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Wang N, He S, Yang B, Zhang H, Liu D, Song P, Chen T, Wang W, Ge H, Ma J. Crystal structure of HPPD inhibitor sensitive protein from Oryza sativa. Biochem Biophys Res Commun 2024; 704:149672. [PMID: 38401306 DOI: 10.1016/j.bbrc.2024.149672] [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: 01/31/2024] [Revised: 02/02/2024] [Accepted: 02/10/2024] [Indexed: 02/26/2024]
Abstract
4-hydroxyphenylpyruvate dioxygenase (HPPD) Inhibitor Sensitive 1 (HIS1) is an endogenous gene of rice, conferring broad-spectrum resistance to β-triketone herbicides. Similar genes, known as HIS1-like genes (HSLs), exhibit analogous functions and can complement the herbicide-resistant characteristics endowed by HIS1. The identification of HIS1 and HSLs represents a valuable asset, as the intentional pairing of herbicides with resistance genes emerges as an effective strategy for crop breeding. Encoded by HIS1 is a Fe(II)/2-oxoglutarate-dependent oxygenase responsible for detoxifying β-triketone herbicides through hydroxylation. However, the precise structure supporting this function remains unclear. This work, which determined the crystal structure of HIS1, reveals a conserved core motif of Fe(II)/2-oxoglutarate-dependent oxygenase and pinpoints the crucial residue dictating substrate preference between HIS1 and HSL.
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Affiliation(s)
- Na Wang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, PR China.
| | - Shibing He
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, PR China
| | - Beibei Yang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, PR China
| | - He Zhang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, PR China
| | - DanDan Liu
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, PR China
| | - Peifan Song
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, PR China
| | - Tiantian Chen
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, PR China
| | - Weiqiang Wang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, PR China
| | - Honghua Ge
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, PR China.
| | - Jinming Ma
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, PR China.
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Ramírez RE, Buendia-Corona RE, Pérez-Xochipa I, Scior T. Computational Binding Study Hints at Ecdysone 20-Mono-Oxygenase as the Hitherto Unknown Target for Ring C-Seco Limonoid-Type Insecticides. Molecules 2024; 29:1628. [PMID: 38611907 PMCID: PMC11013123 DOI: 10.3390/molecules29071628] [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: 03/12/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
The insecticidal property of ring C-seco limonoids has been discovered empirically and the target protein identified, but, to date, the molecular mechanism of action has not been described at the atomic scale. We elucidate on computational grounds whether nine C-seco limonoids present sufficiently high affinity to bind specifically with the putative target enzyme of the insects (ecdysone 20-monooxygenase). To this end, 3D models of ligands and the receptor target were generated and their interaction energies estimated by docking simulations. As a proof of concept, the tetrahydro-isoquinolinyl propenamide derivative QHC is the reference ligand bound to aldosterone synthase in the complex with PDB entry 4ZGX. It served as the 3D template for target modeling via homology. QHC was successfully docked back to its crystal pose in a one-digit nanomolar range. The reported experimental binding affinities span over the nanomolar to lower micromolar range. All nine limonoids were found with strong affinities in the range of -9 < ΔG < -13 kcal/mol. The molt hormone ecdysone showed a comparable ΔG energy of -12 kcal/mol, whereas -11 kcal/mol was the back docking result for the liganded crystal 4ZGX. In conclusion, the nine C-seco limonoids were strong binders on theoretical grounds in an activity range between a ten-fold lower to a ten-fold higher concentration level than insecticide ecdysone with its known target receptor. The comparable or even stronger binding hints at ecdysone 20-monooxygenase as their target biomolecule. Our assumption, however, is in need of future experimental confirmation before conclusions with certainty can be drawn about the true molecular mechanism of action for the C-seco limonoids under scrutiny.
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Affiliation(s)
- Ramsés E. Ramírez
- Departamento de Fisicomatemáticas, Facultad de Ciencias Químicas Benemérita, Universidad Autónoma de Puebla, Prol. 24 Sur, Puebla 72570, Mexico; (R.E.R.); (R.E.B.-C.)
| | - Ricardo E. Buendia-Corona
- Departamento de Fisicomatemáticas, Facultad de Ciencias Químicas Benemérita, Universidad Autónoma de Puebla, Prol. 24 Sur, Puebla 72570, Mexico; (R.E.R.); (R.E.B.-C.)
| | - Ivonne Pérez-Xochipa
- Departamento de Bioquímica Alimentos, Facultad de Ciencias Químicas Benemérita, Universidad Autónoma de Puebla, Prol. 24 Sur, Puebla 72570, Mexico;
| | - Thomas Scior
- Laboratorio de Simulaciones Moleculares Computacionales, Facultad de Ciencias Químicas Benemérita, Universidad Autónoma de Puebla, Prol. 24 Sur, Puebla 72570, Mexico
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Ansari S, Aliasgharzad N, Sarikhani MR, Najafi N, Arzanlou M, Ölmez F. Nitrogen sources alter ligninase and cellulase activities of thermophilic fungi isolated from compost and vermicompost. Folia Microbiol (Praha) 2024; 69:323-332. [PMID: 37338677 DOI: 10.1007/s12223-023-01065-9] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/18/2023] [Indexed: 06/21/2023]
Abstract
Fungi harboring lignocellulolytic activity accelerate the composting process of agricultural wastes; however, using thermophilic fungal isolates for this process has been paid little attention. Moreover, exogenous nitrogen sources may differently affect fungal lignocellulolytic activity. A total of 250 thermophilic fungi were isolated from local compost and vermicompost samples. First, the isolates were qualitative assayed for ligninase and cellulase activities using Congo red (CR) and carboxymethyl cellulose (CMC) as substrates, respectively. Then, twenty superior isolates harboring higher ligninase and cellulase activities were selected and quantitatively assayed for both enzymes in basic mineral (BM) liquid medium supplemented with the relevant substrates and nitrogen sources including (NH4)2SO4 (AS), NH4NO3 (AN), urea (U), AS + U (1:1), or AN + U (1:1) with final nitrogen concentration of 0.3 g/L. The highest ligninase activities of 99.94, 89.82, 95.42, 96.25, and 98.34% of CR decolorization were recorded in isolates VC85, VC94, VC85, C145, and VC85 in the presence of AS, U, AS + U, AN, and AN + U, respectively. Mean ligninase activity of 63.75% in superior isolates was achieved in the presence of AS and ranked the highest among other N compounds. The isolates C200 and C184 exhibited the highest cellulolytic activity in the presence of AS and AN + U by 8.8 and 6.5 U/ml, respectively. Mean cellulase activity of 3.90 U/mL was achieved in AN + U and ranked the highest among other N compounds. Molecular identification of twenty superior isolates confirmed that all of them are belonging to Aspergillus fumigatus group. Focusing on the highest ligninase activity of the isolate VC85 in the presence of AS, the combination can be recommended as a potential bio-accelerator for compost production.
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Affiliation(s)
- Saeideh Ansari
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Nasser Aliasgharzad
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.
| | | | - Nosratollah Najafi
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Mahdi Arzanlou
- Department of Plant Protection, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Fatih Ölmez
- Department of Plant Protection, Faculty of Agriculture, Sivas University of Science and Technology, Sivas, Turkey
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Belle R, Saraç H, Salah E, Bhushan B, Szykowska A, Roper G, Tumber A, Kriaucionis S, Burgess-Brown N, Schofield CJ, Brown T, Kawamura A. Focused Screening Identifies Different Sensitivities of Human TET Oxygenases to the Oncometabolite 2-Hydroxyglutarate. J Med Chem 2024; 67:4525-4540. [PMID: 38294854 PMCID: PMC10983004 DOI: 10.1021/acs.jmedchem.3c01820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/10/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024]
Abstract
Ten-eleven translocation enzymes (TETs) are Fe(II)/2-oxoglutarate (2OG) oxygenases that catalyze the sequential oxidation of 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine in eukaryotic DNA. Despite their roles in epigenetic regulation, there is a lack of reported TET inhibitors. The extent to which 2OG oxygenase inhibitors, including clinically used inhibitors and oncometabolites, modulate DNA modifications via TETs has been unclear. Here, we report studies on human TET1-3 inhibition by a set of 2OG oxygenase-focused inhibitors, employing both enzyme-based and cellular assays. Most inhibitors manifested similar potencies for TET1-3 and caused increases in cellular 5hmC levels. (R)-2-Hydroxyglutarate, an oncometabolite elevated in isocitrate dehydrogenase mutant cancer cells, showed different degrees of inhibition, with TET1 being less potently inhibited than TET3 and TET2, potentially reflecting the proposed role of TET2 mutations in tumorigenesis. The results highlight the tractability of TETs as drug targets and provide starting points for selective inhibitor design.
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Affiliation(s)
- Roman Belle
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Chemistry
− School of Natural and Environmental Sciences, Bedson Building, Newcastle University, NE1 7RU Newcastle upon Tyne, United Kingdom
| | - Hilal Saraç
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Chemistry
− School of Natural and Environmental Sciences, Bedson Building, Newcastle University, NE1 7RU Newcastle upon Tyne, United Kingdom
- Radcliffe
Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human
Genetics, Roosevelt Drive, OX3 7BN Oxford, United Kingdom
| | - Eidarus Salah
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Centre
for Medicines Discovery, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Bhaskar Bhushan
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Radcliffe
Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human
Genetics, Roosevelt Drive, OX3 7BN Oxford, United Kingdom
| | - Aleksandra Szykowska
- Centre
for Medicines Discovery, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Grace Roper
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Chemistry
− School of Natural and Environmental Sciences, Bedson Building, Newcastle University, NE1 7RU Newcastle upon Tyne, United Kingdom
| | - Anthony Tumber
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Skirmantas Kriaucionis
- Ludwig
Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Nicola Burgess-Brown
- Centre
for Medicines Discovery, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Tom Brown
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Akane Kawamura
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Chemistry
− School of Natural and Environmental Sciences, Bedson Building, Newcastle University, NE1 7RU Newcastle upon Tyne, United Kingdom
- Radcliffe
Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human
Genetics, Roosevelt Drive, OX3 7BN Oxford, United Kingdom
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Goupil E, Lacroix L, Brière J, Guga S, Saba-El-Leil MK, Meloche S, Labbé JC. OSGN-1 is a conserved flavin-containing monooxygenase required to stabilize the intercellular bridge in late cytokinesis. Proc Natl Acad Sci U S A 2024; 121:e2308570121. [PMID: 38442170 PMCID: PMC10945809 DOI: 10.1073/pnas.2308570121] [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: 05/22/2023] [Accepted: 01/24/2024] [Indexed: 03/07/2024] Open
Abstract
Cytokinesis is the last step of cell division and is regulated by the small GTPase RhoA. RhoA activity is required for all steps of cytokinesis, including prior to abscission when daughter cells are ultimately physically separated. Like germ cells in all animals, the Caenorhabditis elegans embryonic germline founder cell initiates cytokinesis but does not complete abscission, leaving a stable intercellular bridge between the two daughter cells. Here, we identify and characterize C. elegans OSGN-1 as a cytokinetic regulator that promotes RhoA activity during late cytokinesis. Sequence analyses and biochemical reconstitutions reveal that OSGN-1 is a flavin-containing monooxygenase (MO). Genetic analyses indicate that the MO activity of OSGN-1 is required to maintain active RhoA at the end of cytokinesis in the germline founder cell and to stabilize the intercellular bridge. Deletion of OSGIN1 in human cells results in an increase in binucleation as a result of cytokinetic furrow regression, and this phenotype can be rescued by expressing a catalytically active form of C. elegans OSGN-1, indicating that OSGN-1 and OSGIN1 are functional orthologs. We propose that OSGN-1 and OSGIN1 are conserved MO enzymes required to maintain RhoA activity at the intercellular bridge during late cytokinesis and thus favor its stability, enabling proper abscission in human cells and bridge stabilization in C. elegans germ cells.
