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Yoon J, Lee J, Kim J, Lee SM, Kim S, Park HG. A novel ultrasensitive RNase H assay based on phosphorothioated-terminal hairpin formation and self-priming extension reaction. Biosens Bioelectron 2024; 253:116174. [PMID: 38432074 DOI: 10.1016/j.bios.2024.116174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/16/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024]
Abstract
We herein present a novel ultrasensitive RNase H assay based on phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP) reaction. The detection probe employed as a key component in this technique serves as a substrate for RNase H and triggers the PS-THSP reaction upon the RNase H-mediated degradation of the probe. As a consequence, a large number of long concatemeric amplification products could be produced and used to identify the RNase H activity through the fluorescence signals produced by the nucleic acid-specific fluorescent dye, SYTO 9. Importantly, the use of the gp32 protein allowed the PS-THSP reaction to be performed at 37 °C, ultimately enabling an isothermal one-step RNase H assay. Based on this sophisticated design principle, the RNase H activity was very sensitively detected, down to 0.000237 U mL-1 with high specificity. We further verified its practical applicability through its successful application to the screening of RNase H inhibitors. With its operational convenience and excellent analytical performance, this technique could serve as a new platform for RNase H assay in a wide range of biological applications.
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Affiliation(s)
- Junhyeok Yoon
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jinhwan Lee
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jaemin Kim
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Sang Mo Lee
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Soohyun Kim
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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Karmakar MM, Deb S, Dutta TK. Metabolism of toxic benzonitrile and hydroxybenzonitrile isomers via several distinct central pathway intermediates in a catabolically robust Burkholderia sp. Biochem Biophys Res Commun 2024; 709:149822. [PMID: 38547604 DOI: 10.1016/j.bbrc.2024.149822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024]
Abstract
Aromatic nitriles are of considerable environmental concern, because of their hazardous impacts on the health of both humans and wildlife. In the present study, Burkholderia sp. strain BC1 was observed to be capable of utilizing toxic benzonitrile and hydroxybenzonitrile isomers singly, as sole carbon and energy sources. The results of chromatographic and spectrometric analyses in combination with oxygen uptake and enzyme activity studies, revealed the metabolism of benzonitrile as well as 2-, 3-, and 4-hydroxybenzonitriles by nitrile hydratase-amidase to the corresponding carboxylates. These carboxylates were further metabolized via central pathways, namely benzoate-catechol, salicylate-catechol, 3-hydroxybenzoate-gentisate and 4-hydroxybenzoate-protocatechute pathways in strain BC1, ultimately leading to the TCA cycle intermediates. Studies also evaluated substrate specificity profiles of both nitrile hydratase and amidase(s) involved in the denitrification of the nitriles. In addition, a few metabolic crosstalk events due to the induction of multiple operons by central metabolites were appraised in strain BC1. The present study illustrates the broad degradative potential of strain BC1, harboring diverse catabolic machinery of biotechnological importance, elucidating pathways for the assimilation of benzonitrile and that of hydroxybenzonitrile isomers for the first time.
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Affiliation(s)
- Mriganka M Karmakar
- Department of Microbiology, Bose Institute, EN-80, Sector V, Salt Lake, Kolkata, West Bengal, 700091, India
| | - Satamita Deb
- Department of Microbiology, Bose Institute, EN-80, Sector V, Salt Lake, Kolkata, West Bengal, 700091, India
| | - Tapan K Dutta
- Department of Microbiology, Bose Institute, EN-80, Sector V, Salt Lake, Kolkata, West Bengal, 700091, India.
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Yusof NY, Quay DHX, Kamaruddin S, Jonet MA, Md Illias R, Mahadi NM, Firdaus-Raih M, Abu Bakar FD, Abdul Murad AM. Biochemical and in silico structural characterization of a cold-active arginase from the psychrophilic yeast, Glaciozyma antarctica PI12. Extremophiles 2024; 28:15. [PMID: 38300354 DOI: 10.1007/s00792-024-01333-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 12/30/2023] [Indexed: 02/02/2024]
Abstract
Glaciozyma antarctica PI12 is a psychrophilic yeast isolated from Antarctica. In this work, we describe the heterologous production, biochemical properties and in silico structure analysis of an arginase from this yeast (GaArg). GaArg is a metalloenzyme that catalyses the hydrolysis of L-arginine to L-ornithine and urea. The cDNA of GaArg was reversed transcribed, cloned, expressed and purified as a recombinant protein in Escherichia coli. The purified protein was active against L-arginine as its substrate in a reaction at 20 °C, pH 9. At 10-35 °C and pH 7-9, the catalytic activity of the protein was still present around 50%. Mn2+, Ni2+, Co2+ and K+ were able to enhance the enzyme activity more than two-fold, while GaArg is most sensitive to SDS, EDTA and DTT. The predicted structure model of GaArg showed a very similar overall fold with other known arginases. GaArg possesses predominantly smaller and uncharged amino acids, fewer salt bridges, hydrogen bonds and hydrophobic interactions compared to the other counterparts. GaArg is the first reported arginase that is cold-active, facilitated by unique structural characteristics for its adaptation of catalytic functions at low-temperature environments. The structure and function of cold-active GaArg provide insights into the potentiality of new applications in various biotechnology and pharmaceutical industries.
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Affiliation(s)
- Nik Yusnoraini Yusof
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian, 16150, Kelantan, Malaysia.
- Department of Biological Sciences & Biotechnology, Faculty of Sciences and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
| | - Doris Huai Xia Quay
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor, Malaysia.
| | - Shazilah Kamaruddin
- Department of Biological Sciences & Biotechnology, Faculty of Sciences and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Mohd Anuar Jonet
- Malaysia Genome and Vaccine Institute, Jalan Bangi Lama, 43000, Kajang, Selangor, Malaysia
| | - Rosli Md Illias
- Department of Bioprocess Engineering, Faculty of Chemical Engineering, Universiti Teknologi Malaysia, 81300, Skudai, Johor, Malaysia
| | - Nor Muhammad Mahadi
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Mohd Firdaus-Raih
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor, Malaysia
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Farah Diba Abu Bakar
- Department of Biological Sciences & Biotechnology, Faculty of Sciences and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Abdul Munir Abdul Murad
- Department of Biological Sciences & Biotechnology, Faculty of Sciences and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
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Ouédraogo F, Cornu JY, Fanin N, Janot N, Sourzac M, Parlanti E, Denaix L. Changes over time in organic matter dynamics and copper solubility in a vineyard soil after incorporation of cover crop residues: Insights from a batch experiment. Chemosphere 2024; 350:141137. [PMID: 38199494 DOI: 10.1016/j.chemosphere.2024.141137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/15/2023] [Accepted: 01/04/2024] [Indexed: 01/12/2024]
Abstract
Cover crops (CCs) are increasingly used in viticulture because they benefit the soil and the environment in many ways. This study investigated the extent to which the incorporation of CC residues altered organic matter (OM) and Cu dynamics in a Cu-contaminated vineyard topsoil. A 92-day incubation period was used to monitor changes over time in carbon mineralization, carbon hydrolytic enzyme activity, concentration and optical properties of dissolved organic matter (DOM), and Cu solubility after the addition (or not) of two CC residues, oat or faba bean. The results revealed that adding CCs transitorily increased the concentration of DOM in soil solution, as well as the activity of C hydrolytic enzymes and C mineralization rates. DOM content was approximately two orders of magnitude higher in CC-amended soils than in the control soil on day 0, after which it gradually decreased to reach concentrations similar to those measured in the control soil on day 92. Analyses of DOM optical properties showed that its molecular weight and degree of humification increased over time with a decrease in its concentration. The close relationship between DOM and Cu concentrations in the soil solution suggests that degradation of CCs releases soluble forms of C capable of complexing and solubilizing Cu, and hence that incorporating CC residues can transitorily increase the solubility of Cu in vineyard topsoils. Despite their different C:N ratios, oat and faba bean had almost the same effect on Cu dynamics, implying that C inputs played a prominent role in explaining the interactions between OM and Cu within the timeframe of our experiment. In conclusion, this study enabled recommendations on how to mitigate the risk of Cu ecotoxicity associated with incorporating CCs in Cu-contaminated vineyard soils.
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Affiliation(s)
- Frédéric Ouédraogo
- ISPA, Bordeaux Sciences Agro, INRAE, 33140 Villenave d'Ornon, France; University of Bordeaux, UMR CNRS 5805, EPOC, 33400, Talence, France
| | - Jean-Yves Cornu
- ISPA, Bordeaux Sciences Agro, INRAE, 33140 Villenave d'Ornon, France.
| | - Nicolas Fanin
- ISPA, Bordeaux Sciences Agro, INRAE, 33140 Villenave d'Ornon, France
| | - Noémie Janot
- ISPA, Bordeaux Sciences Agro, INRAE, 33140 Villenave d'Ornon, France
| | - Mahaut Sourzac
- University of Bordeaux, UMR CNRS 5805, EPOC, 33400, Talence, France
| | - Edith Parlanti
- University of Bordeaux, UMR CNRS 5805, EPOC, 33400, Talence, France
| | - Laurence Denaix
- ISPA, Bordeaux Sciences Agro, INRAE, 33140 Villenave d'Ornon, France
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Sellamuthu G, Naseer A, Hradecký J, Chakraborty A, Synek J, Modlinger R, Roy A. Gene expression plasticity facilitates different host feeding in Ips sexdentatus (Coleoptera: Curculionidae: Scolytinae). Insect Biochem Mol Biol 2024; 165:104061. [PMID: 38151136 DOI: 10.1016/j.ibmb.2023.104061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/30/2023] [Accepted: 12/15/2023] [Indexed: 12/29/2023]
Abstract
Host shift is ecologically advantageous and a crucial driver for herbivore insect speciation. Insects on the non-native host obtain enemy-free space and confront reduced competition, but they must adapt to survive. Such signatures of adaptations can often be detected at the gene expression level. It is astonishing how bark beetles cope with distinct chemical environments while feeding on various conifers. Hence, we aim to disentangle the six-toothed bark beetle (Ips sexdentatus) response against two different conifer defences upon host shift (Scots pine to Norway spruce). We conducted bioassay and metabolomic analysis followed by RNA-seq experiments to comprehend the beetle's ability to surpass two different terpene-based conifer defence systems. Beetle growth rate and fecundity were increased when reared exclusively on spruce logs (alternative host) compared to pine logs (native host). Comparative gene expression analysis identified differentially expressed genes (DEGs) related to digestion, detoxification, transporter activity, growth, signalling, and stress response in the spruce-feeding beetle gut. Transporter genes were highly abundant during spruce feeding, suggesting they could play a role in pumping a wide variety of endogenous and xenobiotic compounds or allelochemicals out. Trehalose transporter (TRET) is also up-regulated in the spruce-fed beetle gut to maintain homeostasis and stress tolerance. RT-qPCR and enzymatic assays further corroborated some of our findings. Taken together, the transcriptional plasticity of key physiological genes plays a crucial role after the host shift and provides vital clues for the adaptive potential of bark beetles on different conifer hosts.
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Affiliation(s)
- Gothandapani Sellamuthu
- Czech University of Life Sciences Prague, Forest Molecular Entomology Lab, Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic; Czech University of Life Sciences Prague, Excellent Team for Mitigation (ETM), Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic
| | - Aisha Naseer
- Czech University of Life Sciences Prague, Forest Molecular Entomology Lab, Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic; Czech University of Life Sciences Prague, Excellent Team for Mitigation (ETM), Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic
| | - Jaromír Hradecký
- Czech University of Life Sciences Prague, Excellent Team for Mitigation (ETM), Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic
| | - Amrita Chakraborty
- Czech University of Life Sciences Prague, Forest Molecular Entomology Lab, Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic; Czech University of Life Sciences Prague, Forest Microbiome Team, Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic
| | - Jiří Synek
- Czech University of Life Sciences Prague, Excellent Team for Mitigation (ETM), Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic
| | - Roman Modlinger
- Czech University of Life Sciences Prague, Excellent Team for Mitigation (ETM), Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic
| | - Amit Roy
- Czech University of Life Sciences Prague, Forest Molecular Entomology Lab, Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic; Czech University of Life Sciences Prague, Excellent Team for Mitigation (ETM), Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic; Czech University of Life Sciences Prague, Forest Microbiome Team, Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic.
