increasingly associates to form octamers and larger oligomers with decreasing pH. Only at physiological pH is the enzyme responsive to effector binding, with N-carbamoyl-β-alanine causing association to more active higher molecular mass species, and β-alanine dissociation to inactive dimers. The parallel between the pH and ligand-induced effects suggests that protonation state changes play a crucial role in the allosteric regulation mechanism. Disruption of dimer-dimer interfaces by site-directed mutagenesis generated dimeric, inactive enzyme variants. The crystal structure of the T299C variant refined to 2.08 Å resolution revealed high structural conservation between human and fruit fly βUP, and supports the hypothesis that enzyme activation by oligomer assembly involves ordering of loop regions forming the entrance to the active site at the dimer-dimer interface, effectively positioning the catalytically important Glu207 in the active site.
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9
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Martins MP, Gomes EV, Sanches PR, Pedersoli WR, Martinez-Rossi NM, Rossi A. mus-52 disruption and metabolic regulation in Neurospora crassa: Transcriptional responses to extracellular phosphate availability. PLoS One 2018; 13:e0195871. [PMID: 29668735 PMCID: PMC5905970 DOI: 10.1371/journal.pone.0195871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 03/30/2018] [Indexed: 12/01/2022] Open
Abstract
Advances in the understanding of molecular systems depend on specific tools like the disruption of genes to produce strains with the desired characteristics. The disruption of any mutagen sensitive (mus) genes in the model fungus Neurospora crassa, i.e. mus-51, mus-52, or mus-53, orthologous to the human genes KU70, KU80, and LIG4, respectively, provides efficient tools for gene targeting. Accordingly, we used RNA-sequencing and reverse transcription-quantitative polymerase chain reaction amplification techniques to evaluate the effects of mus-52 deletion in N. crassa gene transcriptional modulation, and thus, infer its influence regarding metabolic response to extracellular availability of inorganic phosphate (Pi). Notably, the absence of MUS-52 affected the transcription of a vast number of genes, highlighting the expression of those coding for transcription factors, kinases, circadian clocks, oxi-reduction balance, and membrane- and nucleolus-related proteins. These findings may provide insights toward the KU molecular mechanisms, which have been related to telomere maintenance, apoptosis, DNA replication, and gene transcription regulation, as well as associated human conditions including immune system disorders, cancer, and aging.
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Affiliation(s)
- Maíra P. Martins
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo, Brazil
| | - Eriston V. Gomes
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo, Brazil
| | - Pablo R. Sanches
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo, Brazil
| | - Wellington R. Pedersoli
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo, Brazil
| | - Nilce M. Martinez-Rossi
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo, Brazil
| | - Antonio Rossi
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo, Brazil
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Lovasoa CR, Hela K, Harinaivo AA, Hamma Y. Bioremediation of soil and water polluted by cyanide: A review. ACTA ACUST UNITED AC 2017. [DOI: 10.5897/ajest2016.2264] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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11
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Park JM, Trevor Sewell B, Benedik MJ. Cyanide bioremediation: the potential of engineered nitrilases. Appl Microbiol Biotechnol 2017; 101:3029-3042. [PMID: 28265723 DOI: 10.1007/s00253-017-8204-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 11/29/2022]
Abstract
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.
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Affiliation(s)
- Jason M Park
- Department of Biology, Texas A&M University, College Station, TX, 77843-3258, USA
| | - B Trevor Sewell
- Structural Biology Research Unit, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7925, South Africa
| | - Michael J Benedik
- Department of Biology, Texas A&M University, College Station, TX, 77843-3258, USA.
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Park JM, Mulelu A, Sewell BT, Benedik MJ. Probing an Interfacial Surface in the Cyanide Dihydratase from Bacillus pumilus, A Spiral Forming Nitrilase. Front Microbiol 2016; 6:1479. [PMID: 26779137 PMCID: PMC4700190 DOI: 10.3389/fmicb.2015.01479] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/08/2015] [Indexed: 11/13/2022] Open
Abstract
Nitrilases are of significant interest both due to their potential for industrial production of valuable products as well as degradation of hazardous nitrile-containing wastes. All known functional members of the nitrilase superfamily have an underlying dimer structure. The true nitrilases expand upon this basic dimer and form large spiral or helical homo-oligomers. The formation of this larger structure is linked to both the activity and substrate specificity of these nitrilases. The sequences of the spiral nitrilases differ from the non-spiral forming homologs by the presence of two insertion regions. Homology modeling suggests that these regions are responsible for associating the nitrilase dimers into the oligomer. Here we used cysteine scanning across these two regions, in the spiral forming nitrilase cyanide dihydratase from Bacillus pumilus (CynD), to identify residues altering the oligomeric state or activity of the nitrilase. Several mutations were found to cause changes to the size of the oligomer as well as reduction in activity. Additionally one mutation, R67C, caused a partial defect in oligomerization with the accumulation of smaller oligomer variants. These results support the hypothesis that these insertion regions contribute to the unique quaternary structure of the spiral microbial nitrilases.