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Affiliation(s)
- Eugénie Goupil
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QCH3C 3J7, Canada
| | - Léa Lacroix
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QCH3C 3J7, Canada
| | - Jonathan Brière
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QCH3C 3J7, Canada
| | - Sandra Guga
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QCH3C 3J7, Canada
| | - Marc K. Saba-El-Leil
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QCH3C 3J7, Canada
| | - Sylvain Meloche
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QCH3C 3J7, Canada
- Department of Pharmacology and Physiology, Université de Montréal, Montréal, QCH3C 3J7, Canada
| | - Jean-Claude Labbé
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QCH3C 3J7, Canada
- Department of Pathology and Cell Biology, Université de Montréal, Montréal, QCH3C 3J7, Canada
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6
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Mori K, Tanase K, Sasaki K. Novel electroporation-based genome editing of carnation plant tissues using RNPs targeting the anthocyanidin synthase gene. Planta 2024; 259:84. [PMID: 38448635 DOI: 10.1007/s00425-024-04358-6] [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: 07/26/2023] [Accepted: 02/02/2024] [Indexed: 03/08/2024]
Abstract
MAIN CONCLUSION A novel electroporation method for genome editing was performed using plant tissue samples by direct RNPs-introduction in carnation. Genome editing is becoming a very useful tool in plant breeding. In this study, a novel electroporation method was performed for genome editing using plant tissue samples. The objective was to create a flower color mutant using the pink-flowered carnation 'Kane Ainou 1-go'. For this purpose, a ribonucleoprotein consisting of guide RNA and clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) was introduced into the stem tissue to induce mutations in the anthocyanidin synthase (ANS) gene, which is involved in anthocyanin biosynthesis. As the ANS of 'Kane Ainou 1-go' has not been previously isolated, we initially isolated the ANS gene from 'Kane Ainou 1-go' for characterization. Southern hybridization analysis confirmed that the ANS gene was present in the genome as a two-allele gene with a pair of homologous sequences (ANS-1 and 2); these sequences were used as the target for genome editing. Genome editing was performed by introducing #2_single-guide RNA into the stem tissue using the ribonucleoprotein. This molecule was used because it exhibited the highest efficiency in an analysis of cleavage activity against the target sequence in vitro. Cleaved amplified polymorphic sequence analysis of genomic DNA extracted from 85 regenerated individuals after genome editing was performed. The results indicated that mutations in the ANS gene may have been introduced into two lines. Cloning of the ANS gene in these two lines confirmed the introduction of a single nucleotide substitution mutation for ANS-1 in both lines, and a single amino acid substitution in one line. We discussed the possibility of color change by the amino acid substitution, and also the future applications of this technology.
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Affiliation(s)
- Kenichiro Mori
- Aichi Agricultural Research Center (AARC), 1-1 Sagamine Yazako, Nagakute, Aichi, 480-1193, Japan
| | - Koji Tanase
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki, 305-0852, Japan
| | - Katsutomo Sasaki
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki, 305-0852, Japan.
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Tan Q, Chen W, Liu H, Yan W, Huang X, Li Y. The programmed sequence-based oxygenase screening for polypropylene degradation. J Hazard Mater 2024; 465:133173. [PMID: 38061126 DOI: 10.1016/j.jhazmat.2023.133173] [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: 10/06/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 02/08/2024]
Abstract
Enzymatic degradation of plastic is an effective means of plastic recycling and pollution control. However, the strong chemical inertness of polypropylene plastic (PP) severely impedes its oxidative cleavage, making it resistant to degradation. In this study, based on sequence screening of Hidden Markov Model (HMM), a dioxygenase (HIS1) was identified and characterized to be effective in PP oxidation. Various kinds of PP products, including plastic films, microplastics, and disposable water cups or bags, were HIS1-degraded with cracks and holes on the surface. The hydrophobic binding was the primary force driving oxidative degradation in the specific cavity of HIS1. The discovery of HIS1 achieved a zero breakthrough in PP biodegradation, providing a promising candidate for the selection and evolution of degrading enzymes.
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Affiliation(s)
- Qianlong Tan
- Life and Science Department, Central South University of Forestry and Technology, Changsha, Hunan 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan 410004, China
| | - Wentao Chen
- Life and Science Department, Central South University of Forestry and Technology, Changsha, Hunan 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan 410004, China
| | - Hong Liu
- Life and Science Department, Central South University of Forestry and Technology, Changsha, Hunan 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan 410004, China
| | - Wende Yan
- Life and Science Department, Central South University of Forestry and Technology, Changsha, Hunan 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan 410004, China
| | - Xiu Huang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - Yong Li
- Life and Science Department, Central South University of Forestry and Technology, Changsha, Hunan 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan 410004, China.
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8
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Zhao H, Li D, Liu Y, Zhang T, Zhao X, Su H, Li J. Flavin-containing mono oxygenases FMO GS-OXs integrate flowering transition and salt tolerance in Arabidopsis thaliana. Physiol Plant 2024; 176:e14287. [PMID: 38606719 DOI: 10.1111/ppl.14287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/27/2024] [Indexed: 04/13/2024]
Abstract
Salt stress substantially leads to flowering delay. The regulation of salt-induced late flowering has been studied at the transcriptional and protein levels; however, the involvement of secondary metabolites has rarely been investigated. Here, we report that FMOGS-OXs (EC 1.14.13.237), the enzymes that catalyze the biosynthesis of glucosinolates (GSLs), promote flowering transition in Arabidopsis thaliana. It has been reported that WRKY75 is a positive regulator, and MAF4 is a negative regulator of flowering transition. The products of FMOGS-OXs, methylsulfinylalkyl GSLs (MS GSLs), facilitate flowering by inducing WRKY75 and repressing the MAS-MAF4 module. We further show that the degradation of MS GSLs is involved in salt-induced late flowering and salt tolerance. Salt stress induces the expression of myrosinase genes, resulting in the degradation of MS GSLs, thereby relieving the promotion of WRKY75 and inhibition of MAF4, leading to delayed flowering. In addition, the degradation products derived from MS GSLs enhance salt tolerance. Previous studies have revealed that FMOGS-OXs exhibit alternative catalytic activity to form trimethylamine N-oxide (TMAO) under salt stress, which activates multiple stress-related genes to promote salt tolerance. Therefore, FMOGS-OXs integrate flowering transition and salt tolerance in various ways. Our study shed light on the functional diversity of GSLs and established a connection between flowering transition, salt resistance, and GSL metabolism.
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Affiliation(s)
- Haiyan Zhao
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Dong Li
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Yuqi Liu
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Tianqi Zhang
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Xiaofei Zhao
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Hongzhu Su
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Jing Li
- College of Life Sciences, Northeast Agricultural University, Harbin, China
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Ganouna-Cohen G, Marcouiller F, Blachot-Minassian B, Demarest M, Beauparlant CJ, Droit A, Belaidi E, Bairam A, Joseph V. Loss of testosterone induces postprandial insulin resistance and increases the expression of the hepatic antioxidant flavin-containing mono oxygenases in mice exposed to intermittent hypoxia. Acta Physiol (Oxf) 2024; 240:e14089. [PMID: 38230898 DOI: 10.1111/apha.14089] [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: 06/25/2023] [Revised: 11/29/2023] [Accepted: 01/01/2024] [Indexed: 01/18/2024]
Abstract
AIM We tested the hypothesis that low testosterone alters the effects of intermittent hypoxia (IH) on glucose homeostasis, hepatic oxidative stress, and transcriptomic profile in male mice. METHODS We used sham-operated or orchiectomized (ORX) mice exposed to normoxia (Nx) or IH for 2 weeks. We performed fasting insulin and glucose tolerance tests and assessed fasting and postprandial insulin resistance with the HOMA-IR. The activity of hepatic prooxidant (NADPH oxidase-NOX), antioxidant enzymes (superoxide dismutase, catalase, and glutathione peroxidase-SOD, Cat, GPx), lipid peroxidation (MDA concentration), and the total concentration of glutathione (GSH) were measured under postprandial conditions. mRNA sequencing and pathway enrichment analyses were used to identify hepatic genes underlying the interactions between IH and testosterone. RESULTS In Sham mice, IH improves fasting insulin sensitivity and glucose tolerance, while there are no effects of IH in ORX mice. In ORX mice, IH induces postprandial hyperinsulinemia, insulin resistance, and a prooxidant profile of enzyme activity (low SOD activity) without altering hepatic MDA and GSH content. ORX and IH altered the expression of genes involved in oxidoreductase activities, cytochromes-dependent pathways, and glutathione metabolism. Among the genes upregulated in ORX-IH mice, the flavin-containing monooxygenases (FMO) are particularly relevant since these are potent hepatic antioxidants that could help prevent overt oxidative stress in ORX-IH mice. CONCLUSION Low levels of testosterone in male mice exposed to IH induce post-prandial hyperinsulinemia and insulin resistance and determine the mechanisms by which the liver handles IH-induced oxidative stress.
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Affiliation(s)
- Gauthier Ganouna-Cohen
- Département de Pédiatrie, Faculté de Médecine, Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec, Quebec, Canada
| | - François Marcouiller
- Département de Pédiatrie, Faculté de Médecine, Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec, Quebec, Canada
| | - Britanny Blachot-Minassian
- Département de Pédiatrie, Faculté de Médecine, Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec, Quebec, Canada
- HP2, INSERM, U1300, Université Grenoble Alpes, Grenoble, France
| | - Maud Demarest
- Département de Pédiatrie, Faculté de Médecine, Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec, Quebec, Canada
| | - Charles Joly Beauparlant
- Département de Médecine Moléculaire, Faculté de Médecine, Centre de Recherche du Centre Hospitalo-Universitaire de Québec, Québec, Quebec, Canada
| | - Arnaud Droit
- Département de Médecine Moléculaire, Faculté de Médecine, Centre de Recherche du Centre Hospitalo-Universitaire de Québec, Québec, Quebec, Canada
| | - Elise Belaidi
- HP2, INSERM, U1300, Université Grenoble Alpes, Grenoble, France
- UMR5305-LBTI, CNRS, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Aida Bairam
- Département de Pédiatrie, Faculté de Médecine, Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec, Quebec, Canada
| | - Vincent Joseph
- Département de Pédiatrie, Faculté de Médecine, Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec, Quebec, Canada
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10
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Gui C, Kalkreuter E, Liu YC, Li G, Steele AD, Yang D, Chang C, Shen B. Cofactorless oxygenases guide anthraquinone-fused enediyne biosynthesis. Nat Chem Biol 2024; 20:243-250. [PMID: 37945897 DOI: 10.1038/s41589-023-01476-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/10/2023] [Indexed: 11/12/2023]
Abstract
The anthraquinone-fused enediynes (AFEs) combine an anthraquinone moiety and a ten-membered enediyne core capable of generating a cytotoxic diradical species. AFE cyclization is triggered by opening the F-ring epoxide, which is also the site of the most structural diversity. Previous studies of tiancimycin A, a heavily modified AFE, have revealed a cryptic aldehyde blocking installation of the epoxide, and no unassigned oxidases could be predicted within the tnm biosynthetic gene cluster. Here we identify two consecutively acting cofactorless oxygenases derived from methyltransferase and α/β-hydrolase protein folds, TnmJ and TnmK2, respectively, that are responsible for F-ring tailoring in tiancimycin biosynthesis by comparative genomics. Further biochemical and structural characterizations reveal that the electron-rich AFE anthraquinone moiety assists in catalyzing deformylation, epoxidation and oxidative ring cleavage without exogenous cofactors. These enzymes therefore fill important knowledge gaps for the biosynthesis of this class of molecules and the underappreciated family of cofactorless oxygenases.
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Affiliation(s)
- Chun Gui
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA
| | - Edward Kalkreuter
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA
| | - Yu-Chen Liu
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA
| | - Gengnan Li
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA
| | - Andrew D Steele
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA
| | - Dong Yang
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA
- Natural Products Discovery Center, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA
| | - Changsoo Chang
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Ben Shen
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA.
- Natural Products Discovery Center, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA.
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA.
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11
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Chen H, Liu R, Cai S, Zhang Y, Zhu C, Yu H, Li S. Intermediate product control in cascade reaction for one-pot production of ε-caprolactone by Escherichia coli. Biotechnol J 2024; 19:e2300210. [PMID: 38403458 DOI: 10.1002/biot.202300210] [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: 05/10/2023] [Revised: 12/11/2023] [Accepted: 12/25/2023] [Indexed: 02/27/2024]
Abstract
ε-Caprolactone is an important non-toxic compound for polymer synthesis like polycaprolactone which has been widely used in drug delivery and degradable plastics. To meet the demand for a green economy, a bi-enzymatic cascade, consisting of an alcohol dehydrogenase (ADH) and a cyclohexanone monooxygenase (CHMO), was designed and introduced into Escherichia coli to synthesize ε-caprolactone from cyclohexanol with a self-sufficient NADPH-cofactor regeneration system. To further improve the catalytic efficiency, a carbonyl group-dependent colorimetric method using inexpensive 2,4-dinitrophenylhydrazine (DNPH) was developed for assay of cyclohexanone, an intermediate production of cascade reaction. It can be used to screen mutant strains with high catalytic efficiency from high-throughput library by detecting the absorbance value in microtiter plates (MTP) instead of gas chromatography (GC) analysis. Moreover, an RBS combinatorial library was constructed for balancing the expression of ADH and CHMO from two independent transcriptional units. After the high-throughput screening based on intermediate product control, an optimal variant with higher substrate tolerance and long-term stability was obtained from RBS combinatorial library. Through a fed-batch process, ε-caprolactone production reached 148.2 mM after 70 h of reaction under the optimized conditions, which was the highest yield achieved to date.