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6
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Elsäßer G, Seidl T, Pfannstiel J, Schaller A, Stührwohldt N. Characterization of Prolyl-4-Hydroxylase Substrate Specificity Using Pichia pastoris as an Efficient Eukaryotic Expression System. Methods Mol Biol 2024; 2731:59-80. [PMID: 38019426 DOI: 10.1007/978-1-0716-3511-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
The use of eukaryotic expression systems facilitates the heterologous expression of complex eukaryotic proteins in their post-translationally modified and biologically active state, as a prerequisite for subsequent biochemical characterization and functional analysis. Here we describe the complete workflow for the expression of Arabidopsis thaliana prolyl-4-hydroxylases (P4Hs) in the methylotrophic yeast Pichia pastoris (renamed as Komagataella phaffii), for the extraction of the recombinant enzymes, purification by affinity chromatography, and characterization of P4H activity and specificity toward oligopeptide substrates by mass spectrometry. We expressed eight of the 13 Arabidopsis P4Hs and show that they are all active against proline-rich extensin-derived peptides. However, three of them differed in substrate specificity and were also able to hydroxylate the CLEL9 signaling peptide, featuring a single proline within its mature peptide sequence.
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Affiliation(s)
- Gerith Elsäßer
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Tim Seidl
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Jens Pfannstiel
- Core Facility Hohenheim, Mass Spectrometry Module, University of Hohenheim, Stuttgart, Germany
| | - Andreas Schaller
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Nils Stührwohldt
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, Stuttgart, Germany.
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7
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Liveris ZJ, Kelley EH, Simmons E, Konczak K, Lutz MR, Ballicora M, Olsen KW, Becker DP. Synthesis and characterization of the N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) alternate substrate analog N,N-dimethyl-l,l-SDAP. Bioorg Med Chem 2023; 91:117415. [PMID: 37459673 DOI: 10.1016/j.bmc.2023.117415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/26/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023]
Abstract
Growing antibiotic resistance by pathogenic bacteria has led to a global crisis. The bacterial enzyme N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) provides a very attractive target for the discovery of a new class of antibiotics, as it resides exclusively in many pathogenic bacterial strains and is a key enzyme in the lysine biosynthetic pathway. This pathway is responsible for the production of lysine as well as meso-diaminopimelate (m-DAP), both of which are required for peptidoglycan cell-wall synthesis, and lysine for peptide synthesis. The enzyme DapE catalyzes the hydrolysis of N-succinyl-l,l-diaminopimelic acid (l,l-SDAP) to succinate and l,l-diaminopimelic acid (l,l-DAP), and due to its absence in humans, inhibition of DapE avoids mechanism-based side effects. We have executed the asymmetric synthesis of N,N-dimethyl-SDAP, an l,l-SDAP substrate analog and an analog of the synthetic substrate of our previously described DapE assay. Previous modeling studies advocated that N,N-dimethyl-SDAP might function as an inhibitor, however the compound behaves as a substrate, and we have demonstrated the use of N,N-dimethyl-SDAP as the substrate in a modified ninhydrin-based DapE assay. Thermal shift experiments of DapE in the presence of N,N-dimethyl-SDAP are consistent with a melt temperature (Tm) shifted by succinate, the product of enzymatic hydrolysis.
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Affiliation(s)
- Zachary J Liveris
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Emma H Kelley
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Emma Simmons
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Katherine Konczak
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Marlon R Lutz
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Miguel Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Kenneth W Olsen
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Daniel P Becker
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States.
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8
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Das J, Kumar R, Shah V, Raghavendra KP, Sharma AK. Identification and functional characterisation of N-acetylglucosamine kinase from Helicoverpa armigera divulge its potential role in growth and development via UDP-GlcNAc salvage pathway. Int J Biol Macromol 2023; 242:124674. [PMID: 37137348 DOI: 10.1016/j.ijbiomac.2023.124674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 04/17/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023]
Abstract
N-acetylglucosamine kinase (NAGK), a major enzyme of sugar-kinase/Hsp70/actin superfamily, catalyses the conversion of N-acetylglucosamine to GlcNAc-6-phosphate, the first step leading to the salvage synthesis of uridine diphosphate N-acetylglucosamine. Here, we present the first report on identification, cloning, recombinant expression and functional characterisation of NAGK from Helicoverpa armigera (HaNAGK). The purified soluble HaNAGK exhibited a molecular mass of ~39 kDa with monomeric conformation. It catalysed the sequential transformation of GlcNAc into UDP-GlcNAc, indicating its role as the initiator of UDP-GlcNAc salvage pathway. HaNAGK exhibited ubiquitous expressions across all the developmental stages and major tissues of H. armigera. The gene was significantly upregulated (80 %; p < 0.01) by the moulting hormone 20-hydroxyecdysone and significantly downregulated (89 %; p < 0.001) by the chitin synthesis inhibitor novaluron, indicating its involvement in ecdysis and chitin metabolism. Furthermore, RNAi of HaNAGK caused poor weight gain, deformed insect bodies, aberrant metamorphosis and pronounced wing abnormalities in >55 % of surviving adults, while recording 7.79 ± 1.52 % and 24.25 ± 7.21 % mortality during larval and pupal stages, respectively. Altogether, the present findings suggest that HaNAGK plays a crucial role in the growth and development of H. armigera and thus, could be considered as a compelling gene of interest while formulating novel pest management strategies.
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Affiliation(s)
- Joy Das
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India; ICAR-Central Institute for Cotton Research, Nagpur, Maharashtra, India
| | - Rakesh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India; ICAR-Central Institute for Cotton Research, Nagpur, Maharashtra, India
| | - Vivek Shah
- ICAR-Central Institute for Cotton Research, Nagpur, Maharashtra, India
| | - K P Raghavendra
- ICAR-Central Institute for Cotton Research, Nagpur, Maharashtra, India
| | - Ashwani Kumar Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India.
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9
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Reichardt S, Stintzi A, Schaller A. Assay for Phytaspase-mediated Peptide Precursor Cleavage Using Synthetic Oligopeptide Substrates. Bio Protoc 2023; 13:e4608. [PMID: 36816990 PMCID: PMC9909310 DOI: 10.21769/bioprotoc.4608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 11/22/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023] Open
Abstract
Proteases control plant growth and development by limited proteolysis of regulatory proteins at highly specific sites. This includes the processing of peptide hormone precursors to release the bioactive peptides as signaling molecules. The proteases involved in this process have long remained elusive. Confirmation of a candidate protease as a peptide precursor-processing enzyme requires the demonstration of protease-mediated precursor cleavage in vitro. In vitro cleavage assays rely on the availability of suitable substrates and the candidate protease with high purity. Here, we provide a protocol for the expression, purification, and characterization of tomato (Solanum lycopersicum) phytaspases as candidate proteases for the processing of the phytosulfokine precursor. We also show how synthetic oligopeptide substrates can be used to demonstrate site-specific precursor cleavage. Graphical abstract.
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Affiliation(s)
- Sven Reichardt
- Dept. Plant Physiology and Biochemistry, University of Hohenheim, 70593 Stuttgart, Germany
| | - Annick Stintzi
- Dept. Plant Physiology and Biochemistry, University of Hohenheim, 70593 Stuttgart, Germany
| | - Andreas Schaller
- Dept. Plant Physiology and Biochemistry, University of Hohenheim, 70593 Stuttgart, Germany
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10
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Barbier E, Fouchet T, Hartmann A, Cambau E, Mougari F, Dubois C, Lubetzki M, Rochelet M. Rapid electrochemical detection of Mycobacterium tuberculosis in sputum by measuring Ag85 activity with disposable carbon sensors. Talanta 2023; 253:123927. [PMID: 36174382 DOI: 10.1016/j.talanta.2022.123927] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 12/13/2022]
Abstract
An electrochemical assay for the detection of the enzymatic activity of the antigen 85 (Ag85) tuberculosis (TB) biomarker was developed and evaluated for the qualitative detection of Mycobacterium tuberculosis in decontaminated sputum. For this purpose, the electroactive properties of both synthetic p-aminophenyl-6-O-octanoyl-3-d-glucopyranoside (p-APOG) substrate and p-aminophenyl-6-3-d-glucopyranoside (p-APG) product released after the removal of the octanoyl fatty acid by the Ag85 were investigated with disposable carbon screen-printed electrodes by cyclic voltammetry. Since specific anodic responses were obtained for the p-APOG substrate and the p-APG product, the intensity of the oxidation peak of the p-APG (E = + 0.35 V vs. Ag/AgCl) was selected as the analytical response for the detection of the Ag85 acyltransferase activity. Once the proof of concept of the Ag85 electrochemical assay was validated with a commercially-available Ag85B protein, its specificity was further assessed by analyzing pure cultures of various bacteria including tuberculous and non-tuberculous mycobacteria as well as different species found in patients' sputum. Finally, with a specificity of 78% and a sensitivity of 89%, the method was successfully compared to microscopy and culture routine tests for TB testing in 36 frozen fluidized and decontaminated sputum. This suggests that owing to its convenience, rapidity, low-cost and portability, the reported Ag85 electrochemical assay is a promising tool to screen patients for TB.
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Affiliation(s)
- Elodie Barbier
- UMR AgroEcologie 1347, INRAe, Université Bourgogne Franche-Comté, BP 87999, Cedex, 21079, Dijon, France
| | - Théo Fouchet
- UMR AgroEcologie 1347, INRAe, Université Bourgogne Franche-Comté, BP 87999, Cedex, 21079, Dijon, France; Inserm UMR 1137 IAME, Université de Paris, 75018, Paris, France; Service de Mycobactériologie Spécialisée et de Référence, Laboratoire Associé du Centre National de Référence des Mycobactéries et Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), APHP-Bichat GHU Nord, 75018, Paris, France; EpiLAB, 4 Rue Anatole France, 78350, Jouy-en-Josas, France
| | - Alain Hartmann
- UMR AgroEcologie 1347, INRAe, Université Bourgogne Franche-Comté, BP 87999, Cedex, 21079, Dijon, France
| | - Emmanuelle Cambau
- Inserm UMR 1137 IAME, Université de Paris, 75018, Paris, France; Service de Mycobactériologie Spécialisée et de Référence, Laboratoire Associé du Centre National de Référence des Mycobactéries et Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), APHP-Bichat GHU Nord, 75018, Paris, France
| | - Faiza Mougari
- Inserm UMR 1137 IAME, Université de Paris, 75018, Paris, France; Service de Mycobactériologie Spécialisée et de Référence, Laboratoire Associé du Centre National de Référence des Mycobactéries et Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), APHP-Bichat GHU Nord, 75018, Paris, France
| | - Clément Dubois
- EpiLAB, 4 Rue Anatole France, 78350, Jouy-en-Josas, France
| | | | - Murielle Rochelet
- UMR AgroEcologie 1347, INRAe, Université Bourgogne Franche-Comté, BP 87999, Cedex, 21079, Dijon, France.
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11
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Petschenka G, Züst T, Hastings AP, Agrawal AA, Jander G. Quantification of plant cardenolides by HPLC, measurement of Na(+)/K(+)-ATPase inhibition activity, and characterization of target enzymes. Methods Enzymol 2023; 680:275-302. [PMID: 36710014 DOI: 10.1016/bs.mie.2022.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The biosynthesis of cardiac glycosides, broadly classified as cardenolides and bufadienolides, has evolved repeatedly among flowering plants. Individual species can produce dozens or even hundreds of structurally distinct cardiac glycosides. Although all cardiac glycosides exhibit biological activity by inhibiting the function of the essential Na+/K+-ATPase in animal cells, they differ in their level of inhibitory activity. For within- and between-species comparisons of cardiac glycosides to address ecological and evolutionary questions, it is necessary to not only quantify their relative abundance, but also their effectiveness in inhibiting the activity of different animal Na+/K+-ATPases. Here we describe protocols for characterizing the amount and toxicity of cardenolides from plant samples and the degree of insect Na+/K+-ATPase tolerance to inhibition: (1) an HPLC-based assay to quantify the abundance of individual cardenolides in plant extracts, (2) an assay to quantify inhibition of Na+/K+-ATPase activity by plant extracts, and (3) extraction of insect Na+/K+-ATPases for inhibition assays.
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12
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Abstract
Assays for measuring enzyme activity can be useful tools for proteomics applications. Enzyme testing can be performed to validate an experimental system prior to a difference gel electrophoresis (DIGE) proteomic experiment and can also be utilized as an integral part of multifaceted experiment in conjunction with DIGE. Data from enzyme tests can be used to corroborate results of DIGE proteomic experiments where an enzyme or enzymes are demonstrated by DIGE to be differentially expressed. Enzyme testing can also be utilized to support data from DIGE experiments that demonstrate metabolic changes in a biological system. The different types of enzyme assays that can be performed in conjunction with DIGE experiments are reviewed alongside a discussion of experimental approaches for designing enzyme assays.
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Affiliation(s)
- Andrew Dowd
- Croda Europe Limited, Daresbury, Cheshire, UK.
