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Telek A, Molnár Z, Takács K, Varga B, Grolmusz V, Tasnádi G, Vértessy BG. Discovery and biocatalytic characterization of opine dehydrogenases by metagenome mining. Appl Microbiol Biotechnol 2024; 108:101. [PMID: 38229296 DOI: 10.1007/s00253-023-12871-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 11/29/2023] [Accepted: 12/06/2023] [Indexed: 01/18/2024]
Abstract
Enzymatic processes play an increasing role in synthetic organic chemistry which requires the access to a broad and diverse set of enzymes. Metagenome mining is a valuable and efficient way to discover novel enzymes with unique properties for biotechnological applications. Here, we report the discovery and biocatalytic characterization of six novel metagenomic opine dehydrogenases from a hot spring environment (mODHs) (EC 1.5.1.X). These enzymes catalyze the asymmetric reductive amination between an amino acid and a keto acid resulting in opines which have defined biochemical roles and represent promising building blocks for pharmaceutical applications. The newly identified enzymes exhibit unique substrate specificity and higher thermostability compared to known examples. The feature that they preferably utilize negatively charged polar amino acids is so far unprecedented for opine dehydrogenases. We have identified two spatially correlated positions in their active sites that govern this substrate specificity and demonstrated a switch of substrate preference by site-directed mutagenesis. While they still suffer from a relatively narrow substrate scope, their enhanced thermostability and the orthogonality of their substrate preference make them a valuable addition to the toolbox of enzymes for reductive aminations. Importantly, enzymatic reductive aminations with highly polar amines are very rare in the literature. Thus, the preparative-scale enzymatic production, purification, and characterization of three highly functionalized chiral secondary amines lend a special significance to our work in filling this gap. KEY POINTS: • Six new opine dehydrogenases have been discovered from a hot spring metagenome • The newly identified enzymes display a unique substrate scope • Substrate specificity is governed by two correlated active-site residues.
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Grants
- K119493 National Research, Development and Innovation Office
- K135231 National Research, Development and Innovation Office
- VEKOP-2.3.2-16-2017-00013 National Research, Development and Innovation Office
- NKP-2018-1.2.1-NKP-2018-00005 National Research, Development and Innovation Office
- TKP2021-EGA-02 National Research, Development and Innovation Office
- ÚNKP-22-4-II-BME-158 National Research, Development and Innovation Office
- RRF-2.3.1-21-2022-000 15 National Research, Development and Innovation Office
- C1580174 Nemzeti Kutatási, Fejlesztési és Innovaciós Alap
- ELTE TKP 2021-NKTA-62 Nemzeti Kutatási, Fejlesztési és Innovaciós Alap
- 2022-1.2.2-TÉT-IPARI-UZ-2022-00003 Nemzeti Kutatási, Fejlesztési és Innovaciós Alap
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Affiliation(s)
- András Telek
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
- Servier Research Institute of Medicinal Chemistry, Budapest, Hungary
| | - Zsófia Molnár
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Budapest, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Kristóf Takács
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös University, Budapest, Hungary
| | - Bálint Varga
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös University, Budapest, Hungary
| | - Vince Grolmusz
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös University, Budapest, Hungary
| | - Gábor Tasnádi
- Servier Research Institute of Medicinal Chemistry, Budapest, Hungary.
| | - Beáta G Vértessy
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary.
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Budapest, Hungary.
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Liu Y, Xu Z, Chen L, Xun W, Shu X, Chen Y, Sun X, Wang Z, Ren Y, Shen Q, Zhang R. Root colonization by beneficial rhizobacteria. FEMS Microbiol Rev 2024; 48:fuad066. [PMID: 38093453 PMCID: PMC10786197 DOI: 10.1093/femsre/fuad066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024] Open
Abstract
Rhizosphere microbes play critical roles for plant's growth and health. Among them, the beneficial rhizobacteria have the potential to be developed as the biofertilizer or bioinoculants for sustaining the agricultural development. The efficient rhizosphere colonization of these rhizobacteria is a prerequisite for exerting their plant beneficial functions, but the colonizing process and underlying mechanisms have not been thoroughly reviewed, especially for the nonsymbiotic beneficial rhizobacteria. This review systematically analyzed the root colonizing process of the nonsymbiotic rhizobacteria and compared it with that of the symbiotic and pathogenic bacteria. This review also highlighted the approaches to improve the root colonization efficiency and proposed to study the rhizobacterial colonization from a holistic perspective of the rhizosphere microbiome under more natural conditions.