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Affiliation(s)
- Hefeng Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ran Liu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Shengliang Cai
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yingjiao Zhang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Chaoyi Zhu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Hao Yu
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, China
| | - Shuang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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12
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Zhou L, Awakawa T, Ushimaru R, Kanaida M, Abe I. Characterization of Aziridine-Forming α-Ketoglutarate-Dependent Oxygenase in l-Isovaline Biosynthesis. Org Lett 2024; 26:724-727. [PMID: 38227980 DOI: 10.1021/acs.orglett.3c04185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
l-Isovaline biosynthesis by TqaLFM-ti from Tolypocladium inflatum was demonstrated in vitro. The biochemical analysis of the α-ketoglutarate-dependent oxygenase TqaL-ti revealed that it produces (2S,3S)-3-ethyl-3-methylaziridine-2-carboxylic acid from l-isoleucine, thus exhibiting a stereoselectivity different from those of the reported homologues. Remarkably, a single mutation on I295 in TqaL-ti completely exchanged its stereoselectivity to produce the C-3 stereoisomer. TqaFM-ti generates d-isovaline from (2S,3R)-aziridine-2-carboxylic acid, suggesting that the stereochemistry of the TqaL product defines that of isovaline.
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Affiliation(s)
- Lu Zhou
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- RIKEN Center for Sustainable Resource Science, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- RIKEN Center for Sustainable Resource Science, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan
| | - Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masahiro Kanaida
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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13
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Zhu W, Wu P, Larson VA, Kumar A, Li XX, Seo MS, Lee YM, Wang B, Lehnert N, Nam W. Electronic Structure and Reactivity of Mononuclear Nonheme Iron-Peroxo Complexes as a Biomimetic Model of Rieske Oxygenases: Ring Size Effects of Macrocyclic Ligands. J Am Chem Soc 2024; 146:250-262. [PMID: 38147793 DOI: 10.1021/jacs.3c08559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
We report the macrocyclic ring size-electronic structure-electrophilic reactivity correlation of mononuclear nonheme iron(III)-peroxo complexes bearing N-tetramethylated cyclam analogues (n-TMC), [FeIII(O2)(12-TMC)]+ (1), [FeIII(O2)(13-TMC)]+ (2), and [FeIII(O2)(14-TMC)]+ (3), as a model study of Rieske oxygenases. The Fe(III)-peroxo complexes show the same δ and pseudo-σ bonds between iron and the peroxo ligand. However, the strength of these interactions varies depending on the ring size of the n-TMC ligands; the overall Fe-O bond strength and the strength of the Fe-O2 δ bond increase gradually as the ring size of the n-TMC ligands becomes smaller, such as from 14-TMC to 13-TMC to 12-TMC. MCD spectroscopy plays a key role in assigning the characteristic low-energy δ → δ* LMCT band, which provides direct insight into the strength of the Fe-O2 δ bond and which, in turn, is correlated with the superoxo character of the iron-peroxo group. In oxidation reactions, reactivities of 1-3 toward hydrocarbon C-H bond activation are compared, revealing the reactivity order of 1 > 2 > 3; the [FeIII(O2)(n-TMC)]+ complex with a smaller n-TMC ring size, 12-TMC, is much more reactive than that with a larger n-TMC ring size, 14-TMC. DFT analysis shows that the Fe(III)-peroxo complex is not reactive toward C-H bonds, but it is the end-on Fe(II)-superoxo valence tautomer that is responsible for the observed reactivity. The hydrogen atom abstraction (HAA) reactivity of these intermediates is correlated with the overall donicity of the n-TMC ligand, which modulates the energy of the singly occupied π* superoxo frontier orbital that serves as the electron acceptor in the HAA reaction. The implications of these results for the mechanism of Rieske oxygenases are further discussed.
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Affiliation(s)
- Wenjuan Zhu
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Peng Wu
- State Key Laboratory of High-Efficiency Utilization of Coal and Green Chemical Engineering, School of Chemistry and Chemical Engineering, Ningxia University, Yinchuan 750021, P. R. China
| | - Virginia A Larson
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Akhilesh Kumar
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Xiao-Xi Li
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, P. R. China
| | - Mi Sook Seo
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Yong-Min Lee
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Binju Wang
- Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
- College of Chemistry and Chemical Engineering, Yan'an University, Yan'an, Shaanxi Province 716000, P. R. China
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14
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Liu M, Yang Y, Huang JW, Dai L, Zheng Y, Cheng S, He H, Chen CC, Guo RT. Structural insights into a novel nonheme iron-dependent oxygenase in selenoneine biosynthesis. Int J Biol Macromol 2024; 256:128428. [PMID: 38013086 DOI: 10.1016/j.ijbiomac.2023.128428] [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: 08/06/2023] [Revised: 11/23/2023] [Accepted: 11/23/2023] [Indexed: 11/29/2023]
Abstract
Selenoneine (SEN) is a natural histidine derivative with radical-scavenging activity and shows higher antioxidant potential than its sulfur-containing isolog ergothioneine (EGT). Recently, the SEN biosynthetic pathway in Variovorax paradoxus was reported. Resembling EGT biosynthesis, the committed step of SEN synthesis is catalyzed by a nonheme Fe-dependent oxygenase termed SenA. This enzyme catalyzes oxidative carbon‑selenium (C-Se) bond formation to conjugate N-α-trimethyl histidine (TMH) and selenosugar to yield selenoxide; the process parallels the EGT biosynthetic route, in which sulfoxide synthases known as EgtB members catalyze the conjugation of TMH and cysteine or γ-glutamylcysteine to afford sulfoxides. Here, we report the crystal structures of SenA and its complex with TMH and thioglucose (SGlc), an analog of selenoglucose (SeGlc) at high resolution. The overall structure of SenA adopts the archetypical fold of EgtB, which comprises a DinB-like domain and an FGE-like domain. While the TMH-binding site is highly conserved to that of EgtB, a various substrate-enzyme interaction network in the selenosugar-binding site of SenA features a number of water-mediated hydrogen bonds. The obtained structural information is beneficial for understanding the mechanism of SenA-mediated C-Se bond formation.
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Affiliation(s)
- Min Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Yu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Jian-Wen Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Longhai Dai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Yingyu Zheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Shujing Cheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Hailin He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China; Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China.
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China; Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China.
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15
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Matienko LI, Mil EM, Albantova AA, Goloshchapov AN. The Role H-Bonding and Supramolecular Structures in Homogeneous and Enzymatic Catalysis. Int J Mol Sci 2023; 24:16874. [PMID: 38069195 PMCID: PMC10707003 DOI: 10.3390/ijms242316874] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
The article analyzes the role of hydrogen bonds and supramolecular structures in enzyme catalysis and model systems. Hydrogen bonds play a crucial role in many enzymatic reactions. However, scientists have only recently attempted to harness the power of hydrogen bonds in homogeneous catalytic systems. One of the newest directions is associated with attempts to control the properties of catalysts by influencing the "second coordination sphere" of metal complexes. The role H-bonding, and the building of stable supramolecular nanostructures due to intermolecular H-bonds, based on catalytic active heteroligand iron (Fe) or nickel (Ni) complexes formed during hydrocarbon oxidations were assessed via the AFM (Atomic-force microscopy) method, which was proposed and applied by authors of this manuscript. Th is article also discusses the roles of hydrogen bonds and supramolecular structures in oxidation reactions catalyzed by heteroligand Ni and Fe complexes, which are not only effective homogeneous catalysts but also structural and functional models of Oxygenases.
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Affiliation(s)
- Ludmila I. Matienko
- N.M. Emanuel Institution of Biochemical Physics Russian Academy of Science, 4 Kosygin Str., 119334 Moscow, Russia; (E.M.M.); (A.A.A.); (A.N.G.)
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16
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Tian J, Liu J, Knapp M, Donnan PH, Boggs DG, Bridwell-Rabb J. Custom tuning of Rieske oxygenase reactivity. Nat Commun 2023; 14:5858. [PMID: 37730711 PMCID: PMC10511449 DOI: 10.1038/s41467-023-41428-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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 08/27/2023] [Indexed: 09/22/2023] Open
Abstract
Rieske oxygenases use a Rieske-type [2Fe-2S] cluster and a mononuclear iron center to initiate a range of chemical transformations. However, few details exist regarding how this catalytic scaffold can be predictively tuned to catalyze divergent reactions. Therefore, in this work, using a combination of structural analyses, as well as substrate and rational protein-based engineering campaigns, we elucidate the architectural trends that govern catalytic outcome in the Rieske monooxygenase TsaM. We identify structural features that permit a substrate to be functionalized by TsaM and pinpoint active-site residues that can be targeted to manipulate reactivity. Exploiting these findings allowed for custom tuning of TsaM reactivity: substrates are identified that support divergent TsaM-catalyzed reactions and variants are created that exclusively catalyze dioxygenation or sequential monooxygenation chemistry. Importantly, we further leverage these trends to tune the reactivity of additional monooxygenase and dioxygenase enzymes, and thereby provide strategies to custom tune Rieske oxygenase reaction outcomes.
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Affiliation(s)
- Jiayi Tian
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jianxin Liu
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Madison Knapp
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Patrick H Donnan
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - David G Boggs
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
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17
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Blagodarov SV, Zheltukhina GA, Nebolsin VE. Iron metabolism in the cell as a target in the development of potential antimicrobial and antiviral agents. Biomed Khim 2023; 69:199-218. [PMID: 37705481 DOI: 10.18097/pbmc20236904199] [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] [Indexed: 09/15/2023]
Abstract
The search and creation of innovative antimicrobial drugs, acting against resistant and multiresistant strains of bacteria and fungi, are one of the most important tasks of modern bioorganic chemistry and pharmaceuticals. Since iron is essential for the vital activity of almost all organisms, including mammals and bacteria, the proteins involved in its metabolism can serve as potential targets in the development of new promising antimicrobial agents. Such targets include endogenous mammalian biomolecules, heme oxygenases, siderophores, protein 24p3, as well as bacterial heme oxygenases and siderophores. Other proteins that are responsible for the delivery of iron to cells and its balance between bacteria and the host organism also attract certain particular interest. The review summarizes data on the development of inhibitors and inducers (activators) of heme oxygenases, selective for mammals and bacteria, and considers the characteristic features of their mechanisms of action and structure. Based on the reviewed literature data, it was concluded that the use of hemin, the most powerful hemooxygenase inducer, and its derivatives as potential antimicrobial and antiviral agents, in particular against COVID-19 and other dangerous infections, would be a promising approach. In this case, an important role is attributed to the products of hemin degradation formed by heme oxygenases in vitro and in vivo. Certain attention has been paid to the data on the antimicrobial action of iron-free protoporphyrinates, namely complexes with Co, Ga, Zn, Mn, their advantages and disadvantages compared to hemin. Modification of the well-known antibiotic ceftazidime with a siderophore molecule increased its effectiveness against resistant bacteria.
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Affiliation(s)
- S V Blagodarov
- MIREA - Russian Technological University (MITHT), Moscow, Russia; LLC "Pharmenterprises", Moscow, Russia
| | - G A Zheltukhina
- MIREA - Russian Technological University (MITHT), Moscow, Russia; LLC "Pharmenterprises", Moscow, Russia
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18
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Gomez CA, Mondal D, Du Q, Chan N, Lewis JC. Directed Evolution of an Iron(II)- and α-Ketoglutarate-Dependent Dioxygenase for Site-Selective Azidation of Unactivated Aliphatic C-H Bonds. Angew Chem Int Ed Engl 2023; 62:e202301370. [PMID: 36757808 PMCID: PMC10050089 DOI: 10.1002/anie.202301370] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 01/27/2023] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/10/2023]
Abstract
FeII - and α-ketoglutarate-dependent halogenases and oxygenases can catalyze site-selective functionalization of C-H bonds via a variety of C-X bond forming reactions, but achieving high chemoselectivity for functionalization using non-native functional groups remains rare. The current study shows that directed evolution can be used to engineer variants of the dioxygenase SadX that address this challenge. Site-selective azidation of succinylated amino acids and a succinylated amine was achieved as a result of mutations throughout the SadX structure. The installed azide group was reduced to a primary amine, and the succinyl group required for azidation was enzymatically cleaved to provide the corresponding amine. These results provide a promising starting point for evolving additional SadX variants with activity on structurally distinct substrates and for enabling enzymatic C-H functionalization with other non-native functional groups.
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Affiliation(s)
- Christian A Gomez
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Dibyendu Mondal
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
- Kalsec Inc., 3713W. Main St., Kalamazoo, MI 49006, USA
| | - Qian Du
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Natalie Chan
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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19
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Abstract
Metalloenzymes have been detailed in The Enzymes since its inception over half a century ago. Here, I review selected metal-containing enzyme highlights from early chapters in this series and I describe advances made since those contributions. Three topics are emphasized: nickel-containing enzymes, Fe(II)/2-oxoglutarate-dependent oxygenases, and enzymes containing non-canonical iron-sulfur clusters.
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Affiliation(s)
- Robert P Hausinger
- Departments of Microbiology & Molecular Genetics and Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States.