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13
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Jung KM, Piomelli D. Assay of Monoacylglycerol Lipase Activity. Methods Mol Biol 2023; 2576:285-297. [PMID: 36152196 DOI: 10.1007/978-1-0716-2728-0_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Monoacylglycerol lipase (MGL/MAGL/MGLL) is a serine hydrolase involved in the biological deactivation of the endocannabinoid 2-arachidonoyl-sn-glycerol (2-AG). 2-AG is the most abundant endogenous lipid agonists for cannabinoid receptors in the brain and elsewhere in the body. In the central nervous system (CNS), MGL is localized to presynaptic nerve terminals of both excitatory and inhibitory synapses, where it controls the regulatory actions of 2-AG on synaptic transmission and plasticity. In this chapter, we describe an in vitro method to assess MGL activity by liquid chromatography/mass spectrometry (LC/MS)-based quantitation of its reaction product. The method may be used to determine basal or altered MGL activity in cells or tissues after pharmacological, genetic, or biological interventions. In addition, the assay can be used for MGL inhibitor screening using purified recombinant enzyme or MGL-overexpressing cells.
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Affiliation(s)
- Kwang-Mook Jung
- Department of Anatomy and Neurobiology, University of California, Irvine, Irvine, CA, USA
| | - Daniele Piomelli
- Department of Anatomy and Neurobiology, University of California, Irvine, Irvine, CA, USA.
- Department of Pharmacology, University of California, Irvine, Irvine, CA, USA.
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA.
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14
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Lin CH, Hsieh YS, Sun YC, Huang WH, Chen SL, Weng ZK, Lin TH, Wu YR, Chang KH, Huang HJ, Lee GC, Hsieh-Li HM, Lee-Chen GJ. Virtual Screening and Testing of GSK-3 Inhibitors Using Human SH-SY5Y Cells Expressing Tau Folding Reporter and Mouse Hippocampal Primary Culture under Tau Cytotoxicity. Biomol Ther (Seoul) 2023; 31:127-138. [PMID: 35790892 PMCID: PMC9810448 DOI: 10.4062/biomolther.2022.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/05/2022] [Accepted: 05/24/2022] [Indexed: 01/13/2023] Open
Abstract
Glycogen synthase kinase-3β (GSK-3β) is an important serine/threonine kinase that implicates in multiple cellular processes and links with the neurodegenerative diseases including Alzheimer's disease (AD). In this study, structure-based virtual screening was performed to search database for compounds targeting GSK-3β from Enamine's screening collection. Of the top-ranked compounds, 7 primary hits underwent a luminescent kinase assay and a cell assay using human neuroblastoma SH-SY5Y cells expressing Tau repeat domain (TauRD) with pro-aggregant mutation ΔK280. In the kinase assay for these 7 compounds, residual GSK-3β activities ranged from 36.1% to 90.0% were detected at the IC50 of SB-216763. In the cell assay, only compounds VB-030 and VB-037 reduced Tau aggregation in SH-SY5Y cells expressing ΔK280 TauRD-DsRed folding reporter. In SH-SY5Y cells expressing ΔK280 TauRD, neither VB-030 nor VB-037 increased expression of GSK-3α Ser21 or GSK-3β Ser9. Among extracellular signal-regulated kinase (ERK), AKT serine/threonine kinase 1 (AKT), mitogen-activated protein kinase 14 (P38) and mitogen-activated protein kinase 8 (JNK) which modulate Tau phosphorylation, VB-037 attenuated active phosphorylation of P38 Thr180/Tyr182, whereas VB-030 had no effect on the phosphorylation status of ERK, AKT, P38 or JNK. However, both VB-030 and VB-037 reduced endogenous Tau phosphorylation at Ser202, Thr231, Ser396 and Ser404 in neuronally differentiated SH-SY5Y expressing ΔK280 TauRD. In addition, VB-030 and VB-037 further improved neuronal survival and/or neurite length and branch in mouse hippocampal primary culture under Tau cytotoxicity. Overall, through inhibiting GSK-3β kinase activity and/or p-P38 (Thr180/Tyr182), both compounds may serve as promising candidates to reduce Tau aggregation/cytotoxicity for AD treatment.
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Affiliation(s)
- Chih-Hsin Lin
- School of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Yu-Shao Hsieh
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Ying-Chieh Sun
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Wun-Han Huang
- School of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Shu-Ling Chen
- School of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Zheng-Kui Weng
- School of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Te-Hsien Lin
- School of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Yih-Ru Wu
- Department of Neurology, Chang Gung Memorial Hospital, Taoyuan 33378, Taiwan
| | - Kuo-Hsuan Chang
- Department of Neurology, Chang Gung Memorial Hospital, Taoyuan 33378, Taiwan
| | - Hei-Jen Huang
- Department of Nursing, Mackay Junior College of Medicine, Nursing and Management, Taipei 11260, Taiwan
| | - Guan-Chiun Lee
- School of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan,Corresponding Authors E-mail: (Lee GC), (Hsieh-Li HM), (Lee-Chen GJ), Tel:+886-2-7749-6351 (Lee GC), +886-2-7749-6354 (Hsieh-Li HM), +886-2-7749-6359 (Lee-Chen GJ), Fax:+886-2-2931-2904 (Lee GC), +886-2-2931-2904 (Hsieh-Li HM), +886-2-2931-2904 (Lee-Chen GJ)
| | - Hsiu Mei Hsieh-Li
- School of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan,Corresponding Authors E-mail: (Lee GC), (Hsieh-Li HM), (Lee-Chen GJ), Tel:+886-2-7749-6351 (Lee GC), +886-2-7749-6354 (Hsieh-Li HM), +886-2-7749-6359 (Lee-Chen GJ), Fax:+886-2-2931-2904 (Lee GC), +886-2-2931-2904 (Hsieh-Li HM), +886-2-2931-2904 (Lee-Chen GJ)
| | - Guey-Jen Lee-Chen
- School of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan,Corresponding Authors E-mail: (Lee GC), (Hsieh-Li HM), (Lee-Chen GJ), Tel:+886-2-7749-6351 (Lee GC), +886-2-7749-6354 (Hsieh-Li HM), +886-2-7749-6359 (Lee-Chen GJ), Fax:+886-2-2931-2904 (Lee GC), +886-2-2931-2904 (Hsieh-Li HM), +886-2-2931-2904 (Lee-Chen GJ)
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15
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Chan YY, Mbenza NM, Chan MC, Leung IKH. Assays to Study Hypoxia-Inducible Factor Prolyl Hydroxylase Domain 2 (PHD2), a Key Human Oxygen Sensing Protein. Methods Mol Biol 2023; 2648:187-206. [PMID: 37039992 DOI: 10.1007/978-1-0716-3080-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Molecular oxygen is essential for all multicellular life forms. In humans, the hypoxia-inducible factor (HIF) prolyl hydroxylase domain-containing enzymes (PHDs) serve as important oxygen sensors by regulating the activity of HIF, the master regulator that mediates cellular oxygen homeostasis, in an oxygen-dependent manner. In normoxia, PHDs catalyze the prolyl hydroxylation of HIF, which leads to its degradation and prevents cellular hypoxic response to be triggered. PHDs are current inhibition targets for the potential treatments of a number of diseases. In this chapter, we discuss in vitro and cell-based methods to study the modulation of PHD2, the most important human PHD isoform in normoxia and mild hypoxia. These include the production and purification of recombinant PHD2, the use of mass spectrometry to follow PHD2-catalyzed reactions and the studies of HIF stabilization in cells by immunoblotting.
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Affiliation(s)
- Yan Ying Chan
- Department of Molecular Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Naasson M Mbenza
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Mun Chiang Chan
- Department of Molecular Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
- GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Ivanhoe K H Leung
- School of Chemistry and the Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.
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16
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Abstract
Enzyme activity assay methods can be used to corroborate the results generated by difference gel electrophoresis (DIGE) proteomic experiments. Two assay methods were chosen to demonstrate how this can be achieved. Assays for determining the activity of superoxide dismutase and NADH dehydrogenase are outlined in detail in this chapter. These methods were chosen as examples because they are frequently used in conjunction with DIGE proteomics.
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Affiliation(s)
- Andrew Dowd
- Croda Europe Limited, Daresbury, Cheshire, UK.
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17
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Dhayalan A, Thillainathan N, Velramar B, Athiyappagounder P, Sundaramoorthy D, Pachiappan P. Pectinase from a Fish Gut Bacterium, Aeromonas guangheii (SS6): Production, Cloning and Characterization. Protein J 2022; 41:572-590. [PMID: 36208356 DOI: 10.1007/s10930-022-10077-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2022] [Indexed: 11/28/2022]
Abstract
During the present research, 11 gut bacteria were isolated from the freshwater fish, Systomus sarana (General name: olive barb) and upon screening, the strains produced extracellular pectinase enzyme. Among them, the SS6 strain was found to produce a high quantity of 208.731 U/ml pectinase and through molecular characterization the SS6 strain was identified as Aeromonas guangheii. During the culture of SS6 strain, a set of parameters were optimized through the response surface methodology with a Box-Behnken design, for the production of the enzyme. The optimal conditions were found to be 2.11% of maltose, 2.20% of yeast extract, 6.5 of pH, and a temperature of 27.3 °C at 32-h incubation. Under the above conditions, the activity of pectinase production was enhanced to 371 U/ml. The purified pectinase's molecular weight was determined to be ~ 50 kDa (by 10% 2-D PAGE). Totally, nine peptides were identified from the purified pectinase enzyme through the MALDI-TOF-MS analysis and MASCOT tool was used to get the mass spectrum of the peak at 2211 of peptide that indicated the reference pectinase protein. The referenced gene primer (pectate lyases) was PCR amplified and its nucleotide sequence was analyzed. The exo-pelA gene was cloned in pREST vector, which was found to be over expressed in Escherichia coli BL21. The ORF encoded for a mature protein comprising of 425 amino acids (1236 nucleotides) with a predicted molecular weight of ~ 48.7 kDa. The present findings underline the potential of the fish-gut microbes as a source of biotechnologically important enzymes.
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Affiliation(s)
- Arul Dhayalan
- Department of Biotechnology, School of Biosciences, Periyar University, Salem, Tamil Nadu, 636011, India.,SRS of ICAR- National Dairy Research Institute, Adugodi, Bengaluru, Karnataka, 560030, India
| | - Natarajan Thillainathan
- Department of Biotechnology, School of Biosciences, Periyar University, Salem, Tamil Nadu, 636011, India.,Department of Biomedical Engineering, Central University of Rajasthan, Ajmer, Rajasthan, 305817, India
| | - Balasubramanian Velramar
- Department of Biotechnology, School of Biosciences, Periyar University, Salem, Tamil Nadu, 636011, India.,Amity Institute of Biotechnology, Amity University, Raipur, Chhattisgarh, 493225, India
| | - Palanisammi Athiyappagounder
- Veterinary College & Research Institute, Tamil Nadu Veterinary & Animal Science University, Tirunelveli, Tamil Nadu, 627358, India
| | - Dhanasundaram Sundaramoorthy
- Department of Marine Science, School of Marine Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India
| | - Perumal Pachiappan
- Department of Biotechnology, School of Biosciences, Periyar University, Salem, Tamil Nadu, 636011, India. .,Department of Marine Science, School of Marine Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India.
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18
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Thomsen TB, Hunt CJ, Meyer AS. Standardized method for controlled modification of poly (ethylene terephthalate) (PET) crystallinity for assaying PET degrading enzymes. MethodsX 2022; 9:101815. [PMID: 36039192 DOI: 10.1016/j.mex.2022.101815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/04/2022] [Indexed: 11/20/2022] Open
Abstract
Poly(ethylene terephthalate) (PET) is a polyester plastic, which is widely used, notably as a material for single-use plastic bottles. Its accumulation in the environment now poses a global pollution threat. A number of enzymes are active on PET providing new options for industrial biorecycling of PET materials. The enzyme activity is strongly affected by the degree of PET crystallinity (XC), and the XC is therefore a relevant factor to consider in enzyme catalyzed PET recycling. Here, we present a new experimental methodology, based on systematic thermal annealing for controlled preparation of PET disks having different XC, to allow systematic quantitative evaluation of the efficiency of PET degrading enzymes at different degrees of PET substrate crystallinity. We discuss the theory of PET crystallinity and compare PET crystallinity data measured by differential scanning calorimetry and attenuated Fourier transform infrared spectroscopy.•This study introduces a simple method for controlling the crystallinity of PET samples via annealing in a heat block.•The present methodology is not limited to the analytical methods included in the methods details.
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19
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Nasuno R, Iwai N, Takagi H. Development of a microtiter plate-based analysis method of nitric oxide dioxygenase activity. J GEN APPL MICROBIOL 2022; 68:38-41. [PMID: 35321969 DOI: 10.2323/jgam.2021.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Nitric oxide (NO) functions in cell protection or cell death, depending on its concentration. Therefore, regulation of the intracellular concentrations of NO by its degradation systems is important for cellular functions. One of the NO degrading enzymes, flavohemoglobin (FHb), which has NO dioxygenase (NOD) activity, is a promising target for antibiotics, based on the finding that FHb-deficient pathogens exhibited reduced host toxicity. Here, we developed a high-throughput method to measure the NOD activity. Our newly developed method could contribute to the screening of potential antibiotics with NOD inhibitory activity.