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Affiliation(s)
- Yunpeng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Lin Chen
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, 1 Shuizha West Road, Beijing 102300, P.R. China
| | - Weibing Xun
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Xia Shu
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, P.R. China
| | - Yu Chen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Xinli Sun
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Zhengqi Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Yi Ren
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Ruifu Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
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Telek A, Molnár Z, Vértessy BG, Tasnádi G. Opine dehydrogenases, an underexplored enzyme family for the enzymatic synthesis of chiral amines. Biotechnol Bioeng 2023; 120:2793-2808. [PMID: 37334502 DOI: 10.1002/bit.28469] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/17/2023] [Accepted: 06/03/2023] [Indexed: 06/20/2023]
Abstract
Opines and opine-type chemicals are valuable natural products with diverse biochemical roles, and potential synthetic building blocks of bioactive compounds. Their synthesis involves reductive amination of ketoacids with amino acids. This transformation has high synthetic potential in producing enantiopure secondary amines. Nature has evolved opine dehydrogenases for this chemistry. To date, only one enzyme has been used as biocatalyst, however, analysis of the available sequence space suggests more enzymes to be exploited in synthetic organic chemistry. This review summarizes the current knowledge of this underexplored enzyme class, highlights key molecular, structural, and catalytic features with the aim to provide a comprehensive general description of opine dehydrogenases, thereby supporting future enzyme discovery and protein engineering studies.
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Affiliation(s)
- András Telek
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
- Servier Research Institute of Medicinal Chemistry, Budapest, Hungary
| | - Zsófia Molnár
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Beáta G Vértessy
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Gábor Tasnádi
- Servier Research Institute of Medicinal Chemistry, Budapest, Hungary
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Veremeichik GN, Bulgakov DV, Solomatina TO, Makhazen DS. In the interkingdom horizontal gene transfer, the small rolA gene is a big mystery. Appl Microbiol Biotechnol 2023; 107:2097-2109. [PMID: 36881118 DOI: 10.1007/s00253-023-12454-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/08/2023]
Abstract
The biological function of the agrobacterial oncogene rolA is very poorly understood compared to other components of the mechanism of horizontal gene transfer during agrobacterial colonization of plants. Research groups around the world have worked on this problem, and available information is reviewed in this review, but other rol oncogenes have been studied much more thoroughly. Having one unexplored element makes it impossible to form a complete picture. However, the limited data suggest that the rolA oncogene and its regulatory apparatus have great potential in plant biotechnology and genetic engineering. Here, we collect and discuss available experimental data about the function and structure of rolA. There is still no clear understanding of the mechanism of RolA and its structure and localization. We believe this is because of the nucleotide structure of a frameshift in the most well-studied rolA gene of the agropine type pRi. In fact, interest in the genes of agrobacteria as natural tools for the phenotypic or biochemical engineering of plants increased. We believe that a detailed understanding of the molecular mechanisms will be forthcoming. KEY POINTS: • Among pRi T-DNA oncogenes, rolA is the least understood in spite of many studies. • Frameshift may be the reason for the failure to elucidate the role of agropine rolA. • Understanding of rolA is promising for the phenotypic and biochemical engineering of plants.
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Affiliation(s)
- Galina N Veremeichik
- Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Russian Academy of Sciences Far Eastern Branch, FGBUN FNC Bioraznoobrazia nazemnoj bioty Vostocnoj Azii Dal'nevostocnogo otdelenia Rossijskoj akademii nauk, 690022, Vladivostok, Russia.