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Affiliation(s)
- Jason M Park
- Department of Biology, Texas A&M University, College Station TX, USA
| | - Andani Mulelu
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - B Trevor Sewell
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - Michael J Benedik
- Department of Biology, Texas A&M University, College Station TX, USA
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Irmer H, Tarazona S, Sasse C, Olbermann P, Loeffler J, Krappmann S, Conesa A, Braus GH. RNAseq analysis of Aspergillus fumigatus in blood reveals a just wait and see resting stage behavior. BMC Genomics 2015; 16:640. [PMID: 26311470 PMCID: PMC4551469 DOI: 10.1186/s12864-015-1853-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 08/17/2015] [Indexed: 12/20/2022] Open
Abstract
Background Invasive aspergillosis is started after germination of Aspergillus fumigatus conidia that are inhaled by susceptible individuals. Fungal hyphae can grow in the lung through the epithelial tissue and disseminate hematogenously to invade into other organs. Low fungaemia indicates that fungal elements do not reside in the bloodstream for long. Results We analyzed whether blood represents a hostile environment to which the physiology of A. fumigatus has to adapt. An in vitro model of A. fumigatus infection was established by incubating mycelium in blood. Our model allowed to discern the changes of the gene expression profile of A. fumigatus at various stages of the infection. The majority of described virulence factors that are connected to pulmonary infections appeared not to be activated during the blood phase. Three active processes were identified that presumably help the fungus to survive the blood environment in an advanced phase of the infection: iron homeostasis, secondary metabolism, and the formation of detoxifying enzymes. Conclusions We propose that A. fumigatus is hardly able to propagate in blood. After an early stage of sensing the environment, virtually all uptake mechanisms and energy-consuming metabolic pathways are shut-down. The fungus appears to adapt by trans-differentiation into a resting mycelial stage. This might reflect the harsh conditions in blood where A. fumigatus cannot take up sufficient nutrients to establish self-defense mechanisms combined with significant growth. Electronic supplementary material The online version of this article (doi10.1186/s12864-015-1853-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Henriette Irmer
- Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstraße 8, D-37077, Göttingen, Germany.
| | - Sonia Tarazona
- Genomics of Gene Expression Lab, Prince Felipe Research Center, Av. Eduardo Primo Yufera 3, 46012, Valencia, Spain.
| | - Christoph Sasse
- Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstraße 8, D-37077, Göttingen, Germany.
| | - Patrick Olbermann
- Research Center for Infectious Diseases, Julius-Maximilians University Würzburg, Würzburg, Germany.
| | - Jürgen Loeffler
- Laboratory WÜ4i, Medical Clinic and Policlinic II, University Clinic Würzburg, Würzburg, Germany.
| | - Sven Krappmann
- Research Center for Infectious Diseases, Julius-Maximilians University Würzburg, Würzburg, Germany. .,Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinik Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
| | - Ana Conesa
- Genomics of Gene Expression Lab, Prince Felipe Research Center, Av. Eduardo Primo Yufera 3, 46012, Valencia, Spain. .,Department of Microbiology and Cell Science, Institute for Food and Agricultura Sciences, University of Florida at Gainesville, Gainesville, FL, USA.
| | - Gerhard H Braus
- Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstraße 8, D-37077, Göttingen, Germany.