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20
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Jang N, Jeong J, Ko M, Song DU, Emelianov G, Kim SK, Rha E, Kwon KK, Kim H, Lee DH, Lee H, Lee SG. High Cell-Density Cultivation of Methylococcus capsulatus Bath for Efficient Methane-Derived Mevalonate Production. J Agric Food Chem 2023; 71:4924-4931. [PMID: 36931885 DOI: 10.1021/acs.jafc.3c00286] [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] [Indexed: 06/18/2023]
Abstract
The engineered Methylococcus capsulatus Bath presents a promising approach for converting methane, a potent greenhouse gas, into valuable chemicals. High cell-density culture (HCDC) is necessary for high-titer growth-associated bioproducts, but it often requires time-consuming and labor-intensive optimization processes. In this study, we aimed to achieve efficient HCDC of M. capsulatus Bath by measuring the residual nutrient levels during bioreactor operations and analyzing the specific uptake of each medium component. By controlling the concentrations of nutrients, particularly calcium and phosphorus via intermittent feeding, we achieved a high cell density of 28.2 g DCW/L and a significantly elevated production of mevalonate at a concentration of 1.8 g/L from methane. Our findings demonstrate that the methanotroph HCDC approach presented herein offers a promising strategy for promoting sustainable development, with an exceptional g-scale production titer for value-added synthetic biochemicals.
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Affiliation(s)
- Nulee Jang
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Jiyeong Jeong
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Minji Ko
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
| | - Dong-Uk Song
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Georgii Emelianov
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
| | - Seong Keun Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Eugene Rha
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Kil Koang Kwon
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Haseong Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
| | - Dae-Hee Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon-si, Gyeonggi-do 16419, Republic of Korea
| | - Hyewon Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
| | - Seung-Goo Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
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21
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Cabello-Yeves PJ, Scanlan DJ, Callieri C, Picazo A, Schallenberg L, Huber P, Roda-Garcia JJ, Bartosiewicz M, Belykh OI, Tikhonova IV, Torcello-Requena A, De Prado PM, Millard AD, Camacho A, Rodriguez-Valera F, Puxty RJ. α-cyanobacteria possessing form IA RuBisCO globally dominate aquatic habitats. ISME J 2022; 16:2421-2432. [PMID: 35851323 PMCID: PMC9477826 DOI: 10.1038/s41396-022-01282-z] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 11/24/2022]
Abstract
RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) is one the most abundant enzymes on Earth. Virtually all food webs depend on its activity to supply fixed carbon. In aerobic environments, RuBisCO struggles to distinguish efficiently between CO2 and O2. To compensate, organisms have evolved convergent solutions to concentrate CO2 around the active site. The genetic engineering of such inorganic carbon concentrating mechanisms (CCMs) into plants could help facilitate future global food security for humankind. In bacteria, the carboxysome represents one such CCM component, of which two independent forms exist: α and β. Cyanobacteria are important players in the planet's carbon cycle and the vast majority of the phylum possess a β-carboxysome, including most cyanobacteria used as laboratory models. The exceptions are the exclusively marine Prochlorococcus and Synechococcus that numerically dominate open ocean systems. However, the reason why marine systems favor an α-form is currently unknown. Here, we report the genomes of 58 cyanobacteria, closely related to marine Synechococcus that were isolated from freshwater lakes across the globe. We find all these isolates possess α-carboxysomes accompanied by a form 1A RuBisCO. Moreover, we demonstrate α-cyanobacteria dominate freshwater lakes worldwide. Hence, the paradigm of a separation in carboxysome type across the salinity divide does not hold true, and instead the α-form dominates all aquatic systems. We thus question the relevance of β-cyanobacteria as models for aquatic systems at large and pose a hypothesis for the reason for the success of the α-form in nature.
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Affiliation(s)
- Pedro J Cabello-Yeves
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain.
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Cristiana Callieri
- National Research Council (CNR), Institute of Water Research (IRSA), Verbania, Italy
| | - Antonio Picazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, E-46980 Paterna, Valencia, Spain
| | | | - Paula Huber
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET., Av. Intendente Marino Km 8,200, 7130, Chascomús, Buenos Aires, Argentina
- Instituto Nacional de Limnología (INALI), CONICET-UNL., Ciudad Universitaria-Paraje el Pozo s/n, 3000, Santa Fé, Argentina
| | - Juan J Roda-Garcia
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Maciej Bartosiewicz
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Olga I Belykh
- Limnological Institute, Russian Academy of Sciences, P.O. Box 278, 664033, Irkutsk, Russia
| | - Irina V Tikhonova
- Limnological Institute, Russian Academy of Sciences, P.O. Box 278, 664033, Irkutsk, Russia
| | | | | | - Andrew D Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Antonio Camacho
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, E-46980 Paterna, Valencia, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Richard J Puxty
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
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22
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Nishiura T, Ohta T, Ogura T, Nakazawa J, Okamura M, Hikichi S. The Conversion of Superoxide to Hydroperoxide on Cobalt(III) Depends on the Structural and Electronic Properties of Azole-Based Chelating Ligands. Molecules 2022; 27:molecules27196416. [PMID: 36234952 PMCID: PMC9571172 DOI: 10.3390/molecules27196416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/24/2022] [Accepted: 09/24/2022] [Indexed: 11/16/2022] Open
Abstract
Conversion from superoxide (O2−) to hydroperoxide (OOH−) on the metal center of oxygenases and oxidases is recognized to be a key step to generating an active species for substrate oxidation. In this study, reactivity of cobalt(III)-superoxido complexes supported by facially-capping tridentate tris(3,5-dimethyl-4-X-pyrazolyl)hydroborate ([HB(pzMe2,X)3]−; TpMe2,X) and bidentate bis(1-methyl-imidazolyl)methylborate ([B(ImN-Me)2Me(Y)]−; LY) ligands toward H-atom donating reagent (2-hydroxy-2-azaadamantane; AZADOL) has been explored. The oxygenation of the cobalt(II) precursors give the corresponding cobalt(III)-superoxido complexes, and the following reaction with AZADOL yield the hydroperoxido species as has been characterized by spectroscopy (UV-vis, resonance Raman, EPR). The reaction of the cobalt(III)-superoxido species and a reducing reagent ([CoII(C5H5)2]; cobaltocene) with proton (trifluoroacetic acid; TFA) also yields the corresponding cobalt(III)-hydroperoxido species. Kinetic analyses of the formation rates of the cobalt(III)-hydroperoxido complexes reveal that second-order rate constants depend on the structural and electronic properties of the cobalt-supporting chelating ligands. An electron-withdrawing ligand opposite to the superoxide accelerates the hydrogen atom transfer (HAT) reaction from AZADOL due to an increase in the electrophilicity of the superoxide ligand. Shielding the cobalt center by the alkyl group on the boron center of bis(imidazolyl)borate ligands hinders the approaching of AZADOL to the superoxide, although the steric effect is insignificant.
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Affiliation(s)
- Toshiki Nishiura
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Takehiro Ohta
- Department of Life Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
| | - Takashi Ogura
- Department of Life Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
| | - Jun Nakazawa
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Masaya Okamura
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Shiro Hikichi
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
- Correspondence: ; Tel.: +81-45-481-5661
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23
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Chen C, Ye G, Tang J, Li J, Liu W, Wu L, Long Y. New Polyketides from Mangrove Endophytic Fungus Penicillium sp. BJR-P2 and Their Anti-Inflammatory Activity. Mar Drugs 2022; 20:md20090583. [PMID: 36135772 PMCID: PMC9502265 DOI: 10.3390/md20090583] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
Four new polyketide compounds, including two new unique isocoumarins penicillol A (1) and penicillol B (2) featuring with spiroketal rings, two new citreoviridin derivatives citreoviridin H (3) and citreoviridin I (4), along with four known analogues were isolated from the mangrove endophytic fungus Penicillium sp. BJR-P2. Their structures were elucidated by extensive spectroscopic methods. The absolute configurations of compounds 1-4 based on electronic circular dichroism (ECD) calculations, DP4+ analysis, and single-crystal X-ray diffraction are presented. All the new compounds were evaluated for anti-inflammatory activity. An anti-inflammatory assay indicated that compound 2 inhibited lipopolysaccharide (LPS)-induced NO production in RAW 264.7 cells, with half-maximal inhibitory concentration (IC50) values of 12 μM, being more potent than the positive control, indomethacin (IC50 = 35.8 ± 5.7 μM). Docking study showed that compound 2 was perfectly docking into the active site of murine inducible nitric oxide oxygenase (iNOS) via forming multiple typical hydrogen bonds.
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24
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Hassan HA, D Enza M, Armengaud J, Pieper DH. Biochemical and genetic characterization comparison of four extradiol di oxygenases in Rhizorhabdus wittichii RW1. Appl Microbiol Biotechnol 2022; 106:5539-5550. [PMID: 35906995 DOI: 10.1007/s00253-022-12099-3] [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: 04/18/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 11/26/2022]
Abstract
Rhizorhabdus (previously Sphingomonas) wittichii RW1 uses a diverse array of aromatic organic compounds as energy and carbon sources, including some extremely recalcitrant compounds such as dibenzo-p-dioxin and dibenzofuran. Extradiol dioxygenases play a key role in the metabolism of dibenzofuran (DBF), dibenzo-p-dioxin (DBD), PCBs, and various other aromatic compounds. In this study, a detailed kinetic analysis of four extradiol dioxygenases identified in R. wittichii RW1 (DbfB, Edo2, Edo3, and Edo4) showed all of them to be typical 2,3dihydroxybiphenyl (DHB) dioxygenases with DHB as preferred substrate (kcat/Km values of 0.13-188 (µM -1 s-1)) and only slightly lower activity against trihydroxybiphenyl (THB) whereas monocyclic substrates were, to different extents, poor substrates due to high km values. All extradiol dioxygenases analyzed were subject to mechanism-based inactivation by 2,2`,3-trihydroxybiphenylether (THBE) the intermediate of DBD degradation. However, Edo4 was superior as reflected by the relatively high partition ratio and the comparably low efficiency of inactivation. Significant differences were observed with respect to their inactivation by 3-chlorocatechol. The absence of any significant mechanism-based inactivation makes Edo3 a perfect candidate for being recruited for chlorobiphenyl degradation where inactivation of extradiol dioxygenases by this intermediate creates significant metabolic problems. KEY POINTS: • Characterization of additional extradiol dioxygenases encoded by RW1 • Identification of differences in 2,2`,3-trihydroxybiphenylether transformation • Identification of differences in inhibition by 3-chlorocatechol.
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Affiliation(s)
- Hamdy A Hassan
- Department of Environmental Biotechnology, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City 32897, Egypt.
- Biology Department, Science and Humanities College, Shaqra University, Al-Quwayiyah, 11726, Riyadh, Saudi Arabia.
| | - Marina D Enza
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Jean Armengaud
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Université Paris-Saclay, CEA, INRAE, Département Médicaments Et Technologies Pour La Santé, Bagnols-sur-Cèze, France
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
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25
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Liu Z, Wu X, Wang E, Liu Y, Wang Y, Zheng Q, Han Y, Chen Z, Zhang Y. PHR1 positively regulates phosphate starvation-induced anthocyanin accumulation through direct upregulation of genes F3'H and LDOX in Arabidopsis. Planta 2022; 256:42. [PMID: 35842503 DOI: 10.1007/s00425-022-03952-w] [Citation(s) in RCA: 2] [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] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Phosphate deficiency promotes anthocyanin accumulation in Arabidopsis through direct binding of PHR1 to the P1BS motifs on the promoters of F3'H and LDOX and thereby upregulating their expression. Phosphorus is one of the essential elements for plants, and plants mainly absorb inorganic phosphate (Pi) from soil. But Pi deficiency is a common factor limiting plant growth and development. Anthocyanin accumulation in green tissues (such as leaves) is one of the characteristics of many plants in response to Pi starvation. However, little is known about the mechanism by which Pi starvation induces anthocyanin accumulation. Here, we found that the mutation of the gene PHOSPHATE STARVATION RESPONSE1 (PHR1), which encodes a key factor involved in Pi starvation signaling in Arabidopsis, significantly attenuates anthocyanin accumulation under Pi-limiting conditions. Moreover, the expression of several Pi deficiency-upregulated genes that are involved in anthocyanin biosyntheses, such as flavanone 3'-hydroxylase (F3'H), dihydroflavonol 4-reductase (DFR), leucoanthocyanidin dioxygenase (LDOX), and production of anthocyanin pigment 1 (PAP1), was significantly lower in the phr1-1 mutant than in the wild type (WT). Both yeast one-hybrid (Y1H) analysis and chromatin immunoprecipitation quantitative PCR (ChIP-qPCR) showed that PHR1 can interact with the promoters of F3'H and LDOX, but not DFR and PAP1. By electrophoretic mobility shift assay (EMSA), it was further confirmed that the PHR1-binding sequence (P1BS) motifs located on the F3'H and LDOX promoters are required for the PHR1 bindings. Also, in Arabidopsis protoplasts, PHR1 enhanced the transcriptional activity of the F3'H and LDOX promoters, but these effects were markedly impaired when the P1BS motifs were mutated. Taken together, these results indicate that PHR1 positively regulates Pi starvation-induced anthocyanin accumulation in Arabidopsis, at least in part, by directly binding the P1BS motifs located on the promoters to upregulate the transcription of anthocyanin biosynthetic genes F3'H and LDOX.
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Affiliation(s)
- Zhongjuan Liu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province Universities, Fuzhou, 350002, People's Republic of China
| | - Xueqian Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Enhui Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Yanan Liu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Yi Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Qinghua Zheng
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Yizhen Han
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Zhongze Chen
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Yongqiang Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province Universities, Fuzhou, 350002, People's Republic of China.