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Affiliation(s)
- Ryo Nasuno
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology
| | - Nozomi Iwai
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology
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20
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Rasor BJ, Vögeli B, Jewett MC, Karim AS. Cell-Free Protein Synthesis for High-Throughput Biosynthetic Pathway Prototyping. Methods Mol Biol 2022; 2433:199-215. [PMID: 34985746 DOI: 10.1007/978-1-0716-1998-8_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Biological systems provide a sustainable and complimentary approach to synthesizing useful chemical products. Metabolic engineers seeking to establish economically viable biosynthesis platforms strive to increase product titers, rates, and yields. Despite continued advances in genetic tools and metabolic engineering techniques, cellular workflows remain limited in throughput. It may take months to test dozens of unique pathway designs even in a robust model organism, such as Escherichia coli. In contrast, cell-free protein synthesis enables the rapid generation of enzyme libraries that can be combined to reconstitute metabolic pathways in vitro for biochemical synthesis in days rather than weeks. Cell-free reactions thereby enable comparison of hundreds to thousands of unique combinations of enzyme homologs and concentrations, which can quickly identify the most productive pathway variants to test in vivo or further characterize in vitro. This cell-free pathway prototyping strategy provides a complementary approach to accelerate cellular metabolic engineering efforts toward highly productive strains for metabolite production.
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Affiliation(s)
- Blake J Rasor
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Bastian Vögeli
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, Center for Synthetic Biology, Robert H. Lurie Comprehensive Cancer Center, and Simpson Querrey Institute, Northwestern University, Evanston, IL, USA.
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
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21
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Tuan PA, Shafai T, Kaur G, Grenier G, Ayele BT. Molecular and functional characterization of a jasmonate resistant gene of wheat (Triticum aestivum L.). J Plant Physiol 2022; 270:153637. [PMID: 35144140 DOI: 10.1016/j.jplph.2022.153637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/01/2022] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Jasmonates play important roles in several plant developmental processes and responses to biotic and abiotic stresses. This study identified a gene encoding jasmonate resistant 1 (JAR1) protein that catalyzes the production of bioactive jasmonoyl-isoleucine (JA-Ile) from hexaploid wheat (Triticum aestivum L), designated as TaJAR1B. The nucleotide sequence of TaJAR1B and amino acid sequence of the corresponding protein exhibited high identity and similarity with other plant JAR1s. Feeding the culture of E. coli cells heterologously expressing TaJAR1B with jasmonic acid (JA) resulted in the production of JA-Ile, indicating the functionality of TaJAR1B in converting JA to JA-Ile. TaJAR1B was highly expressed in the internodes of adult plants and maturing seeds. Salt treatment induced the expression level of TaJAR1B in seedling tissues. Our results indicate that TaJAR1B encodes a functional JAR and is involved in the regulation of plant growth and developmental processes and response to salinity in wheat.
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Affiliation(s)
- Pham Anh Tuan
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Talia Shafai
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Gurkamal Kaur
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Ginelle Grenier
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Belay T Ayele
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, Manitoba, R3T 2N2, Canada.
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22
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Dhayalan A, Velramar B, Govindasamy B, Ramalingam KR, Dilipkumar A, Pachiappan P. Isolation of a bacterial strain from the gut of the fish, Systomus sarana, identification of the isolated strain, optimized production of its protease, the enzyme purification, and partial structural characterization. J Genet Eng Biotechnol 2022; 20:24. [PMID: 35142906 PMCID: PMC8831710 DOI: 10.1186/s43141-022-00299-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 01/07/2022] [Indexed: 01/12/2023]
Abstract
BACKGROUND The present study focuses on the isolation of Bacillus thuringiensis bacterium from the gut of fresh water fish, Systomus sarana, the innovative optimization of culture parameters to produce maximum protease enzyme, by the isolated bacterium, and the elucidation of peptide profile of the protease. And the experimental data and results were authenticated through the response surface method (RSM) and Box-Behnken design (BBD) model. RESULTS During the RSM optimization, the interaction of the highest concentrations (%) of 2.2 maltose, 2.2 beef extract, and 7.0 pH, at 37 °C incubation, yielded a maximum protease enzyme of 245 U/ml by the fish gut-isolated, B. thuringiensis. The spectral analysis of the obtained enzyme revealed the presence of major functional groups at the range of 610-3852 cm-1 viz., alkynes (-C≡C-H: C-H stretch), misc (P-H phosphine sharp), α, β-unsaturated aldehydes, and through PAGE analysis, its molecular weight was determined as 27 kDa. The enzyme's MALDI-TOF/MS analysis revealed the presence of 15 peptides from which the R.YHTVCDPR.L peptide has been found to be a major one. CONCLUSIONS The fish gut-isolated bacterium, B. thuringiensis, SS4 exhibited the potential for high protease production under the innovatively optimized culture conditions, and the obtained result provides scope for applications in food and pharmaceutical industries.
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Affiliation(s)
- Arul Dhayalan
- Department of Biotechnology, School of Biosciences, Periyar University, Salem, 636011, Tamil Nadu, India.,ICAR- National Dairy Research Institute, SRS, Adugodi, Bengaluru, 560030, Karnataka, India
| | - Balasubramanian Velramar
- Department of Biotechnology, School of Biosciences, Periyar University, Salem, 636011, Tamil Nadu, India.,Amity Institute of Biotechnology, Amity University, Raipur, 493225, Chhattisgarh, India
| | - Balasubramani Govindasamy
- Department of Biotechnology, School of Biosciences, Periyar University, Salem, 636011, Tamil Nadu, India.,ICAR- Central Institute of Brackishwater Aquaculture, Chennai, 600028, Tamil Nadu, India
| | - Karthik Raja Ramalingam
- Department of Biotechnology, School of Biosciences, Periyar University, Salem, 636011, Tamil Nadu, India.,Department of Microbiology, Alagappa University, Karaikudi, 630003, Tamil Nadu, India
| | - Aiswarya Dilipkumar
- Department of Biotechnology, School of Biosciences, Periyar University, Salem, 636011, Tamil Nadu, India.,1/145, New Mariyaman Kovil Street, Bominayakanpatti post, Pagalpatti, Salem, 636304, Tamil Nadu, India
| | - Perumal Pachiappan
- Department of Biotechnology, School of Biosciences, Periyar University, Salem, 636011, Tamil Nadu, India. .,Department of Marine Science, School of Marine Sciences, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India.
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Bijali J, Halder T, Acharya K. Elucidation of the biochemical and molecular basis of the differential disease expression in two cultivars of chili ( Capsicum annuum) in response to Colletotrichum capsici infection. Acta Physiol Plant 2021; 43:155. [PMID: 34776557 PMCID: PMC8578917 DOI: 10.1007/s11738-021-03334-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/22/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Abstract
Chili plants are affected by the hemibiotrophic ascomycota fungus Colletotrichum capsici causing Anthracnose. Infection results in yield and marketability loss due to a decrease in the quality of fruits. The study of morphological symptom development in two cultivars, Bullet, and Beldanga, showed very different disease expression pattern. To understand the reasons behind such differential response, we investigated, in a time-dependent manner, biochemical activities of important defense enzymes, PR proteins, like peroxidase, polyphenol-oxidase, phenylalanine ammonia lyase, β-glucanase, chitinase, catalase, as well as phenols, flavonoids, chlorophyll and the key signaling molecule nitric oxide in their leaves. We further performed real-time nitric oxide (NO) detection studies. The results showed striking differences in the activity profile of these defense molecules through the course of the study. We monitored the gene expression levels of 12 important defense-related genes under in vivo condition. The transcription levels were mostly increased in the tolerant cultivar till 7 days post-infection (DPI), while downregulation of some of the genes were observed in the susceptible one. These data indicated that disease manifestation is a simulated response of these defense molecules which can nullify the effect of the pathogen and its products, when resistance occurs. Alternatively, the pathogen suppresses the host defense when the disease develops. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11738-021-03334-x.
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Affiliation(s)
- Jayeeta Bijali
- Molecular and Applied Mycology and Plant Pathology Laboratory Centre of Advanced Study, Department of Botany, University of Calcutta, Kolkata, West Bengal 700019 India
| | - Tanmoy Halder
- Plant Functional Genomics Lab, Department of Botany, Centre of Advanced Study, University of Calcutta, Kolkata, West Bengal 700019 India
| | - Krishnendu Acharya
- Molecular and Applied Mycology and Plant Pathology Laboratory Centre of Advanced Study, Department of Botany, University of Calcutta, Kolkata, West Bengal 700019 India
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Zhang ZP, Xue WY, Hu JX, Xiong DC, Wu YF, Ye XS. Novel carbohydrate-triazole derivatives as potential α-glucosidase inhibitors. Chin J Nat Med 2021; 18:729-737. [PMID: 33039052 DOI: 10.1016/s1875-5364(20)60013-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Indexed: 10/23/2022]
Abstract
A series of novel pyrano[2, 3-d]trizaole compounds were synthesized and their α-glucosidase inhibitory activities were evaluated by in vitro enzyme assay. The experimental data demonstrated that compound 10f showed up to 10-fold higher inhibition (IC5074.0 ± 1.3 μmol·L-1) than acarbose. The molecular docking revealed that compound 10f could bind to α-glucosidase via the hydrophobic, π-π stacking, and hydrogen bonding interactions. The results may benefit further structural modifications to find new and potent α-glucosidase inhibitors.
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Affiliation(s)
- Zi-Pei Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Wan-Ying Xue
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Jian-Xing Hu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - De-Cai Xiong
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yan-Fen Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Xin-Shan Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
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Siwach A, Kaushal S, Baishya R. Terricolous mosses impact soil microbial biomass carbon and enzymatic activity under temperate forest types of the Garhwal Himalayas. Environ Monit Assess 2021; 193:516. [PMID: 34308502 DOI: 10.1007/s10661-021-09295-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
Estimates of enzymatic activity are used as indices for soil quality, microbial nutrient demand, microbial growth, and activity. Mosses trap soil moisture, influence soil temperature, and create a microenvironment promoting an overall higher level of microbial activity, thus making the decomposition of organic matter more favorable. This study determines the role of mosses in influencing soil biochemical properties in three temperate forest types of the Garhwal Himalayas, Uttarakhand, viz., moist temperate deciduous forest, Ban oak forest, and moist deodar forest. Activities of major soil enzymes (dehydrogenase, β-glucosidase, acid phosphatase, aryl sulfatase, phenol oxidase, and urease) and soil microbial biomass carbon (SMBC) were determined under two different substrates, i.e., with and without moss cover in two different seasons, viz., monsoon and winter. The Pearson correlation of enzymes with specific soil nutrients they act upon has also been shown. The SMBC and on average activities of all the enzymes were predominantly higher in soil with moss cover during monsoon season and without moss cover in the winter season. SMBC in the three study sites ranged from 280.55 to 1707.64 µg C/g. Statistically significant differences (p < 0.01) were observed for all the properties within the substrates among all the three sites and across the two seasons. Our results suggest that mosses play a significant role in positively influencing soil biochemical properties in both seasons by creating a microscale mosaic that offers a high degree of heterogeneity in soil function. Our study emphasizes that mosses strongly affect soil enzyme activities and microbial biomass, thus improving soil health.
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Affiliation(s)
- Anshu Siwach
- Ecology and Ecosystem Research Laboratory, Department of Botany, University of Delhi, Delhi, 110007, India
| | - Siddhartha Kaushal
- Ecology and Ecosystem Research Laboratory, Department of Botany, University of Delhi, Delhi, 110007, India
| | - Ratul Baishya
- Ecology and Ecosystem Research Laboratory, Department of Botany, University of Delhi, Delhi, 110007, India.