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Crum MAN, Park JM, Mulelu AE, Sewell BT, Benedik MJ. Probing C-terminal interactions of the Pseudomonas stutzeri cyanide-degrading CynD protein. Appl Microbiol Biotechnol 2014; 99:3093-102. [PMID: 25549622 DOI: 10.1007/s00253-014-6335-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 12/10/2014] [Accepted: 12/14/2014] [Indexed: 12/01/2022]
Abstract
The cyanide dihydratases from Bacillus pumilus and Pseudomonas stutzeri share high amino acid sequence similarity throughout except for their highly divergent C-termini. However, deletion or exchange of the C-termini had different effects upon each enzyme. Here we extended previous studies and investigated how the C-terminus affects the activity and stability of three nitrilases, the cyanide dihydratases from B. pumilus (CynDpum) and P. stutzeri (CynDstut) and the cyanide hydratase from Neurospora crassa. Enzymes in which the C-terminal residues were deleted decreased in both activity and thermostability with increasing deletion lengths. However, CynDstut was more sensitive to such truncation than the other two enzymes. A domain of the P. stutzeri CynDstut C-terminus not found in the other enzymes, 306GERDST311, was shown to be necessary for functionality and explains the inactivity of the previously described CynDstut-pum hybrid. This suggests that the B. pumilus C-terminus, which lacks this motif, may have specific interactions elsewhere in the protein, preventing it from acting in trans on a heterologous CynD protein. We identify the dimerization interface A-surface region 195-206 (A2) from CynDpum as this interaction site. However, this A2 region did not rescue activity in C-terminally truncated CynDstutΔ302 or enhance the activity of full-length CynDstut and therefore does not act as a general stability motif.
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Affiliation(s)
- Mary Abou-Nader Crum
- Department of Biology, Texas A&M University, College Station, TX, 77843-3258, USA
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Kaplan O, Bezouška K, Plíhal O, Ettrich R, Kulik N, Vaněk O, Kavan D, Benada O, Malandra A, Sveda O, Veselá AB, Rinágelová A, Slámová K, Cantarella M, Felsberg J, Dušková J, Dohnálek J, Kotik M, Křen V, Martínková L. Heterologous expression, purification and characterization of nitrilase from Aspergillus niger K10. BMC Biotechnol 2011; 11:2. [PMID: 21210990 PMCID: PMC3023689 DOI: 10.1186/1472-6750-11-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 01/06/2011] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Nitrilases attract increasing attention due to their utility in the mild hydrolysis of nitriles. According to activity and gene screening, filamentous fungi are a rich source of nitrilases distinct in evolution from their widely examined bacterial counterparts. However, fungal nitrilases have been less explored than the bacterial ones. Nitrilases are typically heterogeneous in their quaternary structures, forming short spirals and extended filaments, these features making their structural studies difficult. RESULTS A nitrilase gene was amplified by PCR from the cDNA library of Aspergillus niger K10. The PCR product was ligated into expression vectors pET-30(+) and pRSET B to construct plasmids pOK101 and pOK102, respectively. The recombinant nitrilase (Nit-ANigRec) expressed in Escherichia coli BL21-Gold(DE3)(pOK101/pTf16) was purified with an about 2-fold increase in specific activity and 35% yield. The apparent subunit size was 42.7 kDa, which is approx. 4 kDa higher than that of the enzyme isolated from the native organism (Nit-ANigWT), indicating post-translational cleavage in the enzyme's native environment. Mass spectrometry analysis showed that a C-terminal peptide (Val327 - Asn₃₅₆) was present in Nit-ANigRec but missing in Nit-ANigWT and Asp₂₉₈-Val₃₁₃ peptide was shortened to Asp₂₉₈-Arg₃₁₀ in Nit-ANigWT. The latter enzyme was thus truncated by 46 amino acids. Enzymes Nit-ANigRec and Nit-ANigWT differed in substrate specificity, acid/amide ratio, reaction optima and stability. Refolded recombinant enzyme stored for one month at 4°C was fractionated by gel filtration, and fractions were examined by electron microscopy. The late fractions were further analyzed by analytical centrifugation and dynamic light scattering, and shown to consist of a rather homogeneous protein species composed of 12-16 subunits. This hypothesis was consistent with electron microscopy and our modelling of the multimeric nitrilase, which supports an arrangement of dimers into helical segments as a plausible structural solution. CONCLUSIONS The nitrilase from Aspergillus niger K10 is highly homologous (≥86%) with proteins deduced from gene sequencing in Aspergillus and Penicillium genera. As the first of these proteins, it was shown to exhibit nitrilase activity towards organic nitriles. The comparison of the Nit-ANigRec and Nit-ANigWT suggested that the catalytic properties of nitrilases may be changed due to missing posttranslational cleavage of the former enzyme. Nit-ANigRec exhibits a lower tendency to form filaments and, moreover, the sample homogeneity can be further improved by in vitro protein refolding. The homogeneous protein species consisting of short spirals is expected to be more suitable for structural studies.
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Affiliation(s)
- Ondřej Kaplan
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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