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26
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Moradzad M, Abdi M, Sheikh Esmaeili F, Ghaderi D, Rahmani K, Moloudi MR, Vahabzadeh Z. Possible correlation between high circulatory levels of trimethylamine-N-oxide and 2177G>C polymorphisms of hepatic flavin containing monooxygenase 3 in Kurdish Population with non-alcoholic fatty liver disease. Mol Biol Rep 2022; 49:5927-5937. [PMID: 35348964 DOI: 10.1007/s11033-022-07375-4] [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: 01/06/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Non-alcoholic fatty liver disease (NAFLD) is a multifactorial disorder with complicated pathophysiology. Trimethylamine-N-oxide (TMAO) has been thought to be correlated with the pathogenesis of NAFLD. The single nucleotide polymorphisms (SNPs) of hepatic flavin-containing monooxygenase 3 (FMO3) regulate the concentration of TMAO. This case-control study investigated the plasma levels of TMAO as well as its possible correlation with the frequency of specific genotype of FMO3 (-2650C>G, -2543T>A, -2177G>C, -2589C>T, -2106G>A polymorphisms) in Kurdish patients with NAFLD. METHODS AND RESULTS: In 85 confirmed NAFLD patients and 30 healthy individuals, triglycerides (TG), total cholesterol (Chol), low-density lipoprotein (LDL), high-density lipoprotein (HDL), alanine aminotransferase (ALT), and aspartate aminotransferase (AST) activities were measured. TMAO was also measured using the LC-MS/MS method. High-resolution melting analysis was applied to determine FMO3 genotypes. Plasma TMAO levels were significantly higher in patients (p = 0.030). A CC genotype with a frequency of 12.9% for SNP -2177G>C was found in Kurdish NAFLD patients. The distribution of the GC genotype was also significantly different (p = 0.017). CONCLUSIONS The current results provide documentation for high circulatory levels of TMAO and its possible correlation with the presence of the specific genotype -2177G>C FMO3 in Kurdish NAFLD patients.
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Affiliation(s)
- Mohammad Moradzad
- Student Research Committee, Kurdistan University of Medical Sciences, Sanandaj, Iran
- Department of Clinical Biochemistry, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Mohammad Abdi
- Department of Clinical Biochemistry, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Farshad Sheikh Esmaeili
- Liver & Digestive Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Dana Ghaderi
- Student Research Committee, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Khaled Rahmani
- Liver & Digestive Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Mohammad Raman Moloudi
- Liver & Digestive Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Zakaria Vahabzadeh
- Department of Clinical Biochemistry, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran.
- Cellular and Molecular Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran.
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27
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Yu Y, Zhang Q, Sun S, Yang J. Upregulated expression of RESPIRATORY BURST OXIDASE HOMOLOG D underlies lesion-mimic phenotype in dark-treated Arabidopsis pheide a oxygenase mutant leaves. Planta 2022; 255:110. [PMID: 35471712 DOI: 10.1007/s00425-022-03895-2] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
Upregulated expression of RESPIRATORY BURST OXIDASE HOMOLOG D (RBOHD) encoding a plasma membrane NADPH oxidase is responsible for the lesion-mimic phenotype in detached Arabidopsis leaves with mutation of PHEIDE a OXYGENASE during extended darkness. Chlorophyll degradation is an indispensable process in leaf senescence, either age-dependent or dark-induced. Besides higher chlorophyll retention, a lesion-mimic phenotype (abbreviated as LMP afterwards) was exhibited in Arabidopsis leaves with mutation of PHEIDE a OXYGENASE (PaO) involved in chlorophyll degradation during dark incubation, but the associated mechanism remains elusive. We found that dark-treated pao leaves showed higher membrane damage and H2O2 accumulation, while scavenging H2O2 by its chemical scavenger diminished LMP. RBOHD which encodes NADPH oxidase was strikingly up-regulated in pao leaves during dark treatment. Chemical inhibition of NADPH oxidase or mutation of RBOHD in pao leaves suppressed LMP. Thus, our study suggests that up-regulated RBOHD transcription is responsible for the formation of LMP in dark-treated pao leaves and there may be a retrograde signaling pathway mediating upregulation of RBOHD which remains to be elucidated.
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Affiliation(s)
- Yongfan Yu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Qiang Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Sujing Sun
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Jiading Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.
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Wang Y, Lai CY, Wu M, Lu X, Hu S, Yuan Z, Guo J. Copper stimulation on methane-supported perchlorate reduction in a membrane biofilm reactor. J Hazard Mater 2022; 425:127917. [PMID: 34915291 DOI: 10.1016/j.jhazmat.2021.127917] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/05/2021] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
The present study demonstrated that the perchlorate reduction rate in a methane-based membrane biofilm reactor was significantly enhanced from 14.4 to 25.6 mg-Cl/L/d by increasing copper concentration in the feeding medium from 1 to 10 μM, indicating a stimulatory effect of copper on the methane-supported perchlorate reduction process. Batch tests further confirmed that the increased copper concentration enhanced both methane oxidation and perchlorate reduction rates, which was supported by an increasing trend of functional genes (pmoA for methanotrophs and pcrA for specific perchlorate reducers) abundances through quantitative polymerase chain reaction (qPCR). Both 16S rRNA gene sequencing and functional genes (pmoA and pcrA) sequencing jointly revealed that the biofilm supplied with a higher copper concentration exhibited a more diverse microbial community. The methane-supported perchlorate reduction was accomplished through a synergistic association of methanotrophs (Methylocystis, Methylomonas, and Methylocystaceae) and perchlorate reducers (Dechloromonas, Azospira, Magnetospirillum, and Denitratisoma). Acetate may function as the key syntrophic linkage between methanotrophs and perchlorate reducers. It was proposed that the increased copper concentration improved the activity of particulate methane monooxygenase (pMMO) for methane oxidation or promoted the biosynthesis of intracellular carbon storage compounds polyhydroxybutyrate (PHB) in methanotrophs for generating more acetate available for perchlorate reduction.
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Affiliation(s)
- Yulu Wang
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Chun-Yu Lai
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Mengxiong Wu
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Xuanyu Lu
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Shihu Hu
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Zhiguo Yuan
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St Lucia, Queensland 4072, Australia.
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29
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Pokhrel S, Ponniah SK, Jia Y, Yu O, Manoharan M. Transgenic Rice Expressing Isoflavone Synthase Gene from Soybean Shows Resistance Against Blast Fungus ( Magnaporthe oryzae). Plant Dis 2021; 105:3141-3146. [PMID: 33616428 DOI: 10.1094/pdis-08-20-1777-re] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The isoflavones are a group of plant secondary metabolites primarily synthesized in legumes and are known for their role in improving human health and plant disease resistance. The isoflavones, especially genistein, act as precursors for the production of phytoalexins, which may induce broad-spectrum disease resistance in plants. In this study, we screened transgenic rice lines expressing the isoflavone synthase (GmIFS1) gene from soybean for rice blast (Magnaporthe oryzae) resistance. Two homozygous transgenic lines (I2 and I10), based on single copy gene integration, were identified. The expression of GmIFS1 in transgenic lines was confirmed by quantitative real-time PCR. Genistein was detected in the transgenic lines using liquid chromatography with tandem mass spectrometry. Subsequently, the transgenic lines were evaluated against the rice blast pathogen, isolate YJ54 (race IB-54). The results indicated that >60% of the plants in both the lines (I2 and I10) showed resistance against the blast pathogen. The progenies of one of the resistant transgenic lines (I10) also showed >65% resistance against rice blast. The resistance of these transgenic lines against rice blast may be attributed to the synthesis of isoflavone (genistein) in rice.
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Affiliation(s)
- Suresh Pokhrel
- Department of Agriculture, University of Arkansas at Pine Bluff, Pine Bluff, AR 71601
| | - Sathish K Ponniah
- Department of Agriculture, University of Arkansas at Pine Bluff, Pine Bluff, AR 71601
| | - Yulin Jia
- Dale Bumpers National Rice Research Center, U.S. Department of Agriculture-Agricultural Research Service, Stuttgart, AR 72160
| | | | - Muthusamy Manoharan
- Department of Agriculture, University of Arkansas at Pine Bluff, Pine Bluff, AR 71601
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Li N, Wang X, Ma B, Wu Z, Zheng L, Qi Z, Wang Y. A leucoanthocyanidin dioxygenase gene (RtLDOX2) from the feral forage plant Reaumuria trigyna promotes the accumulation of flavonoids and improves tolerance to abiotic stresses. J Plant Res 2021; 134:1121-1138. [PMID: 34037878 DOI: 10.1007/s10265-021-01315-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 03/05/2021] [Accepted: 05/19/2021] [Indexed: 05/27/2023]
Abstract
Reaumuria trigyna, a Tamaricaceae archaic recretohalophyte, is an important feral forage plant in the desert steppe of northwestern China. We identified two significantly differentially expressed leucoanthocyanidin dioxygenase genes (RtLDOX/RtLDOX2) and investigated the function and characteristics of RtLDOX2. RtLDOX2 from R. trigyna was rapidly upregulated by salt, drought, and abscisic acid, consistent with the stress-related cis-regulatory elements in the promoter region. Recombinant RtLDOX2 converted dihydrokaempferol to kaempferol in vitro, and was thus interchangeable with flavonol synthase, a dioxygenase in the flavonoid pathway. Transgenic plants overexpressing RtLDOX2 accumulated more anthocyanin and flavonols under abiotic stresses, speculating that RtLDOX2 may act as a multifunctional dioxygenase in the synthesis of anthocyanins and flavonols. Overexpression of RtLDOX2 enhanced the primary root length, biomass accumulation, and chlorophyll content of salt-, drought-, and ultraviolet-B-stressed transgenic Arabidopsis. Antioxidant enzyme activity; proline content; and expression of antioxidant enzyme, proline biosynthesis, and ion-transporter genes were increased in transgenic plants. Therefore, RtLDOX2 confers tolerance to abiotic stress on transgenic Arabidopsis by promoting the accumulation of anthocyanins and flavonols. This in turn increases reactive oxygen species scavenging and activates other stress responses, such as osmotic adjustment and ion transport, and so improves tolerance to abiotic stresses.
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Affiliation(s)
- Ningning Li
- College of Agricultural, Inner Mongolia Agricultural University, Hohhot, 010019, China
- The Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, the State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, and College of Life Sciences, Inner Mongolia University, 24 Zhaojun Road, Hohhot, 010070, China
| | - Xue Wang
- The Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, the State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, and College of Life Sciences, Inner Mongolia University, 24 Zhaojun Road, Hohhot, 010070, China
| | - Binjie Ma
- The Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, the State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, and College of Life Sciences, Inner Mongolia University, 24 Zhaojun Road, Hohhot, 010070, China
| | - Zhigang Wu
- The Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, the State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, and College of Life Sciences, Inner Mongolia University, 24 Zhaojun Road, Hohhot, 010070, China
| | - Linlin Zheng
- The Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, the State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, and College of Life Sciences, Inner Mongolia University, 24 Zhaojun Road, Hohhot, 010070, China
| | - Zhi Qi
- The Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, the State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, and College of Life Sciences, Inner Mongolia University, 24 Zhaojun Road, Hohhot, 010070, China
| | - Yingchun Wang
- The Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, the State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, and College of Life Sciences, Inner Mongolia University, 24 Zhaojun Road, Hohhot, 010070, China.
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Liu Z, Zhao F, Zhao B, Yang J, Ferrara J, Sankaran B, Venkataram Prasad BV, Kundu BB, Phillips GN, Gao Y, Hu L, Zhu T, Gao X. Structural basis of the stereoselective formation of the spirooxindole ring in the biosynthesis of citrinadins. Nat Commun 2021; 12:4158. [PMID: 34230497 PMCID: PMC8260726 DOI: 10.1038/s41467-021-24421-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/17/2021] [Indexed: 11/09/2022] Open
Abstract
Prenylated indole alkaloids featuring spirooxindole rings possess a 3R or 3S carbon stereocenter, which determines the bioactivities of these compounds. Despite the stereoselective advantages of spirooxindole biosynthesis compared with those of organic synthesis, the biocatalytic mechanism for controlling the 3R or 3S-spirooxindole formation has been elusive. Here, we report an oxygenase/semipinacolase CtdE that specifies the 3S-spirooxindole construction in the biosynthesis of 21R-citrinadin A. High-resolution X-ray crystal structures of CtdE with the substrate and cofactor, together with site-directed mutagenesis and computational studies, illustrate the catalytic mechanisms for the possible β-face epoxidation followed by a regioselective collapse of the epoxide intermediate, which triggers semipinacol rearrangement to form the 3S-spirooxindole. Comparing CtdE with PhqK, which catalyzes the formation of the 3R-spirooxindole, we reveal an evolutionary branch of CtdE in specific 3S spirocyclization. Our study provides deeper insights into the stereoselective catalytic machinery, which is important for the biocatalysis design to synthesize spirooxindole pharmaceuticals.