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Mukherjee S, De Buck J. Autotransporter-based surface expression and complementation of split TreA fragments utilized for the detection of antibodies against bovine leukemia virus. J Immunol Methods 2021; 495:113084. [PMID: 34118226 DOI: 10.1016/j.jim.2021.113084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/30/2021] [Accepted: 06/02/2021] [Indexed: 11/17/2022]
Abstract
Bovine Leukemia Virus (BLV) is an oncogenic virus which is the etiological agent of a neoplastic disease in infected cattle called enzootic bovine leukemia (EBL). The most common and sensitive diagnostic methods for EBL like enzyme-linked immunosorbent assay (ELISA) is time-consuming and requires manual handling which makes it unsuitable as an on-farm diagnostic test. Hence, there is a need for an alternative test with rapid detection and reduced manual labour. We have previously reported the use of E. coli periplasmic trehalase (TreA) in a split enzyme sensor diagnostic technology to detect immunoglobulins and antigen-specific antibodies. In the current study, a more sensitive detection was attempted by bacterial surface display of split TreA fragment by fusion with the autotransporter AIDA-I. The split TreA fragments fused to antigens require antigen-specific antibodies for complementation and to trigger trehalase activity. This surface complementation strategy was used to detect anti-BLV antibodies in clinical serum by incorporating the antigenic BLV capsid protein in the fusion proteins. To validate this assay, a panel of serum samples obtained from BLV positive and negative cattle were tested in comparison with ELISA results. Evaluation of this panel resulted in positive detection of all true positive samples. We further demonstrated that this assay can be enhanced by pre-adsorption of clinical serum samples using E. coli cells to increase the specificity and help reduce nonspecific binding. In conclusion, the p24 antigen specific BLV assay is a potential tool for simple and rapid diagnosis of BLV infection, which is compatible with both lab-based and a more user friendly on-farm format.
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Affiliation(s)
- Sonia Mukherjee
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Jeroen De Buck
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada.
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Tang W, Gordon A, Wang HY, Li P, Chen J, Li B. Development of MALDI MS peptide array for thrombin inhibitor screening. Talanta 2021; 226:122129. [PMID: 33676683 DOI: 10.1016/j.talanta.2021.122129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/11/2021] [Accepted: 01/16/2021] [Indexed: 11/20/2022]
Abstract
The development of in situ methods for the analysis and visualization of enzyme activity is of paramount importance in drug discovery, research, and development. In this work, the functionalized and array patterned indium tin oxide (ITO) glass slides were fabricated by non-covalent immobilization of amphipathic phospholipid-tagged peptides encompassing the thrombin cleavage site on steric acid-modified ITO slides. The fabricated peptide arrays provide 60 spots per slide, and are compatible with matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) measurement, free matrix peak interference, and tolerance to repeated aqueous washing. The peptide arrays were used for the investigation of thrombin activity and screening for its potential inhibitors. The thrombin activity and its Michaelis-Menten constant (Km) for immobilized peptide substrate was determined using developed MALDI MS peptide array. To investigate the applicability and effectiveness of peptide arrays, the anti-thrombin activity of grape seed proanthocyanidins with different degrees of polymerization (DP) was monitored and visualized. MALDI MS imaging results showed that the fractions of proanthocyanidins with the mean DP of 4.61-6.82 had good thrombin inhibitory activity and their half-maximal inhibitory concentration (IC50) were below 10 μg/mL. Therefore, the developed peptide array is a reliable platform for the discovery of natural thrombin inhibitors.
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Kamate M, Reddy N, Detroja M, Hattiholi V. Neuronal Ceroid Lipofuscinoses in Children. Ann Indian Acad Neurol 2021; 24:192-197. [PMID: 34220062 PMCID: PMC8232483 DOI: 10.4103/aian.aian_61_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/08/2020] [Accepted: 02/10/2020] [Indexed: 11/22/2022] Open
Abstract
Background: The neuronal ceroid lipofuscinoses (NCL) constitute a group of gray matter neurodegenerative disorders characterized by the accumulation of ceroid lipopigment in lysosomes in neurons and other cell types. There are very few published studies on NCL from India, especially in children. Methods: A retrospective study of confirmed patients of NCL diagnosed over a period of 10 years from January 2019 to December 2019. Results: Fifty children had a definitive diagnosis of NCL based on enzymatic studies or genetic testing using next-generation sequencing. Around 15 children were diagnosed to have CLN-1 (ceroid lipofuscinoses, neuronal-1) based on palmitoyl protein thioesterase-1 deficiency; 24 children were diagnosed with CLN2 (ceroid lipofuscinoses, neuronal-2) based on deficient tripeptidyl-peptidase-1 activity; three patients were diagnosed as CLN6, five patients as CLN7, one case each of CLN8, CLN11, and CLN14 based on genetic testing. Clinical presentation was quite varied and included refractory seizures, developmental delay/regression, and abnormal movements. Visual failure was not common in the present case series. Neuroimaging patterns in different types of NCL were different. All children had a progressive downhill course resulting in death in many over a period of 5–10 years of disease onset. Conclusion: NCL is not uncommon and diagnosis can be suspected based on clinical investigations and neuroimaging findings. Diagnosis can be confirmed by enzymatic assays or genetic testing.
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Affiliation(s)
- Mahesh Kamate
- Division of Pediatric Neurology and In-Charge Child Development Clinic, Department of Pediatrics, KAHER's J N Medical College, Belgaum, Karnataka, India
| | - Narendranadha Reddy
- Department of Pediatrics, KAHER's J N Medical College, Belgaum, Karnataka, India
| | - Mayank Detroja
- Department of Child Development and Pediatric Neurology Centre, KLES PK Hospital, Belgaum, Karnataka, India
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Lapis-Gaza HR, Pattison AB. Functional Soil Biological Measurements to Support Healthy Soils. Methods Mol Biol 2021; 2232:265-81. [PMID: 33161553 DOI: 10.1007/978-1-0716-1040-4_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Soil microorganisms contribute significantly to terrestrial ecosystem functioning through their activities. Various methods exist to characterize soil microbial activity and functional diversity including those that focus on potential enzyme activities and the respiratory responses of microbes to different substrates. Here, we describe: (1) the fluorescein diacetate hydrolysis assay for total potential microbial enzyme activity; (2) measurement of beta-glucosidase activity using ρ-nitrophenyl (pNP); (3) multienzyme assay using 4-methylumbelliferone (MUB); and (4) MicroResp assays to measure the respiratory responses of microbes to different substrates and generate a community level physiological profile (CLPP).
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Pederick JL, Bruning JB. An antimony-phosphomolybdate microassay of ATPase activity through the detection of inorganic phosphate. Anal Biochem 2021; 623:114170. [PMID: 33736971 DOI: 10.1016/j.ab.2021.114170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/28/2021] [Accepted: 03/06/2021] [Indexed: 11/22/2022]
Abstract
Colorimetric methods are convenient for the determination of inorganic phosphate. However, the acidic conditions required can complicate measurement of ATPase through non-enzymatic ATP hydrolysis. Here we present an optimized antimony-phosphomolybdate microassay for the simple and rapid detection of ATPase activity, with micromolar sensitivity. The low acidity of the color reagent results in no interference for samples containing up to 0.5-5 mM ATP, dependent on the sample volume. The assay is compatible with common assay conditions and was similar in accuracy to an established continuous method. The simplicity of this method makes it ideal for medium to high throughput applications.
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Song Y, Zhao M, Wu Y, Yu B, Liu HM. A multifunctional cross-validation high-throughput screening protocol enabling the discovery of new SHP2 inhibitors. Acta Pharm Sin B 2021; 11:750-762. [PMID: 33777680 PMCID: PMC7982506 DOI: 10.1016/j.apsb.2020.10.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/01/2020] [Accepted: 08/21/2020] [Indexed: 12/11/2022] Open
Abstract
The protein tyrosine phosphatase Src homology phosphotyrosyl phosphatase 2 (SHP2) is implicated in various cancers, and targeting SHP2 has become a promising therapeutic approach. We herein described a robust cross-validation high-throughput screening protocol that combined the fluorescence-based enzyme assay and the conformation-dependent thermal shift assay for the discovery of SHP2 inhibitors. The established method can effectively exclude the false positive SHP2 inhibitors with fluorescence interference and was also successfully employed to identify new protein tyrosine phosphatase domain of SHP2 (SHP2-PTP) and allosteric inhibitors. Of note, this protocol showed potential for identifying SHP2 inhibitors against cancer-associated SHP2 mutation SHP2-E76A. After initial screening of our in-house compound library (∼2300 compounds), we identified 4 new SHP2-PTP inhibitors (0.17% hit rate) and 28 novel allosteric SHP2 inhibitors (1.22% hit rate), of which SYK-85 and WS-635 effectively inhibited SHP2-PTP (SYK-85: IC50 = 0.32 μmol/L; WS-635: IC50 = 4.13 μmol/L) and thus represent novel scaffolds for designing new SHP2-PTP inhibitors. TK-147, an allosteric inhibitor, inhibited SHP2 potently (IC50 = 0.25 μmol/L). In structure, TK-147 could be regarded as a bioisostere of the well characterized SHP2 inhibitor SHP-099, highlighting the essential structural elements for allosteric inhibition of SHP2. The principle underlying the cross-validation protocol is potentially feasible to identify allosteric inhibitors or those inactivating mutants of other proteins.
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Key Words
- AKT, protein kinase B
- ALK, anaplastic lymphoma kinase
- AML, acute myelogenous leukemia
- Allosteric inhibitors
- BTLA, B and T lymphocyte attenuator
- Bis-tris, bis-(2-hydroxyethyl)amino-tris(hydroxymethyl)methane
- DTT, dithiothreitol
- DiFMU, 6,8-difluoro-4-methylumbelliferyl hydroxid
- DiFMUP, 6,8-difluoro-4-methylumbelliferyl phosphate
- Enzyme assay
- FI, fluorescence intensity
- HEPES, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
- HTS, high-throughput screening
- High-throughput screening
- IC50, half maximal inhibitory concentration
- JAK, janus kinase
- JMML, juvenile myelomonocytic leukaemia
- LB, lysogeny broth
- LOC, ligand only control
- LS, LEOPARD syndrome
- MAPK, mitogen-activated protein kinase
- MEK, extracellular regulated protein kinase kinases
- NPC, no protein control
- NS, Noonan syndrome
- OD, optical density
- PD-1, programmed death 1
- PI3K, phosphatidylinositol 3 kinase
- PMSF, phenylmethanesulfonyl fluoride
- PTP, protein tyrosine phosphatase
- R2, coefficient of determination
- RAS, rat sarcoma
- S/B, signal over background
- SD, standard deviation
- SDS-PAGE, sodium dodecyl sulphate polyacyrlamide gel electrophoresis
- SH2, Src homology 2
- SHP2
- SHP2, Src homology phosphotyrosyl phosphatase 2
- SHP2-PTP, protein tyrosine phosphatase domain of Src homology phosphotyrosyl phosphatase 2
- SHP2-WT, wild type Src homology phosphotyrosyl phosphatase 2
- STAT, signal transducer and activator of transcription
- Thermal shift assay
- Tm, melting temperature
- p-IRS1, phosphorylated insulin receptor substrate 1
- ΔTm, melting temperature change
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Affiliation(s)
- Yihui Song
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Min Zhao
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Yahong Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Bin Yu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Hong-Min Liu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
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Brander S, Lausten S, Ipsen JØ, Falkenberg KB, Bertelsen AB, Nørholm MHH, Østergaard LH, Johansen KS. Colorimetric LPMO assay with direct implication for cellulolytic activity. Biotechnol Biofuels 2021; 14:51. [PMID: 33640002 PMCID: PMC7916272 DOI: 10.1186/s13068-021-01902-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 02/16/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Lytic polysaccharide monooxygenases (LPMOs) are important industrial enzymes known for their catalytic degradation of recalcitrant polymers such as cellulose or chitin. Their activity can be measured by lengthy HPLC methods, while high-throughput methods are less specific. A fast and specific LPMO assay would simplify screening for new or engineered LPMOs and accelerate biochemical characterization. RESULTS A novel LPMO activity assay was developed based on the production of the dye phenolphthalein (PHP) from its reduced counterpart (rPHP). The colour response of rPHP oxidisation catalysed by the cellulose-specific LPMO from Thermoascus aurantiacus (TaAA9A), was found to increase tenfold by adding dehydroascorbate (DHA) as a co-substrate. The assay using a combination of rPHP and DHA was tested on 12 different metallo-enzymes, but only the LPMOs catalysed this reaction. The assay was optimized for characterization of TaAA9A and showed a sensitivity of 15 nM after 30 min incubation. It followed apparent Michaelis-Menten kinetics with kcat = 0.09 s-1 and KM = 244 µM, and the assay was used to confirm stoichiometric copper-enzyme binding and enzyme unfolding at a temperature of approximately 60 °C. DHA, glutathione and fructose were found to enhance LPMO oxidation of rPHP and in the optimized assay conditions these co-substrates also enabled cellulose degradation. CONCLUSIONS This novel and specific LPMO assay can be carried out in a convenient microtiter plate format ready for high-throughput screening and enzyme characterization. DHA was the best co-substrate tested for oxidation of rPHP and this preference appears to be LPMO-specific. The identified co-substrates DHA and fructose are not normally considered as LPMO co-substrates but here they are shown to facilitate both oxidation of rPHP and degradation of cellulose. This is a rare example of a finding from a high-throughput assay that directly translate into enzyme activity on an insoluble substrate. The rPHP-based assay thus expands our understanding of LPMO catalysed reactions and has the potential to characterize LPMO activity in industrial settings, where usual co-substrates such as ascorbate and oxygen are depleted.