| | - Dmitrii V Bulgakov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Russian Academy of Sciences Far Eastern Branch, FGBUN FNC Bioraznoobrazia nazemnoj bioty Vostocnoj Azii Dal'nevostocnogo otdelenia Rossijskoj akademii nauk, 690022, Vladivostok, Russia
| | - Taisia O Solomatina
- Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Russian Academy of Sciences Far Eastern Branch, FGBUN FNC Bioraznoobrazia nazemnoj bioty Vostocnoj Azii Dal'nevostocnogo otdelenia Rossijskoj akademii nauk, 690022, Vladivostok, Russia
| | - Dmitrii S Makhazen
- Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Russian Academy of Sciences Far Eastern Branch, FGBUN FNC Bioraznoobrazia nazemnoj bioty Vostocnoj Azii Dal'nevostocnogo otdelenia Rossijskoj akademii nauk, 690022, Vladivostok, Russia
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Alcalde MA, Müller M, Munné-Bosch S, Landín M, Gallego PP, Bonfill M, Palazon J, Hidalgo-Martinez D. Using machine learning to link the influence of transferred Agrobacterium rhizogenes genes to the hormone profile and morphological traits in Centella asiatica hairy roots. FRONTIERS IN PLANT SCIENCE 2022; 13:1001023. [PMID: 36119596 PMCID: PMC9479193 DOI: 10.3389/fpls.2022.1001023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Hairy roots are made after the integration of a small set of genes from Agrobacterium rhizogenes in the plant genome. Little is known about how this small set is linked to their hormone profile, which determines development, morphology, and levels of secondary metabolite production. We used C. asiatica hairy root line cultures to determine the putative links between the rol and aux gene expressions with morphological traits, a hormone profile, and centelloside production. The results obtained after 14 and 28 days of culture were processed via multivariate analysis and machine-learning processes such as random forest, supported vector machines, linear discriminant analysis, and neural networks. This allowed us to obtain models capable of discriminating highly productive root lines from their levels of genetic expression (rol and aux genes) or from their hormone profile. In total, 12 hormones were evaluated, resulting in 10 being satisfactorily detected. Within this set of hormones, abscisic acid (ABA) and cytokinin isopentenyl adenosine (IPA) were found to be critical in defining the morphological traits and centelloside content. The results showed that IPA brings more benefits to the biotechnological platform. Additionally, we determined the degree of influence of each of the evaluated genes on the individual hormone profile, finding that aux1 has a significant influence on the IPA profile, while the rol genes are closely linked to the ABA profile. Finally, we effectively verified the gene influence on these two specific hormones through feeding experiments that aimed to reverse the effect on root morphology and centelloside content.
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Affiliation(s)
- Miguel Angel Alcalde
- Department of Biology, Healthcare and the Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Maren Müller
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Sergi Munné-Bosch
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Mariana Landín
- Department of Pharmacology, Pharmacy and Pharmaceutical Technology, Group I+D Farma (GI-1645), Faculty of Pharmacy, University of Santiago, Santiago de Compostela, Spain
| | - Pedro Pablo Gallego
- Agrobiotech for Health, Department of Plant Biology and Soil Science, Faculty of Biology, University of Vigo, Vigo, Spain
| | - Mercedes Bonfill
- Department of Biology, Healthcare and the Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Javier Palazon
- Department of Biology, Healthcare and the Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Diego Hidalgo-Martinez
- Department of Biology, Healthcare and the Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
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Asenstorfer RE, Ryder MH, Jones GP. Agrocinopine C, a Ti-plasmid-coded enzyme-product, is a 2-O, 6-O linked phosphodiester of D-Glucose and sucrose. PHYTOCHEMISTRY 2022; 194:113013. [PMID: 34839131 DOI: 10.1016/j.phytochem.2021.113013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/06/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
Agrocinopine C is a small molecule found in crown gall tumours induced by pathogenic Agrobacterium radiobacter carrying the tumour-inducing plasmid pTi Bo542. This phosphodiester opine was isolated (at 0.02 g/100 g fresh wt.) from sunflower (Helianthus annuus L.) galls. It is structurally related to agrocinopine A and is a glucose-2-phosphodiester linked to the C6-hydroxy-methyl group of the glucose moiety of sucrose. Sugar-2-phosphates are uncommon in plant tissues, whether transformed by Agrobacterium or not. 1H and 31P NMR signal multiplicity indicates five-fold anomeric complexity of agrocinopine C in solution, implying that the permeases taking up these sucrose-phosphodiesters could recognise any one of the five anomers. Data suggests that the open chain aldehyde forms of the 2-phosphorylated opines agrocinopine C and agrocinopine A and the corresponding phosphorylated glucose-2-phosphoramidate component of the antibiotic agrocin 84 play a central role in agrocin's selective toxicity to certain strains of Agrobacterium after uptake via Ti plasmid-encoded permeases.
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Affiliation(s)
- Robert E Asenstorfer
- School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, PMB 1, Glen Osmond, South Australia, 5064, Australia
| | - Maarten H Ryder
- School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, PMB 1, Glen Osmond, South Australia, 5064, Australia.
| | - Graham P Jones
- School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, PMB 1, Glen Osmond, South Australia, 5064, Australia
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