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Affiliation(s)
- Zhiwen Liu
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Fanglong Zhao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Boyang Zhao
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Jie Yang
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | | | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - B V Venkataram Prasad
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Biki Bapi Kundu
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
| | - Yang Gao
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Tong Zhu
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.
- Department of Chemistry, Rice University, Houston, TX, USA.
- Department of Bioengineering, Rice University, Houston, TX, USA.
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Jawaharraj K, Sudha Dhiman S, Bedwell S, Vemuri B, Islam J, Sani RK, Gadhamshetty V. Electricity from methane by Methylococcus capsulatus (Bath) and Methylosinus trichosporium OB3b. Bioresour Technol 2021; 321:124398. [PMID: 33257167 DOI: 10.1016/j.biortech.2020.124398] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 08/30/2020] [Revised: 10/31/2020] [Accepted: 11/06/2020] [Indexed: 06/12/2023]
Abstract
Given the difficulties valorizing methane (CH4) via catalytic routes, this study explores use of CH4-oxidizing bacteria ("methanotrophs") for generating electricity directly from CH4. A preconditioned methanotrophic biofilm on 3D nickel foam with reduced graphene oxide (rGO/Ni) was used as the anode in two-compartment microbial fuel cells (MFCs). This study demonstrates a proof of concept for turning CH4 into electricity by two model methanotrophs including Methylosinus trichosposium OB3b and Methylococcus capsulatus (Bath). Both OB3b (205 mW.m-2) and Bath (110 mW.m-2) strains yielded a higher electricity from CH4 when grown on rGO/Ni compared to graphite felt electrodes. Based on electrochemistry tests, molecular dynamics simulations, genome annotations and interaction analysis, a mechanistic understanding of reasons behind enhanced performance of methanotrophs grown on rGO/Ni are presented.
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Affiliation(s)
- Kalimuthu Jawaharraj
- Department of Civil and Environmental Engineering, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, USA; BuG ReMeDEE Consortia, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, USA; 2D-materials for Biofilm Engineering, Science and Technology (2DBEST) Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD 57701, USA
| | - Saurabh Sudha Dhiman
- BuG ReMeDEE Consortia, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, USA; Chemical and Biological Engineering, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD 57701, USA; 2D-materials for Biofilm Engineering, Science and Technology (2DBEST) Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD 57701, USA
| | - Sierra Bedwell
- Department of Microbiology and Immunology, Montana State University, Culbertson Hall, 100, Bozeman, MT 59717, USA
| | - Bhuvan Vemuri
- Department of Civil and Environmental Engineering, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, USA; BuG ReMeDEE Consortia, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, USA
| | - Jamil Islam
- Department of Civil and Environmental Engineering, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, USA; BuG ReMeDEE Consortia, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, USA
| | - Rajesh Kumar Sani
- BuG ReMeDEE Consortia, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, USA; Chemical and Biological Engineering, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD 57701, USA; 2D-materials for Biofilm Engineering, Science and Technology (2DBEST) Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD 57701, USA
| | - Venkataramana Gadhamshetty
- Department of Civil and Environmental Engineering, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, USA; BuG ReMeDEE Consortia, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, USA; 2D-materials for Biofilm Engineering, Science and Technology (2DBEST) Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD 57701, USA.
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Maxwell O, Adewoyin Olusegun O, Joel ES, Ikechukwu B I, Timothy-Terhile Mary A, Okoro Emeka E, Uchechukwu OA, Adeleye BN, Michael OM, Ifeanyi OA, Ogunrinola IE, Ahuekwe Eze F, Saeed MA. MEASUREMENTS OF SEASONAL VARIATIONS OF RADIOACTIVITY DISTRIBUTIONS IN RIVERINE SOIL SEDIMENT OF ADO-ODO OTA, SOUTH-WEST NIGERIA: PROBABILISTIC APPROACH USING MONTE CARLO. Radiat Prot Dosimetry 2021; 193:76-89. [PMID: 33779760 DOI: 10.1093/rpd/ncab027] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/14/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
The radioactivity levels were measured using a hand-held gamma-ray survey meter and NaI (Tl) based gamma spectroscopy to evaluate the seasonal variation of radioactivity levels in the riverine area of Ado-Odo Ota. The measured iso-dose map reported higher gamma dose rate of 79 nGy/h, approximately 34% higher than the world average of 59 nGy/h. The values for U-238, Th-232 and K-40 activity levels ranged between 29.9 and 21.6; 103.2 and 31.2; 802.2 and 233.5 with mean values of 26.1, 55.6 and 499.3 Bq/kg, respectively. According to the mean, 5th and 95th percentiles of the probabilities using the Monte Carlo simulation, the Radium equivalent activities and the absorbed dose rates are within their respective recommended limits of 370 Bq/kg and 84 nGy/h. This study could be used to monitor dose rates and radiological risks for the areas covering the small area (Ado-Odo Ota) to the larger area (West African Region) as baseline data.
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Affiliation(s)
- Omeje Maxwell
- Department of Physics, College of Science and Technology, Covenant University, P.M.B 1023, Ota, Ogun State, Nigeria
| | - O Adewoyin Olusegun
- Department of Physics, College of Science and Technology, Covenant University, P.M.B 1023, Ota, Ogun State, Nigeria
| | - Emmanuel S Joel
- Department of Physics, College of Science and Technology, Covenant University, P.M.B 1023, Ota, Ogun State, Nigeria
| | - Ijeh Ikechukwu B
- Department of Physics, Michael Okpara University of Agriculture, Umudike, Umuahia, Abia State, Nigeria
| | - A Timothy-Terhile Mary
- Department of Physics, Michael Okpara University of Agriculture, Umudike, Umuahia, Abia State, Nigeria
| | - E Okoro Emeka
- Department of Petroleum Engineering, College of Engineering, Covenant University, P.M.B 1023, Ota, Ogun State, Nigeria
| | - Omeje Anne Uchechukwu
- Department of Public and Community Health Care, College of Medicine, Idiaraba, University of Lagos, Nigeria
| | - Bosede Ngozi Adeleye
- Department of Economics and Development Studies, Covenant University, P.M.B. 1023, Ota, Ogun State, Nigeria
| | | | - Oha A Ifeanyi
- Department of Geology, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Iyanuoluwa E Ogunrinola
- Department of Physics, College of Science and Technology, Covenant University, P.M.B 1023, Ota, Ogun State, Nigeria
| | - F Ahuekwe Eze
- Department of Biological Sciences, College of Science and Technology, Covenant University, P.M.B 1023, Ota, Ogun State, Nigeria
| | - M A Saeed
- Department of Physics, Division of Science and Technology, University of Education, Lahore-Pakistan
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Chiang Y, Wei ST, Wang P, Wu P, Yu C. Microbial degradation of steroid sex hormones: implications for environmental and ecological studies. Microb Biotechnol 2020; 13:926-949. [PMID: 31668018 PMCID: PMC7264893 DOI: 10.1111/1751-7915.13504] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/09/2019] [Accepted: 10/09/2019] [Indexed: 12/13/2022] Open
Abstract
Steroid hormones modulate development, reproduction and communication in eukaryotes. The widespread occurrence and persistence of steroid hormones have attracted public attention due to their endocrine-disrupting effects on both wildlife and human beings. Bacteria are responsible for mineralizing steroids from the biosphere. Aerobic degradation of steroid hormones relies on O2 as a co-substrate of oxygenases to activate and to cleave the recalcitrant steroidal core ring. To date, two oxygen-dependent degradation pathways - the 9,10-seco pathway for androgens and the 4,5-seco pathways for oestrogens - have been characterized. Under anaerobic conditions, denitrifying bacteria adopt the 2,3-seco pathway to degrade different steroid structures. Recent meta-omics revealed that microorganisms able to degrade steroids are highly diverse and ubiquitous in different ecosystems. This review also summarizes culture-independent approaches using the characteristic metabolites and catabolic genes to monitor steroid biodegradation in various ecosystems.
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Affiliation(s)
- Yin‐Ru Chiang
- Biodiversity Research CenterAcademia SinicaTaipei115Taiwan
| | | | - Po‐Hsiang Wang
- Biodiversity Research CenterAcademia SinicaTaipei115Taiwan
- Present address:
Earth‐Life Science InstituteTokyo Institute of TechnologyTokyoJapan
| | - Pei‐Hsun Wu
- Graduate Institute of Environmental EngineeringNational Taiwan UniversityTaipei106Taiwan
| | - Chang‐Ping Yu
- Graduate Institute of Environmental EngineeringNational Taiwan UniversityTaipei106Taiwan
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Agrawal D, Kaur B, Kaur Brar K, Chadha BS. An innovative approach of priming lignocellulosics with lytic polysaccharide mono- oxygenases prior to saccharification with glycosyl hydrolases can economize second generation ethanol process. Bioresour Technol 2020; 308:123257. [PMID: 32244131 DOI: 10.1016/j.biortech.2020.123257] [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] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 06/11/2023]
Abstract
Two Lytic polysaccharide Mono-Oxygenases (LPMOs), non-modular (PMO_08942) and modular (PMO_07920), from thermotolerant fungus Aspergillus terreus 9DR cloned and expressed in Pichia pastoris X33 and purified to homogeneity using ion-exchange chromatography were found to be of ~29 and ~40 kDa, respectively. Both LPMOs were optimally active at 50 °C; PMO_08942 was active under acidic condition (pH 5.0) and PMO_07920 at pH 7.0. Modular LPMO (PMO_07920) tethered to CBM-1 was found to be versatile as it showed appreciable activity on complex polysaccharide (both cellulose and xylans) as compared to non-modular (PMO_08942). The t1/2 of PMO_08942 (~192 h, pH 5.0) and PMO_0792 (~192 h, pH 7.0) at 50 °C, suggests highly stable nature of these LPMOs. Fluorescently tagged modular AA9 was studied microscopically to understand interaction with pretreated biomass. Priming of biomass for up to 6 h with LPMOs prior to initiating hydrolysis with core cellulase enzyme resulted in significantly higher saccharification.
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Affiliation(s)
- Dhruv Agrawal
- Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Baljit Kaur
- Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Kamalpreet Kaur Brar
- Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005, India
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Mathai C, Jourd'heuil FL, Lopez-Soler RI, Jourd'heuil D. Emerging perspectives on cytoglobin, beyond NO dioxygenase and peroxidase. Redox Biol 2020; 32:101468. [PMID: 32087552 PMCID: PMC7033357 DOI: 10.1016/j.redox.2020.101468] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/05/2020] [Accepted: 02/13/2020] [Indexed: 12/18/2022] Open
Abstract
Cytoglobin is an evolutionary ancient hemoglobin with poor functional annotation. Rather than constrained to penta coordination, cytoglobin's heme iron may exist either as a penta or hexacoordinated arrangement when exposed to different intracellular environments. Two cysteine residues at the surface of the protein form an intramolecular disulfide bond that regulates iron coordination, ligand binding, and peroxidase activity. Overall, biochemical results do not support a role for cytoglobin as a direct antioxidant enzyme that scavenges hydrogen peroxide because the rate of the reaction of cytoglobin with hydrogen peroxide is several orders of magnitude slower than metal and thiol-based peroxidases. Thus, alternative substrates such as fatty acids have been suggested and regulation of nitric oxide bioavailability through nitric oxide dioxygenase and nitrite reductase activities has received experimental support. Cytoglobin is broadly expressed in connective, muscle, and nervous tissues. Rational for differential cellular distribution is poorly understood but inducibility in response to hypoxia is one of the most established features of cytoglobin expression with regulation through the transcription factor hypoxia-inducible factor (HIF). Phenotypic characterization of cytoglobin deletion in the mouse have indicated broad changes that include a heightened inflammatory response and fibrosis, increase tumor burden, cardiovascular dysfunction, and hallmarks of senescence. Some of these changes might be reversed upon inhibition of nitric oxide synthase. However, subcellular and molecular interactions have been seldom characterized. In addition, specific molecular mechanisms of action are still lacking. We speculate that cytoglobin functionality will extend beyond nitric oxide handling and will have to encompass indirect regulatory antioxidant and redox sensing functions.
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Affiliation(s)
- Clinton Mathai
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Frances L Jourd'heuil
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | | | - David Jourd'heuil
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA.
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Todorova Y, Yotinov I, Topalova Y, Benova E, Marinova P, Tsonev I, Bogdanov T. Evaluation of the effect of cold atmospheric plasma on oxygenases' activities for application in water treatment technologies. Environ Technol 2019; 40:3783-3792. [PMID: 29923777 DOI: 10.1080/09593330.2018.1491631] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 12/22/2017] [Accepted: 06/06/2018] [Indexed: 06/08/2023]
Abstract
Plasma-based technologies take an increasing place in the new conceptions of wastewater management as a promising tool for the treatment of persistent organic pollutants with low biodegradability. Plasma major advantage is the synergy of diverse active components with high oxidative action and additional benefits as disinfection of treated water. But the bactericidal effect of plasma can influence the treatment effectiveness when this technology is used in combination with biological methods for the removal of pollutants. The aim of this paper is to study the effect of non-thermal atmospheric plasma torch on key enzymes from phenol biodegradation pathways in Pseudomonas aureofaciens (chlororaphis) AP-9. The strain was isolated from contaminated soils and had a high potential for biodegradation of aromatic compounds. The used plasma source is surface-wave-sustained discharge operating at 2.45 GHz in argon produced by an electromagnetic wave launcher surfatron type. The enzyme activities of phenol 2-monooxygenase (P2MO), catechol 1,2-dioxygenase (C12DO), catechol 2,3-dioxygenase (C23DO), protocatechuate 3,4-dioxygenase (P34DO) and succinate dehydrogenase (SDH) were measured in control and after plasma treatment of 10, 30 and 60 s. At short-time treatment, the activities of intradiol dioxygenases increased with 26% and 59% for C12DO and P34DO, respectively. Other oxygenases and SDH were inhibited with 35% even at 10 s treatment. Longer treatment times had a clear negative effect but SDH kept the higher activity at 60 s treatment compared to the oxygenases. Our data suggest that plasma-based technologies are a useful approach for post-treatment of aryl-containing wastewater in order to increase the effectiveness of biological removal.