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Affiliation(s)
- Søren Brander
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 1958, Copenhagen, Denmark
| | - Stine Lausten
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Copenhagen, Denmark
| | - Johan Ø Ipsen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Copenhagen, Denmark
| | - Kristoffer B Falkenberg
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Andreas B Bertelsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Morten H H Nørholm
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | | | - Katja S Johansen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 1958, Copenhagen, Denmark.
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Gargiulo S, Soumillion P. Directed evolution for enzyme development in biocatalysis. Curr Opin Chem Biol 2020; 61:107-113. [PMID: 33385931 DOI: 10.1016/j.cbpa.2020.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/25/2020] [Accepted: 11/29/2020] [Indexed: 02/07/2023]
Abstract
As an important sector of the chemical industry, biocatalysis requires the continuous development of enzymes with tailor-made activity, selectivity, stability, or tolerance to unnatural environments. This is now routinely achieved by directed evolution based on iterative cycles of genetic diversification and activity screening. Here, we highlight its recent developments. First, the design of "smarter" libraries by focused mutagenesis may be a crucial start-up for a fast and successful outcome. Then library assembly and expression are also key steps that benefits from modern molecular biology progresses. Finally, various strategies may be considered for library screening depending on the final objective: while low-throughput direct assays have been very successful in generating enzymes for important biocatalytic processes, even in bringing completely new chemistries to the enzyme world, ultrahigh-throughput screening methods are emerging as powerful approaches for engineering the next generation of industrial enzymes.
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Affiliation(s)
- Serena Gargiulo
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Place Croix du Sud 4-5, 1390 Louvain-la-Neuve, Belgium
| | - Patrice Soumillion
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Place Croix du Sud 4-5, 1390 Louvain-la-Neuve, Belgium.
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Calderaro F, Keser M, Akeroyd M, Bevers LE, Eijsink VGH, Várnai A, van den Berg MA. Characterization of an AA9 LPMO from Thielavia australiensis, TausLPMO9B, under industrially relevant lignocellulose saccharification conditions. Biotechnol Biofuels 2020; 13:195. [PMID: 33292403 PMCID: PMC7706046 DOI: 10.1186/s13068-020-01836-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 11/19/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND The discovery of lytic polysaccharide monooxygenases (LPMO) has changed our perspective on enzymatic degradation of plant biomass. Through an oxidative mechanism, these enzymes are able to cleave and depolymerize various polysaccharides, acting not only on crystalline substrates such as chitin and cellulose, but also on other polysaccharides, such as xyloglucan, glucomannan and starch. Despite their widespread use, uncertainties related to substrate specificity and stereospecificity, the nature of the co-substrate, in-process stability, and the nature of the optimal reductant challenge their exploitation in biomass processing applications. RESULTS In this work, we studied the properties of a novel fungal LPMO from the thermophilic fungus Thielavia australiensis, TausLPMO9B. Heterologous expression of TausLPMO9B in Aspergillus niger yielded a glycosylated protein with a methylated N-terminal histidine showing LPMO activity. High sequence identity of the AA9 domain to that of MtLPMO9B (MYCTH_80312) from Myceliophthora thermophila (84%) indicated strictly C1-oxidizing activity on cellulose, which was confirmed experimentally by the analysis of products released from cellulose using HPAEC. The enzyme was stable and active at a pH ranging from 4 to 6, thus matching the conditions commonly used in industrial biomass processing, where a low pH (between 4 and 5) is used due to the pH-optima of commercial cellulases and a desire to limit microbial contamination. CONCLUSION While the oxidative cleavage of phosphoric acid swollen cellulose (PASC) by TausLPMO9B was boosted by the addition of H2O2 as a co-substrate, this effect was not observed during the saccharification of acid pretreated corn stover. This illustrates key differences between the lab-scale tests with artificial, lignin-free substrates and industrial settings with lignocellulosic biomass as substrate.
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Affiliation(s)
- F Calderaro
- DSM Biotechnology Center, PP 699-0310, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands.
- Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
| | - M Keser
- DSM Biotechnology Center, PP 699-0310, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
| | - M Akeroyd
- DSM Biotechnology Center, PP 699-0310, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
| | - L E Bevers
- DSM Biotechnology Center, PP 699-0310, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
| | - V G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - A Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - M A van den Berg
- DSM Biotechnology Center, PP 699-0310, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
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Miners JO, Rowland A, Novak JJ, Lapham K, Goosen TC. Evidence-based strategies for the characterisation of human drug and chemical glucuronidation in vitro and UDP-glucuronosyltransferase reaction phenotyping. Pharmacol Ther 2020; 218:107689. [PMID: 32980440 DOI: 10.1016/j.pharmthera.2020.107689] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/26/2022]
Abstract
Enzymes of the UDP-glucuronosyltransferase (UGT) superfamily contribute to the elimination of drugs from almost all therapeutic classes. Awareness of the importance of glucuronidation as a drug clearance mechanism along with increased knowledge of the enzymology of drug and chemical metabolism has stimulated interest in the development and application of approaches for the characterisation of human drug glucuronidation in vitro, in particular reaction phenotyping (the fractional contribution of the individual UGT enzymes responsible for the glucuronidation of a given drug), assessment of metabolic stability, and UGT enzyme inhibition by drugs and other xenobiotics. In turn, this has permitted the implementation of in vitro - in vivo extrapolation approaches for the prediction of drug metabolic clearance, intestinal availability, and drug-drug interaction liability, all of which are of considerable importance in pre-clinical drug development. Indeed, regulatory agencies (FDA and EMA) require UGT reaction phenotyping for new chemical entities if glucuronidation accounts for ≥25% of total metabolism. In vitro studies are most commonly performed with recombinant UGT enzymes and human liver microsomes (HLM) as the enzyme sources. Despite the widespread use of in vitro approaches for the characterisation of drug and chemical glucuronidation by HLM and recombinant enzymes, evidence-based guidelines relating to experimental approaches are lacking. Here we present evidence-based strategies for the characterisation of drug and chemical glucuronidation in vitro, and for UGT reaction phenotyping. We anticipate that the strategies will inform practice, encourage development of standardised experimental procedures where feasible, and guide ongoing research in the field.
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Affiliation(s)
- John O Miners
- Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, Australia.
| | - Andrew Rowland
- Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, Australia
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Umar AA, Liddell S, Hussain R, Siligardi G, Harris G, Carr S, Asiani K, Gowers DM, Odell M, Scott DJ. Allosteric inhibition of human exonuclease1 (hExo1) through a novel extended β-sheet conformation. Biochim Biophys Acta Gen Subj 2020; 1864:129730. [PMID: 32926959 DOI: 10.1016/j.bbagen.2020.129730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 08/21/2020] [Accepted: 09/08/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND Human Exonuclease1 (hExo1) participates in the resection of DNA double-strand breaks by generating long 3'-single-stranded DNA overhangs, critical for homology-based DNA repair and activation of the ATR-dependent checkpoint. The C-terminal region is essential for modulating the activity of hExo1, containing numerous sites of post-translational modification and binding sites for partner proteins. METHODS Analytical Ultracentrifugation (AUC), Dynamic Light Scattering (DLS), Circular Dichroism (CD) spectroscopy and enzymatic assays. RESULTS AUC and DLS indicates the C-terminal region has a highly extended structure while CD suggest a tendency to adopt a novel left-handed β-sheet structure, together implying the C-terminus may exhibit a transient fluctuating structure that could play a role in binding partner proteins known to regulate the activity of hExo1. Interaction with 14-3-3 protein has a cooperative inhibitory effect upon DNA resection activity, which indicates an allosteric transition occurs upon binding partner proteins. CONCLUSIONS This study has uncovered that hExo1 consist of a folded N-terminal nuclease domain and a highly extended C-terminal region which is known to interact with partner proteins that regulates the activity of hExo1. A positively cooperative mechanism of binding allows for stringent control of hExo1 activity. Such a transition would coordinate the control of hExo1 by hExo1 regulators and hence allow careful coordination of the process of DNA end resection. SIGNIFICANCE The assays presented herein could be readily adapted to rapidly identify and characterise the effects of modulators of the interaction between the 14-3-3 proteins and hExo1. It is conceivable that small molecule modulators of 14-3-3 s-hExo1 interaction may serve as effective chemosensitizers for cancer therapy.
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Affiliation(s)
- Aminu Argungu Umar
- School of Biosciences, University of Nottingham Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom; Department of Biochemistry, Kebbi State University of Science and Technology, Aliero, P.M.B 1144, Birnin Kebbi, Nigeria.
| | - Susan Liddell
- School of Biosciences, University of Nottingham Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Rohanah Hussain
- Diamond Light Source, Rutherford Appleton Laboratory, Oxfordshire OX11 0DE, United Kingdom
| | - Giuliano Siligardi
- Diamond Light Source, Rutherford Appleton Laboratory, Oxfordshire OX11 0DE, United Kingdom
| | - Gemma Harris
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire OX11 0FA, United Kingdom
| | - Stephen Carr
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire OX11 0FA, United Kingdom
| | - Karishma Asiani
- School of Biosciences, University of Nottingham Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Darren M Gowers
- School of Biological Science, King Henry Building, King Henry 1(st) Street, Portsmouth, Hampshire PO1 2DY, United Kingdom
| | - Mark Odell
- Department of Life Sciences, University of Westminster, 115 New Cavendish Street, London W1W 6UW, United Kingdom
| | - David J Scott
- School of Biosciences, University of Nottingham Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom; Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire OX11 0FA, United Kingdom; ISIS Spallation Neutron and Muon source, Rutherford Appleton Laboratory, Oxfordshire OX11 0QX, United Kingdom
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Goulet DL, Fraaz U, Zulich CJ, Pilkington TJ, Siemann S. Specificity-directed design of a FRET-quenched heptapeptide for assaying thermolysin-like proteases. Anal Biochem 2020; 604:113826. [PMID: 32622975 DOI: 10.1016/j.ab.2020.113826] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/08/2020] [Indexed: 11/18/2022]
Abstract
Thermolysin (TL) is an industrially important zinc endopeptidase, and the prototype of the M4 family of metallopeptidases. The catalytic function of TL and its relatives is typically assessed using chromogenic or more sensitive fluorescent peptides, with the latter substrates relying on Förster resonance energy transfer (FRET). Here, we demonstrate that a FRET-quenched heptapeptide designed on the basis of the enzyme's substrate specificity (Dabcyl-FKFLGKE-EDANS) is efficiently cleaved by TL and dispase (a TL-like protease) in between the Phe3 and Leu4 residues. The specificity constants (determined at pH 7.4 and 25 °C) for TL and dispase (3.6 × 106 M-1 s-1 and 4.6 × 106 M-1 s-1, respectively) were found to be amongst the highest documented for any TL substrate. Maximal peptide cleavage rates were achieved at pH 6.5 and a temperature of 65 °C. In view of the sensitivity of the assay, concentrations as low as 10 pM TL could be detected. Furthermore, the rate of hydrolysis of Dabcyl-FKFLGKE-EDANS was slow or immeasurable with some other unrelated metallo-, serine- and cysteine proteases, suggesting that the peptide has the potential to serve as a selective substrate for TL and TL-like proteases.
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Affiliation(s)
- Danica L Goulet
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Usama Fraaz
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Carly J Zulich
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Tyson J Pilkington
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Stefan Siemann
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada.
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Amjadi M, Hallaj T, Hildebrandt N. A sensitive homogeneous enzyme assay for euchromatic histone-lysine-N-methyltransferase 2 (G9a) based on terbium-to-quantum dot time-resolved FRET. ACTA ACUST UNITED AC 2020; 11:173-179. [PMID: 34336605 PMCID: PMC8314039 DOI: 10.34172/bi.2021.23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 06/01/2020] [Accepted: 06/13/2020] [Indexed: 12/20/2022]
Abstract
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Introduction: Histone modifying enzymes include several classes of enzymes that are responsible for various post-translational modifications of histones such as methylation and acetylation. They are important epigenetic factors, which may involve several diseases and so their assay, as well as screening of their inhibitors, are of great importance. Herein, a bioassay based on terbium-to-quantum dot (Tb-to-QD) time-resolved Förster resonance energy transfer (TR-FRET) was developed for monitoring the activity of G9a, the euchromatic histone-lysine N-methyltransferase 2. Overexpression of G9a has been reported in some cancers such as ovarian carcinoma, lung cancer, multiple myeloma and brain cancer. Thus, inhibition of this enzyme is important for therapeutic purposes. Methods: In this assay, a biotinylated peptide was used as a G9a substrate in conjugation with streptavidin-coated ZnS/CdSe QD as FRET acceptor, and an anti-mark antibody labeled with Tb as a donor. Time-resolved fluorescence was used for measuring FRET ratios. Results: We examined three QDs, with emission wavelengths of 605, 655 and 705 nm, as FRET acceptors and investigated FRET efficiency between the Tb complex and each of them. Since the maximum FRET efficiency was obtained for Tb to QD705 (more than 50%), this pair was exploited for designing the enzyme assay. We showed that the method has excellent sensitivity and selectivity for the determination of G9a at concentrations as low as 20 pM. Furthermore, the designed assay was applied for screening of an enzyme inhibitor, S-(5’-Adenosyl)-L-homocysteine (SAH). Conclusion: It was shown that Tb-to-QD FRET is an outstanding platform for developing a homogenous assay for the G9a enzyme and its inhibitors. The obtained results confirmed that this assay was quite sensitive and could be used in the field of inhibitor screening.