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Affiliation(s)
- Yovana Todorova
- Department of General and Applied Hydrobiology, Faculty of Biology, Sofia University St. Kliment Ohridski, Sofia, Bulgaria
| | - Ivaylo Yotinov
- Department of General and Applied Hydrobiology, Faculty of Biology, Sofia University St. Kliment Ohridski, Sofia, Bulgaria
| | - Yana Topalova
- Department of General and Applied Hydrobiology, Faculty of Biology, Sofia University St. Kliment Ohridski, Sofia, Bulgaria
| | - Evgenia Benova
- DLTIS, Sofia University St. Kliment Ohridski, Sofia, Bulgaria
| | - Plamena Marinova
- Faculty of Physics, Sofia University St. Kliment Ohridski, Sofia, Bulgaria
| | - Ivan Tsonev
- Faculty of Physics, Sofia University St. Kliment Ohridski, Sofia, Bulgaria
| | - Todor Bogdanov
- Faculty of Medicine, Medical University Sofia, Sofia, Bulgaria
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Guerrero-Cruz S, Stultiens K, van Kessel MAHJ, Versantvoort W, Jetten MSM, Op den Camp HJM, Kartal B. Key Physiology of a Nitrite-Dependent Methane-Oxidizing Enrichment Culture. Appl Environ Microbiol 2019; 85:e00124-19. [PMID: 30770408 PMCID: PMC6450021 DOI: 10.1128/aem.00124-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 01/15/2019] [Accepted: 02/11/2019] [Indexed: 11/20/2022] Open
Abstract
Nitrite-dependent methane-oxidizing bacteria couple the reduction of nitrite to the oxidation of methane via a unique oxygen-producing pathway. This process is carried out by members of the genus Methylomirabilis that belong to the NC10 phylum. Contrary to other known anaerobic methane oxidizers, they do not employ the reverse methanogenesis pathway for methane activation but instead a canonical particulate methane monooxygenase similar to those used by aerobic methanotrophs. Methylomirabilis-like bacteria are detected in many natural and manmade ecosystems, but their physiology is not well understood. Here, using continuous cultivation techniques, batch activity assays, and state-of-the-art membrane-inlet mass spectrometry, we determined growth rate, doubling time, and methane and nitrite affinities of the nitrite-dependent methane-oxidizing bacterium "Candidatus Methylomirabilis lanthanidiphila." Our results provide insight into understanding the interactions of these microorganisms with methanotrophs and other nitrite-reducing microorganisms, such as anaerobic ammonium-oxidizing bacteria. Furthermore, our data can be used in modeling studies as well as wastewater treatment plant design.IMPORTANCE Methane is an important greenhouse gas with a radiative forcing 28 times that of carbon dioxide over a 100-year time scale. The emission of methane to the atmosphere is controlled by aerobic and anaerobic methanotrophs, which are microorganisms that are able to oxidize methane to conserve energy. While aerobic methanotrophs have been studied for over a century, knowledge on the physiological characteristics of anaerobic methanotrophs is scarce. Here, we describe kinetic properties of "Candidatus Methylomirabilis lanthanidiphila," a nitrite-dependent methane-oxidizing microorganism, which is ecologically important and can be applied in wastewater treatment.
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Affiliation(s)
- Simon Guerrero-Cruz
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | - Karin Stultiens
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | | | - Wouter Versantvoort
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Nijmegen, the Netherlands
| | | | - Boran Kartal
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
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Schulte SM, Jochmann MA, Wolbert JB, Gehrke T, Schmidt TC. A centrifuge tube reactor for the determination of bacterial methane oxidation enrichment factors without influence of diffusion related isotope fractionation. Sci Total Environ 2019; 659:1382-1386. [PMID: 31096348 DOI: 10.1016/j.scitotenv.2018.12.283] [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: 11/12/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
Biotransformation of methane at landfill sites can be estimated by applying compound specific stable isotope analysis of methane from the anaerobic and the cover layer surface zone. Next to these two input parameters, merely the knowledge of the carbon isotopic fractionation of the bacterial methane oxidation in terms of the enrichment factor (ε) is required. However, many factors and conditions have been described to affect ε. These include temperature, the applied landfill cover, the type of expressed methane monooxygenase (MMO), and cell density. In this work we investigated the microbial methane oxidation with respect to temperature and type of methanotrophic enrichment culture. A newly designed setup was used to overcome potential CH4-substrate limitations such as diffusion that could affect the determined values of ε by improper and inhomogeneous mixing. The isotopic fractionation was determined based on the stable carbon isotope analysis of methane and carbon dioxide. The obtained value for isotopic fractionation was ε22°C = -0.0136 ± 0.0036. Also for the first time, bulk stable isotope analysis of bacterial cell mass was performed by flow injection analysis isotope ratio mass spectrometry.
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Affiliation(s)
- S M Schulte
- Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitätsstr. 15, 45117 Essen, Germany
| | - M A Jochmann
- Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitätsstr. 15, 45117 Essen, Germany.
| | - J-B Wolbert
- Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitätsstr. 15, 45117 Essen, Germany
| | - T Gehrke
- Ruhrverband, Stabsstelle Qualitätsmanagment, Kronprinzenstr. 37, 45128 Essen, Germany; Department of Water and Waste Management, University of Duisburg-Essen, Universitätsstr. 15, 45117 Essen, Germany
| | - T C Schmidt
- Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitätsstr. 15, 45117 Essen, Germany; University of Duisburg-Essen, Centre for Water and Environmental Research (ZWU), Universitaetsstr. 5, 45141 Essen, Germany
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Tupa PR, Masuda H. Comparative Proteomic Analysis of Propane Metabolism in Mycobacterium sp. Strain ENV421 and Rhodococcus sp. Strain ENV425. J Mol Microbiol Biotechnol 2018; 28:107-115. [PMID: 30153684 DOI: 10.1159/000490494] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/17/2018] [Indexed: 11/19/2022] Open
Abstract
While growing on propane as a sole source of carbon, many strains cometabolically degrade environmental pollutants, such as ethers and chlorinated hydrocarbons. To gain insights into the molecular basis behind such a high metabolic versatility of propanotrophs, we examined the propane-inducible protein expression patterns of 2 soil actinobacteria that are known to degrade a variety of ethers (i.e., Mycobacterium sp. strain ENV421 and Rhodococcus sp. strain ENV425). In both strains, soluble diiron monooxygenase(s), that would catalyze the first step of the pathway, were induced by propane. However, despite their phylogenetic similarity, different sets of additional putative propane oxygenases (e.g., cytochrome P450 and particulate methane monooxygenases) were overexpressed in the 2 strains. They also diverged in the expression of enzymes responsible for downstream reactions. This study revealed a diversity of expression of putative propane oxygenases, which may be responsible for xenobiotic degradation, as well as a variety of metabolic pathways for propane in these bacterial species.
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Li Y, Wang Y, Lin Z, Wang J, He Q, Zhou J. A novel methanotrophic co-metabolic system with high soluble methane monooxygenase activity to biodegrade refractory organics in pulping wastewater. Bioresour Technol 2018; 256:358-365. [PMID: 29471231 DOI: 10.1016/j.biortech.2018.02.048] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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: 12/15/2017] [Revised: 02/09/2018] [Accepted: 02/10/2018] [Indexed: 06/08/2023]
Abstract
Pulping wastewater still contains massive refractory organics after biotreatment, with high colority, low biodegradability, and lasting biotoxicity. To eliminate refractory organics in pulping wastewater, a methanotrophic co-metabolic system in a gas cycle Sequencing Batch Biofilm Reactor (gcSBBR) seeded by soil at a ventilation opening of coal mine was quickly built on the 92nd day. The removal rate of COD, colority and TOC was 53.28%, 50.59% and 51.60%, respectively. Analysis of 3D-EEM indicated that glycolated protein-like, melanoidin-like or lignocellulose-like, and humic acid-like decreased by 7.85%, 5.02% and 1.74%, respectively. Moreover, this system exhibited high activity of soluble methane monooxygenase (sMMO) and mmoX encoding sMMO reached up to 7.89 × 105 copies/μL. Methanotrophs, namely, Methylocaldum (8.28%), Methylococcus (6.06%) and Methylomonas (0.07%), were detected by 16S rRNA sequencing. And other bacteria were dominated by Denitratisoma, Anaerolineaceae_uncultured and Methylophilaceae_uncultured. Refractory organics was biodegraded through the synergy among microorganisms, and a postulated synergy pathway was put forward.
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Affiliation(s)
- Yancheng Li
- Key Laboratory of the Three Gorges Reservoir's Eco-Environments, Chongqing University, Chongqing 400045, PR China
| | - Yingmu Wang
- Key Laboratory of the Three Gorges Reservoir's Eco-Environments, Chongqing University, Chongqing 400045, PR China
| | - Ziyuan Lin
- Key Laboratory of the Three Gorges Reservoir's Eco-Environments, Chongqing University, Chongqing 400045, PR China
| | - Jiale Wang
- Key Laboratory of the Three Gorges Reservoir's Eco-Environments, Chongqing University, Chongqing 400045, PR China
| | - Qiang He
- Key Laboratory of the Three Gorges Reservoir's Eco-Environments, Chongqing University, Chongqing 400045, PR China
| | - Jian Zhou
- Key Laboratory of the Three Gorges Reservoir's Eco-Environments, Chongqing University, Chongqing 400045, PR China.
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Gunasekera B, Abou Diwan C, Altawallbeh G, Kalil H, Maher S, Xu S, Bayachou M. Functional Layer-by-Layer Thin Films of Inducible Nitric Oxide (NO) Synthase Oxygenase and Polyethylenimine: Modulation of Enzyme Loading and NO-Release Activity. ACS Appl Mater Interfaces 2018; 10:7745-7755. [PMID: 29359547 DOI: 10.1021/acsami.7b17575] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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] [Indexed: 06/07/2023]
Abstract
Nitric oxide (NO) release counteracts platelet aggregation and prevents the thrombosis cascade in the inner walls of blood vessels. NO-release coatings also prevent thrombus formation on the surface of blood-contacting medical devices. Our previous work has shown that inducible nitric oxide synthase (iNOS) films release NO fluxes upon enzymatic conversion of the substrate l-arginine. In this work, we report on the modulation of enzyme loading in layer-by-layer (LbL) thin films of inducible nitric oxide synthase oxygenase (iNOSoxy) on polyethylenimine (PEI). The layer of iNOSoxy is electrostatically adsorbed onto the PEI layer. The pH of the iNOSoxy solution affects the amount of enzyme adsorbed. The overall negative surface charge of iNOSoxy in solution depends on the pH and hence determines the density of adsorbed protein on the positively charged PEI layer. We used buffered iNOSoxy solutions adjusted to pHs 8.6 and 7.0, while saline PEI solution was used at pH 7.0. Atomic force microscopy imaging of the outermost layer shows higher protein adsorption with iNOSoxy at pH 8.6 than with a solution of iNOSoxy at pH 7.0. Graphite electrodes with PEI/iNOSoxy films show higher catalytic currents for nitric oxide reduction mediated by iNOSoxy. The higher enzyme loading translates into higher NO flux when the enzyme-modified surface is exposed to a solution containing the substrate and a source of electrons. Spectrophotometric assays showed higher NO fluxes with iNOSoxy/PEI films built at pH 8.6 than with films built at pH 7.0. Fourier transform infrared analysis of iNOSoxy adsorbed on PEI at pH 8.6 and 7.0 shows structural differences of iNOSoxy in films, which explains the observed changes in enzymatic activity. Our findings show that pH provides a strategy to optimize the NOS loading and enzyme activity in NOS-based LbL thin films, which enables improved NO release with minimum layers of PEI/NOS.