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Affiliation(s)
- Mohammad Amjadi
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz 5166616471, Iran
| | - Tooba Hallaj
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz 5166616471, Iran.,Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Niko Hildebrandt
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, Orsay, France.,Laboratoire Chimie Organique, Bioorganique, Réactivité et Analyse (COBRA), Université de Rouen Normandie, CNRS, INSA, 76821 Mont-Saint-Aignan, France
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39
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Yun KI, Han TS. Relationship between enzyme concentration and Michaelis constant in enzyme assays. Biochimie 2020; 176:12-20. [PMID: 32585228 DOI: 10.1016/j.biochi.2020.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/07/2020] [Accepted: 06/09/2020] [Indexed: 11/28/2022]
Abstract
The upper bound of enzyme concentration for accurately estimating the parameters in Michaelis-Menten (MM) equation is not completely determined and still under discussion, even though many researchers have investigated the equation's validity for a long time. In the paper, we broadly investigated the correlation between the system of ordinary differential equations for monosubstrate irreversible enzyme reaction (HMM-system) and its derivative MM equation focusing on the relationship between initial enzyme concentration [E]0 and Michaelis constant Km by numerical simulation. According to the results, the initial reaction velocity v0 is still a function of initial substrate concentration [S]0 at [E]0<Km. The function is identical to the MM equation at [E]0≦0.01Km, while it is described as a new type of equation at 0.01Km≦[E]0<Km. This function is of great significance in enzyme assays as a comprehensive approximation for the HMM-system.
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Affiliation(s)
- Kyong-Il Yun
- Department of Biophysics, Faculty of Life Science, KIM IL SUNG University, Taesong District, Pyongyang, Democratic People's Republic of Korea.
| | - Tong-Sul Han
- Department of Biophysics, Faculty of Life Science, KIM IL SUNG University, Taesong District, Pyongyang, Democratic People's Republic of Korea
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Golmohammadzadeh S, Rojano-Delgado AM, Vázquez-García JG, Romano Y, Osuna MD, Gherekhloo J, De Prado R. Cross-resistance mechanisms to ACCase-inhibiting herbicides in short-spike canarygrass (Phalaris brachystachys). Plant Physiol Biochem 2020; 151:681-688. [PMID: 32353674 DOI: 10.1016/j.plaphy.2020.03.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 03/24/2020] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
Herbicides that inhibit acetyl-coenzyme A carboxylase (ACCase) are commonly used to control weedy grasses such as short-spike canarygrass (Phalaris brachystachys). Two resistant biotypes of P. brachystachys (R1 and R2) were found in different winter wheat fields in Iran. This study was done to confirm the suspected resistance observed in the field and to elucidate the resistance mechanisms involved. The results indicated that the both resistant biotypes showed cross-resistance to diclofop-methyl (DM), pinoxaden (PN) and cycloxydim (CD) herbicides. Based on the herbicide dose that inhibited 50% of the ACCase activity (I50), the ACCase activity of the resistant biotypes was less sensitive than the S biotype to DM, CD, and PN. No differences in translocation were detected between biotypes; most of the herbicide remained in the treated leaves. The 14C-DM metabolites were identified using thin-layer chromatography. Pre-treatment with the cytochrome P450 inhibitor ABT inhibited 14C-DM metabolism in the R1 biotype, indicating that metabolism is involved in the DM resistance in the R1 biotype. DNA sequencing studies found an Ile-1781-Thr change in both resistant biotypes, conferring cross-resistance to ACCase inhibitors. In general, in the R1 biotype which showed a higher level of resistance than that of the R2 biotype, cross-resistance was observed because of mutation and DM metabolism, while in the R2 biotype, the mutation confers resistance to ACCase-inhibiting herbicides. This is the first reported evidence of the mechanisms responsible for the resistance to ACCase herbicides in P. brachystachys. These results could be useful for improved management of resistant biotypes carrying similar mutations.
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Affiliation(s)
- Sajedeh Golmohammadzadeh
- Department of Agronomy, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, 4918943464, Iran
| | - Antonia M Rojano-Delgado
- Department of Agricultural Chemistry and Soil Science, University of Córdoba, 14014, Córdoba, Spain
| | - Jose G Vázquez-García
- Department of Agricultural Chemistry and Soil Science, University of Córdoba, 14014, Córdoba, Spain
| | - Yolanda Romano
- Center for Scientific and Technological Research of Extremadura (CICYTEX), 06187, Badajoz, Spain
| | - Maria D Osuna
- Center for Scientific and Technological Research of Extremadura (CICYTEX), 06187, Badajoz, Spain
| | - Javid Gherekhloo
- Department of Agronomy, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, 4918943464, Iran
| | - Rafael De Prado
- Department of Agricultural Chemistry and Soil Science, University of Córdoba, 14014, Córdoba, Spain.
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Olp MD, Kalous KS, Smith BC. ICEKAT: an interactive online tool for calculating initial rates from continuous enzyme kinetic traces. BMC Bioinformatics 2020; 21:186. [PMID: 32410570 PMCID: PMC7222511 DOI: 10.1186/s12859-020-3513-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 04/23/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Continuous enzyme kinetic assays are often used in high-throughput applications, as they allow rapid acquisition of large amounts of kinetic data and increased confidence compared to discontinuous assays. However, data analysis is often rate-limiting in high-throughput enzyme assays, as manual inspection and selection of a linear range from individual kinetic traces is cumbersome and prone to user error and bias. Currently available software programs are specialized and designed for the analysis of complex enzymatic models. Despite the widespread use of initial rate determination for processing kinetic data sets, no simple and automated program existed for rapid analysis of initial rates from continuous enzyme kinetic traces. RESULTS An Interactive Continuous Enzyme Kinetics Analysis Tool (ICEKAT) was developed for semi-automated calculation of initial rates from continuous enzyme kinetic traces with particular application to the evaluation of Michaelis-Menten and EC50/IC50 kinetic parameters, as well as the results of high-throughput screening assays. ICEKAT allows users to interactively fit kinetic traces using convenient browser-based selection tools, ameliorating tedious steps involved in defining ranges to fit in general purpose programs like Microsoft Excel and Graphpad Prism, while still maintaining simplicity in determining initial rates. As a test case, we quickly analyzed over 500 continuous enzyme kinetic traces resulting from experimental data on the response of the protein lysine deacetylase SIRT1 to small-molecule activators. CONCLUSIONS ICEKAT allows simultaneous visualization of individual initial rate fits and the resulting Michaelis-Menten or EC50/IC50 kinetic model fits, as well as hits from high-throughput screening assays. In addition to serving as a convenient program for practicing enzymologists, ICEKAT is also a useful teaching aid to visually demonstrate in real-time how incorrect initial rate fits can affect calculated Michaelis-Menten or EC50/IC50 kinetic parameters. For the convenience of the research community, we have made ICEKAT freely available online at https://icekat.herokuapp.com/icekat.
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Affiliation(s)
- Michael D Olp
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, 53226, USA
| | - Kelsey S Kalous
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, 53226, USA
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, 53226, USA.
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Busch H, Tonin F, Alvarenga N, van den Broek M, Lu S, Daran JM, Hanefeld U, Hagedoorn PL. Exploring the abundance of oleate hydratases in the genus Rhodococcus-discovery of novel enzymes with complementary substrate scope. Appl Microbiol Biotechnol 2020; 104:5801-5812. [PMID: 32358760 PMCID: PMC7306040 DOI: 10.1007/s00253-020-10627-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 04/02/2020] [Accepted: 04/14/2020] [Indexed: 11/24/2022]
Abstract
Oleate hydratases (Ohys, EC 4.2.1.53) are a class of enzymes capable of selective water addition reactions to a broad range of unsaturated fatty acids leading to the respective chiral alcohols. Much research was dedicated to improving the applications of existing Ohys as well as to the identification of undescribed Ohys with potentially novel properties. This study focuses on the latter by exploring the genus Rhodococcus for its plenitude of oleate hydratases. Three different Rhodococcus clades showed the presence of oleate hydratases whereby each clade was represented by a specific oleate hydratase family (HFam). Phylogenetic and sequence analyses revealed HFam-specific patterns amongst conserved amino acids. Oleate hydratases from two Rhodococcus strains (HFam 2 and 3) were heterologously expressed in Escherichia coli and their substrate scope investigated. Here, both enzymes showed a complementary behaviour towards sterically demanding and multiple unsaturated fatty acids. Furthermore, this study includes the characterisation of the newly discovered Rhodococcus pyridinivorans Ohy. The steady-state kinetics of R. pyridinivorans Ohy was measured using a novel coupled assay based on the alcohol dehydrogenase and NAD+-dependent oxidation of 10-hydroxystearic acid.
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Affiliation(s)
- Hanna Busch
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Fabio Tonin
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Natália Alvarenga
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Simona Lu
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Ulf Hanefeld
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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Shakeel T, Fatma Z, Yazdani SS. In vivo Quantification of Alkanes in Escherichia coli. Bio Protoc 2020; 10:e3593. [PMID: 33659559 DOI: 10.21769/bioprotoc.3593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 11/02/2022] Open
Abstract
Microbial production of alkanes employing synthetic biology tools has gained tremendous attention owing to the high energy density and similarity of alkanes to existing petroleum fuels. One of the most commonly studied pathways includes the production of alkanes by AAR (acyl-ACP (acyl carrier protein) reductase)-ADO (aldehyde deformylating oxygenase) pathway. Here, the intermediates of fatty acid synthesis pathway are used as substrate by the AAR enzyme to make fatty aldehyde, which is then deformylated by ADO to make linear chain alkane. However, the variation in substrate availability to the first enzyme of the pathway, i.e., AAR, via fatty acid synthesis pathway and low turnover of the ADO enzyme make calculation of yields and titers under in vivo conditions extremely difficult. In vivo assay employing external addition of defined substrates for ADO enzyme into the medium helps to monitor the influx of substrate hence providing a more accurate measurement of the product yields. In this protocol, we include a detailed guide for implementing the in vivo assay for monitoring alkane production in E. coli.
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Affiliation(s)
- Tabinda Shakeel
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Zia Fatma
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Syed Shams Yazdani
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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44
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Piroozmand F, Ghadam P, Zarrabi M, Abdi-Ali A. Biochemical and computational study of an alginate lyase produced by Pseudomonas aeruginosa strain S21. Iran J Basic Med Sci 2020; 23:454-460. [PMID: 32489560 PMCID: PMC7239423 DOI: 10.22038/ijbms.2020.37277.8874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVES Alginates play a key role in mucoid Pseudomonas aeruginosa colonization, biofilm formation, and driving out of cationic antibiotics. P. aeruginosa alginate lyase (AlgL) is a periplasmic enzyme that is necessary for alginate synthesis and secretion. It also has a role in depolymerization of alginates. Using AlgLs in cystic fibrosis patients along with antibiotics enhances bacterial killing and host healing. In this study, we investigated the different biochemical properties of a newly isolated AlgL from P. aeruginosa S21 to complete the databank of AlgLs. MATERIALS AND METHODS The enzyme was extracted from the periplasmic space of the bacteria by the heat shock method. Using the TBA method, the enzyme activity and biochemical properties were assessed. The mutability of P. aeruginosa S21 AlgL to increase its thermal stability was investigated. The most favorable mutations were studied computationally. The molecular dynamics simulation (MDS) package GROMACS was used for determining the effect of S34R mutation on enzyme's thermal stability. RESULTS Data showed that this enzyme has the best activity at 37 °C and pH 7.5 and it can degrade mannuronate blocks, guluronate blocks, and sodium alginate. After 7 hr at 80 °C, 45% of the enzyme activity was retained. This enzyme needed 15 min to completely degrade accessible sodium alginate. Tris buffer, pH 8.5 and Britton-Robinson buffer, pH 7.0 were the preferable buffers for the enzyme activity. MDS of native and mutated enzymes showed desirable results. CONCLUSION P. aeruginosa S21 AlgL can be used in medical and industrial applications to degrade alginates.