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Affiliation(s)
- Bhagya Gunasekera
- Department of Chemistry , Cleveland State University , 2399 Euclid Avenue SR 397 , Cleveland , Ohio 44120 , United States
| | - Charbel Abou Diwan
- Department of Chemistry , Cleveland State University , 2399 Euclid Avenue SR 397 , Cleveland , Ohio 44120 , United States
| | - Ghaith Altawallbeh
- Department of Chemistry , Cleveland State University , 2399 Euclid Avenue SR 397 , Cleveland , Ohio 44120 , United States
| | - Haitham Kalil
- Department of Chemistry , Cleveland State University , 2399 Euclid Avenue SR 397 , Cleveland , Ohio 44120 , United States
| | - Shaimaa Maher
- Department of Chemistry , Cleveland State University , 2399 Euclid Avenue SR 397 , Cleveland , Ohio 44120 , United States
| | - Song Xu
- Keysight Technologies , 1400 Foutaingrove Parkway , Santa Rosa 95403 , California , United States
| | - Mekki Bayachou
- Department of Chemistry , Cleveland State University , 2399 Euclid Avenue SR 397 , Cleveland , Ohio 44120 , United States
- Department of Pathobiology , Lerner Research Institute , The Cleveland Clinic , Cleveland , Ohio 44106 , United States
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Lin YJ, Chang JJ, Lin HY, Thia C, Kao YY, Huang CC, Li WH. Metabolic engineering a yeast to produce astaxanthin. Bioresour Technol 2017; 245:899-905. [PMID: 28931206 DOI: 10.1016/j.biortech.2017.07.116] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [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: 06/27/2017] [Revised: 07/17/2017] [Accepted: 07/21/2017] [Indexed: 05/21/2023]
Abstract
In this study, an astaxanthin-biosynthesis Kluyveromyces marxianus strain Sm23 was first constructed, which could produce 31µg/g DCW astaxanthin. Then, repeated genome integration of the key astaxanthin biosynthesis genes Hpchyb and bkt was done to increase gene copy number and astaxanthin yield. Four improved strains were obtained and the yield of astaxanthin and the total yield of carotenoids in a strain increased with the copy numbers of Hpchyb and bkt. To improve the yield further, the gene Hpchyb from Haematococcus pluvialis was modified by site-directed mutagenesis to increase the enzyme efficiency or/and to prevent the heterologous protein degradation by ubiquitination. Using repeated-integration approach of bkt and the mutated Hpchyb into Sm23, the S3-2 strain was obtained and shown to produce the 3S, 3'S-astaxanthin at 9972µg/g DCW in a 5L fermentor.
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Affiliation(s)
- Yu-Ju Lin
- Biodiversity Research Center, Academia Sinica, No. 128 Academia Road, Sec. 2, Nankang, Taipei 115, Taiwan; Department of Life Sciences, National Chung Hsing University, No. 250, Kuo Kuang Rd, Taichung 402, Taiwan
| | - Jui-Jen Chang
- Department of Medical Research, China Medical University Hospital, China Medical University, No. 91 Hsueh-Shih Road, Taichung 402, Taiwan
| | - Hao-Yeh Lin
- Biodiversity Research Center, Academia Sinica, No. 128 Academia Road, Sec. 2, Nankang, Taipei 115, Taiwan
| | - Caroline Thia
- Biodiversity Research Center, Academia Sinica, No. 128 Academia Road, Sec. 2, Nankang, Taipei 115, Taiwan
| | - Yi-Ying Kao
- Biodiversity Research Center, Academia Sinica, No. 128 Academia Road, Sec. 2, Nankang, Taipei 115, Taiwan
| | - Chieh-Chen Huang
- Department of Life Sciences, National Chung Hsing University, No. 250, Kuo Kuang Rd, Taichung 402, Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, No. 128 Academia Road, Sec. 2, Nankang, Taipei 115, Taiwan; Department of Life Sciences, National Chung Hsing University, No. 250, Kuo Kuang Rd, Taichung 402, Taiwan; Department of Medical Research, China Medical University Hospital, China Medical University, No. 91 Hsueh-Shih Road, Taichung 402, Taiwan; Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, United States.
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Ishikawa M, Tanaka Y, Suzuki R, Kimura K, Tanaka K, Kamiya K, Ito H, Kato S, Kamachi T, Hori K, Nakanishi S. Real-time monitoring of intracellular redox changes in Methylococcus capsulatus (Bath) for efficient bioconversion of methane to methanol. Bioresour Technol 2017; 241:1157-1161. [PMID: 28578808 DOI: 10.1016/j.biortech.2017.05.107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 03/30/2017] [Revised: 05/16/2017] [Accepted: 05/17/2017] [Indexed: 06/07/2023]
Abstract
This study aimed to develop a novel method for real-time monitoring of the intracellular redox states in a methanotroph Methylococcus capsulatus, using Peredox as a genetically encoded fluorescent sensor of the NADH:NAD+ ratio. As expected, the fluorescence derived from the Peredox-expressing M. capsulatus transformant increased by supplementation of electron donor compounds (methane and formate), while it decreased by specifically inhibiting the methanol oxidation reaction. Electrochemical measurements confirmed that the Peredox fluorescence reliably represents the intracellular redox changes. This study is the first to construct a reliable redox-monitoring method for methanotrophs, which will facilitate to develop more efficient methane-to-methanol bioconversion processes.
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Affiliation(s)
- Masahito Ishikawa
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan; Research Center for Solar Energy Chemistry, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Yuya Tanaka
- Department of Chemistry, Graduate School of Engineering Science, Osaka University, Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Risa Suzuki
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Kota Kimura
- Department of Chemistry, Graduate School of Engineering Science, Osaka University, Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Kenya Tanaka
- Department of Chemistry, Graduate School of Engineering Science, Osaka University, Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Kazuhide Kamiya
- Research Center for Solar Energy Chemistry, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan; Department of Chemistry, Graduate School of Engineering Science, Osaka University, Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Hidehiro Ito
- Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Souichiro Kato
- Research Center for Solar Energy Chemistry, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan; Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido 062-8517, Japan
| | - Toshiaki Kamachi
- Department of Life Science and Technology, Graduated School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Katsutoshi Hori
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Shuji Nakanishi
- Research Center for Solar Energy Chemistry, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan; Department of Chemistry, Graduate School of Engineering Science, Osaka University, Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
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Strong PJ, Kalyuzhnaya M, Silverman J, Clarke WP. A methanotroph-based biorefinery: Potential scenarios for generating multiple products from a single fermentation. Bioresour Technol 2016; 215:314-323. [PMID: 27146469 DOI: 10.1016/j.biortech.2016.04.099] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [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: 01/29/2016] [Revised: 04/17/2016] [Accepted: 04/19/2016] [Indexed: 05/12/2023]
Abstract
Methane, a carbon source for methanotrophic bacteria, is the principal component of natural gas and is produced during anaerobic digestion of organic matter (biogas). Methanotrophs are a viable source of single cell protein (feed supplement) and can produce various products, since they accumulate osmolytes (e.g. ectoine, sucrose), phospholipids (potential biofuels) and biopolymers (polyhydroxybutyrate, glycogen), among others. Other cell components, such as surface layers, metal chelating proteins (methanobactin), enzymes (methane monooxygenase) or heterologous proteins hold promise as future products. Here, scenarios are presented where ectoine, polyhydroxybutyrate or protein G are synthesised as the primary product, in conjunction with a variety of ancillary products that could enhance process viability. Single or dual-stage processes and volumetric requirements for bioreactors are discussed, in terms of an annual biomass output of 1000 tonnesyear(-1). Product yields are discussed in relation to methane and oxygen consumption and organic waste generation.
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Affiliation(s)
- P J Strong
- Centre for Solid Waste Bioprocessing, School of Civil Engineering, School of Chemical Engineering, The University of Queensland, Brisbane 4072, Australia.
| | - M Kalyuzhnaya
- Biology Department, San Diego State University, San Diego, CA 92182-4614, United States
| | - J Silverman
- Calysta, 1140 O'Brien Drive, Menlo Park, CA 94025, United States
| | - W P Clarke
- Centre for Solid Waste Bioprocessing, School of Civil Engineering, School of Chemical Engineering, The University of Queensland, Brisbane 4072, Australia
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Affiliation(s)
- Kathy E Schwinn
- The New Zealand Institute for Plant & Food Research Ltd, Private Bag 11600, Palmerston North, 4442, New Zealand
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Nick S, Meurer J, Soll J, Ankele E. Nucleus-encoded light-harvesting chlorophyll a/b proteins are imported normally into chlorophyll b-free chloroplasts of Arabidopsis. Mol Plant 2013; 6:860-871. [PMID: 23041941 DOI: 10.1093/mp/sss113] [Citation(s) in RCA: 11] [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] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Chloroplast-located proteins which are encoded by the nuclear genome have to be imported from the cytosol into the organelle in a posttranslational manner. Among these nuclear-encoded chloroplast proteins are the light-harvesting chlorophyll a/b-binding proteins (LHCPs). After translation in the cytosol, precursor proteins of LHCPs are imported via the TOC/TIC translocase, processed to their mature size to insert into thylakoid membranes where they recruit chlorophylls a and b to form pigment-protein complexes. The translocation of proteins is a highly regulated process which employs several regulators. To analyze whether CAO (chlorophyll a oxigenase) which converts chlorophyll a to chlorophyll b at the inner chloroplast membrane, is one of these regulators, we performed import reactions utilizing a homozygous loss-of-function mutant (cao-1). We imported in vitro translated and (35)S-labeled precursor proteins of light-harvesting proteins of photosystem II LHCB1, LHCB4, and LHCB5 into chloroplasts isolated from cao-1 and show that import of precursor proteins and their processing to mature forms are not impaired in the mutant. Therefore, regulation of the import machinery cannot be responsible for the decreased steady-state levels of light-harvesting complex (LHC) proteins. Regulation does not take place at the transcriptional level either, because Lhcb mRNAs are not down-regulated. Additionally, reduced steady-state levels of LHCPs also do not occur due to posttranslational turnover of non-functional LHCPs in chloroplasts. Taken together, our data show that plants in the absence of CAO and therefore devoid of chlorophyll b are not influenced in their import behavior of LHC proteins.
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Affiliation(s)
- Sabine Nick
- Dept Biologie I-Botanik, Biozentrum LMU München, Grosshadernerstrasse 2-4, D-82152 Planegg-Martinsried, Germany
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Luo M, Liu YJ, Xia LM, Yan W, Zhu Q, Tian DA. Very low density lipoprotein receptor subtype II silencing by RNA interference inhibits cell proliferation in hepatoma cell lines. Hepatogastroenterology 2010; 57:882-890. [PMID: 21033246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Very low density lipoprotein receptor (VLDLR) belongs to the low density lipoprotein receptor family, it is divided into two subtypes according to forms with an absence (type II) or a presence (type I) of the O-linked sugar domain. VLDLR have been detected in kinds of cancers so far; however, the subtype of VLDLR in hepatocellular carcinoma (HCC) tissues and hepatoma cell lines has yet to be reported. We detected the VLDLR expression in 39 cases of hepatocellular carcinoma and in three kinds of hepatoma cell lines: HepG2, HBV transfected HepG2.2.15, SMMC-7721 and normal human fetal liver cell line LO2 using RT-PCR and western blotting. The results showed that both type I and type II VLDLR were detected in HCC tissues and hepatoma cell lines, and the type II VLDLR expression was significantly higher than that of type I in cell lines. We inhibited the type II VLDLR expression by shRNA-mediated RNA interference in HepG2, SMMC-7721 cell and then subsequently found the cell proliferation slowed down. The cyclinD1 expression confirmed the cell cycle was arrested at the G0/G1 phase, suggesting that inhibiting the type II VLDLR expression may have a positive impact on carcinogenesis of HCC.
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Affiliation(s)
- Min Luo
- Institute of Liver Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
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Strieker M, Kopp F, Mahlert C, Essen LO, Marahiel MA. Mechanistic and structural basis of stereospecific Cbeta-hydroxylation in calcium-dependent antibiotic, a daptomycin-type lipopeptide. ACS Chem Biol 2007; 2:187-96. [PMID: 17373765 DOI: 10.1021/cb700012y] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Non-ribosomally synthesized lipopeptide antibiotics of the daptomycin type are known to contain unnatural beta-modified amino acids, which are essential for bioactivity. Here we present the biochemical and structural basis for the incorporation of 3-hydroxyasparagine at position 9 in the 11-residue acidic lipopeptide lactone calcium-dependent antibiotic (CDA). Direct hydroxylation of l-asparagine by AsnO, a non-heme Fe(2+)/alpha-ketoglutarate-dependent oxygenase encoded by the CDA biosynthesis gene cluster, was validated by Fmoc derivatization of the reaction product and LC/MS analysis. The 1.45, 1.92, and 1.66 A crystal structures of AsnO as apoprotein, Fe(2+) complex, and product complex, respectively, with (2S,3S)-3-hydroxyasparagine and succinate revealed the stereoselectivity and substrate specificity of AsnO. The comparison of native and product-complex structures of AsnO showed a lid-like region (residues F208-E223) that seals the active site upon substrate binding and shields it from sterically demanding peptide substrates. Accordingly, beta-hydroxylated asparagine is synthesized prior to its incorporation into the growing CDA peptide. The AsnO structure could serve as a template for engineering novel enzymes for the synthesis of beta-hydroxylated amino acids.
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Affiliation(s)
- Matthias Strieker
- Department of Chemistry/Biochemistry, Philipps University of Marburg, Marburg, Germany
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