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Affiliation(s)
- Firoozeh Piroozmand
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Parinaz Ghadam
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran,Corresponding author: Parinaz Ghadam. Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran. Tel: +98-21-88044051;
| | - Mahboobe Zarrabi
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Ahya Abdi-Ali
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
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Lee J, Chen J, Sarkar P, Xue M, Hooley RJ, Zhong W. Monitoring the crosstalk between methylation and phosphorylation on histone peptides with host-assisted capillary electrophoresis. Anal Bioanal Chem 2020; 412:6189-6198. [PMID: 32064571 DOI: 10.1007/s00216-020-02486-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/27/2020] [Accepted: 02/03/2020] [Indexed: 11/29/2022]
Abstract
Post-translational modifications (PTMs) greatly increase protein diversity and regulate their functions by changing the structures, properties, and molecular interactions of proteins. In peptide regions with high density of PTMs, PTMs can influence modification on residues in proximity or even at distal positions, adding another layer of regulation. Methods that can monitor the activities of PTM enzymes on peptides carrying multiple modifications are valuable tools for better understanding of PTM crosstalk. Herein, we developed a host-assisted capillary electrophoresis (CE) method to separate histone peptides with methylation and phosphorylation and applied it to monitor the crosstalk between serine phosphorylation and lysine methylation when they were added by Aurora B kinase and G9a lysine methyltransferase, respectively. A synthetic receptor molecule, 4-hexasulfonatocalix[6]arene (CX6), was included in the CE buffer to improve the resolution of the corresponding substrates and products. A linear polyacrylamide-coated capillary was employed to effectively reduce wall adsorption of the cationic histone peptides. The peptide substrates were labeled with fluorescein to enhance their detectability during CE separation. Our method successfully revealed that the activity of G9a methyltransferase was completely inhibited by the adjacent phosphorylation, while 25% reduction in the activity of Aurora B kinase was observed with the presence of dimethylation on the nearby residue. The PTM crosstalk was examined not only using a pure peptide substrate, but also in a competitive reaction environment, in which the modified and unmodified peptides were mixed and the enzyme actions on both peptides were monitored simultaneously. Our work demonstrates that host-assisted CE is an effective method for study of PTM crosstalk, which could offer the advantages of fast separation, high resolution, and low sample consumption. Graphical abstract.
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Affiliation(s)
- Jiwon Lee
- Department of Chemistry, University of California-Riverside, 900 University Ave., Riverside, CA, 92521, USA
| | - Junyi Chen
- Department of Environmental Toxicology Program, University of California-Riverside, 00 University Ave., Riverside, CA, 92521, USA
| | - Priyanka Sarkar
- Department of Chemistry, University of California-Riverside, 900 University Ave., Riverside, CA, 92521, USA
| | - Min Xue
- Department of Chemistry, University of California-Riverside, 900 University Ave., Riverside, CA, 92521, USA.,Department of Environmental Toxicology Program, University of California-Riverside, 00 University Ave., Riverside, CA, 92521, USA
| | - Richard J Hooley
- Department of Chemistry, University of California-Riverside, 900 University Ave., Riverside, CA, 92521, USA.,Department of Biochemistry and Molecular Biology, University of California-Riverside, 900 University Ave., Riverside, CA, 92521, USA
| | - Wenwan Zhong
- Department of Chemistry, University of California-Riverside, 900 University Ave., Riverside, CA, 92521, USA. .,Department of Environmental Toxicology Program, University of California-Riverside, 00 University Ave., Riverside, CA, 92521, USA.
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46
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Abstract
Phytoene synthase (PSY) is the rate-limiting step in carotenoid biosynthesis, and accordingly subjected to a number of regulatory mechanisms at various levels, including transcriptional, posttranscriptional, and posttranslational. Several PSY genes are present in most taxa and show various degrees of tissue and/or stress-specific responses providing an additional layer of regulating carotenogenesis. Moreover, only a small number of amino acid differences between paralogs or even single nucleotide polymorphisms distinguishing orthologs greatly affect enzyme properties, suggesting that different enzymatic parameters determined by intrinsic properties of PSY protein sequences also determine pathway flux. The characterization of enzyme properties of PSY variants from different origins requires in vitro enzyme assays with recombinant PSY. In this protocol, we present detailed instructions how to purify several milligrams of active PSY enzyme from bacterial lysates, which includes initial recombinant PSY enrichment through inclusion body purification, chaotropic unfolding, refolding in presence of detergents and purification through immobilized metal affinity chromatography. In addition, we provide a protocol to obtain active geranylgeranyl pyrophosphate (GGPP) synthase as active supply of GGPP substrate is a requirement for high in vitro PSY activity. The activity assay requires 14C-labeled substrate and allows to determine its incorporation into phytoene as well as GGPP. The protocol described here was successfully applied to a variety of PSY and GGPP synthase homologs from various plant species.
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Affiliation(s)
- Maurizio Camagna
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ralf Welsch
- Institute for Biology II, University of Freiburg, Freiburg, Germany.
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47
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Arafa AS, Ragab AE, Ibrahim ARS, Abdel-Mageed WS, Nasr ME. Cloning and Overexpression of Strictosidine β-D-Glucosidase Gene Short Sequence from Catharanthus roseus in Escherichia coli. Adv Pharm Bull 2019; 9:655-661. [PMID: 31857971 PMCID: PMC6912177 DOI: 10.15171/apb.2019.076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 06/07/2019] [Accepted: 06/15/2019] [Indexed: 11/18/2022] Open
Abstract
Purpose: Strictosidine-β-D-glucosidase (SGD) is considered as a key enzyme in the production of bisindole alkaloids in Catharanthus roseus. The present study illustrated the production of a short sequence of this enzyme in Escherichia coli without codon optimization. Methods: Strictosidine-β-D-glucosidase (sgd) gene short sequence (1434 bp), which lacks the conserved sequence KGFFVWS and the localization peptide sequence at the C-terminal, was amplified from cDNA of C. roseus leaves, cloned and expressed in Escherichia coli. The activity of the produced protein in cell free lysate was tested using total alkaloid extract of C. roseus leaves. Results: HPLC and LC-MS analysis of the assay mixture revealed the disappearance of the strictosidine peak. Conclusion: SGD short sequence can be produced in Escherichia coli in active form without codon optimization.
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Affiliation(s)
- Ahmed Saeed Arafa
- Pharmacognosy Department, Faculty of Pharmacy, Tanta University, Tanta, Egypt, 31527
| | - Amany Elsayed Ragab
- Pharmacognosy Department, Faculty of Pharmacy, Tanta University, Tanta, Egypt, 31527
| | | | - Wael Saad Abdel-Mageed
- Molecular Biology Department, Genetic Engineering and Biotechnology Research Institute, Sadat City University, Sadat City, Egypt, 32897.,Genetics Department, Faculty of Agriculture, Beni-Suef University, Beni-Suef, Egypt, 62511
| | - Mahmoud Emam Nasr
- Molecular Biology Department, Genetic Engineering and Biotechnology Research Institute, Sadat City University, Sadat City, Egypt, 32897
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48
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Ohta Y, Wakita H, Kawaguchi M, Ieda N, Osada S, Nakagawa H. Ratiometric assay of CARM1 activity using a FRET-based fluorescent probe. Bioorg Med Chem Lett 2019; 29:126728. [PMID: 31607607 DOI: 10.1016/j.bmcl.2019.126728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/25/2019] [Accepted: 10/01/2019] [Indexed: 10/25/2022]
Abstract
One of the regulatory mechanisms of epigenetic gene expression is the post-translational methylation of arginine residues, which is catalyzed by protein arginine methyltransferases (PRMTs). Abnormal expression of PRMT4/CARM1, one of the PRMTs, is associated with various diseases, including cancers. Here, we designed and synthesized a Förster resonance energy transfer (FRET)-based probe, FRC, which contains coumarin and fluorescein fluorophores at the N-terminus and C-terminus of a peptide containing an arginine residue within an appropriate amino acid sequence to serve as a substrate of CARM1; the two fluorophores act as a FRET donor and a FRET acceptor, respectively. Since trypsin specifically hydrolyzes the arginine residue, but not a monomethylarginine or dimethylarginine residue, CARM1 activity can be evaluated from the change of the coumarin/fluorescein fluorescence ratio of FRC in the presence of trypsin.
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Affiliation(s)
- Yuhei Ohta
- Graduate School of Pharmaceutical Science, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, Japan
| | - Hiroo Wakita
- Graduate School of Pharmaceutical Science, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, Japan
| | - Mitsuyasu Kawaguchi
- Graduate School of Pharmaceutical Science, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, Japan
| | - Naoya Ieda
- Graduate School of Pharmaceutical Science, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, Japan
| | - Shigehiro Osada
- Daiichi University of Pharmacy, 22-1 Tamagawa-cho, Minami-ku, Fukuoka, Japan
| | - Hidehiko Nakagawa
- Graduate School of Pharmaceutical Science, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, Japan.
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49
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Yu J, Zhang Y, Ning S, Ye Q, Tan H, Chen R, Bu Q, Zhang R, Gong P, Ma X, Zhang L, Wei D. Molecular cloning and metabolomic characterization of the 5-enolpyruvylshikimate-3-phosphate synthase gene from Baphicacanthus cusia. BMC Plant Biol 2019; 19:485. [PMID: 31706293 PMCID: PMC6842527 DOI: 10.1186/s12870-019-2035-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 09/12/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Indigo alkaloids, such as indigo, indirubin and its derivatives, have been identified as effective antiviral compounds in Baphicacanthus cusia. Evidence suggests that the biosynthesis of indigo alkaloids in plants occurs via the shikimate pathway. The enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) is involved in plant metabolism; however, its underlying putative mechanism of regulating the production of indigo alkaloids is currently unknown. RESULTS One gene encoding EPSPS was isolated from B. cusia. Quantitative real-time PCR analysis revealed that BcEPSPS was expressed at the highest level in the stem and upregulated by methyl jasmonate (MeJA), salicylic acid (SA) and abscisic acid (ABA) treatment. The results of subcellular localization indicated that BcEPSPS is mainly expressed in both the plastids and cytosol, which has not been previously reported. An enzyme assay revealed that the heterogeneously expressed BcEPSPS protein catalysed the generation of 5-enolpyruvyl shikimate-3-phosphate. The overexpression of BcEPSPS in Isatis indigotica hairy roots resulted in the high accumulation of indigo alkaloids, such as indigo, secologanin, indole and isorhamnetin. CONCLUSIONS The function of BcEPSPS in catalysing the production of EPSP and regulating indigo alkaloid biosynthesis was revealed, which provided a distinct view of plant metabolic engineering. Our findings have practical implications for understanding the effect of BcEPSPS on active compound biosynthesis in B. cusia.
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Affiliation(s)
- Jian Yu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fuzhou, 350002, People's Republic of China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fuzhou, 350002, People's Republic of China
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
- School of Life Sciences, East China Normal University, Shanghai, 200433, People's Republic of China
| | - Yihan Zhang
- Department of Pharmaceutical Changzheng Hosipital, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Shuju Ning
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Qi Ye
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fuzhou, 350002, People's Republic of China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fuzhou, 350002, People's Republic of China
| | - Hexin Tan
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Ruibing Chen
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Qitao Bu
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Rui Zhang
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Peimin Gong
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fuzhou, 350002, People's Republic of China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fuzhou, 350002, People's Republic of China
| | - Xiaoli Ma
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fuzhou, 350002, People's Republic of China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fuzhou, 350002, People's Republic of China
| | - Lei Zhang
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China.
| | - Daozhi Wei
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fuzhou, 350002, People's Republic of China.
- Key Laboratory of Crop Ecology and Molecular Physiology, Fuzhou, 350002, People's Republic of China.
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50
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Abstract
Heparanase, an endo-β-D-glucuronidase, cleaves cell surface and extracellular matrix heparan sulfate (HS) chains at distinct sites and plays important biological roles including modulation of cell growth and metastasis. Although a number of different types of heparanase assays have been reported to date, most are labor intensive, complex and/or expensive to carry out. We reasoned that a simpler heparanase assay could be developed using heparin labeled with Dabcyl and EDANS as donor and acceptor fluorophores so as to generate a FRET signal. Our results show that a more robust heparanase assay could be developed based on the principle studied herein and more homogeneous preparation of heparin. Yet, the assay in its current form could be used for routine screening of potential inhibitors in a high-throughput manner as well as for studying heparanase activity expressed in tumors as well as biological fluids like plasma.
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Affiliation(s)
- Jyothi C Sistla
- Institute for Structural Biology, Drug Discovery, and Development, Virginia Commonwealth University, Richmond, VA 23219, USA.,Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Umesh R Desai
- Institute for Structural Biology, Drug Discovery, and Development, Virginia Commonwealth University, Richmond, VA 23219, USA.,Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA
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