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Lu Y, Kronzucker HJ, Yu M, Shabala S, Shi W. Nitrogen-loss and carbon-footprint reduction by plant-rhizosphere exudates. TRENDS IN PLANT SCIENCE 2024; 29:469-481. [PMID: 37802692 DOI: 10.1016/j.tplants.2023.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 09/02/2023] [Accepted: 09/08/2023] [Indexed: 10/08/2023]
Abstract
Low-carbon approaches to agriculture constitute a pivotal measure to address the challenge of global climate change. In agroecosystems, rhizosphere exudates are significantly involved in regulating the nitrogen (N) cycle and facilitating belowground chemical communication between plants and soil microbes to reduce direct and indirect emissions of greenhouse gases (GHGs) and control N runoff from cultivated sites into natural water bodies. Here, we discuss specific rhizosphere exudates from plants and microorganisms and the mechanisms by which they reduce N loss and subsequent N pollution in terrestrial and aquatic environments, including biological nitrification inhibitors (BNIs), biological denitrification inhibitors (BDIs), and biological denitrification promoters (BDPs). We also highlight promising application scenarios and challenges in relation to rhizosphere exudates in terrestrial and aquatic environments.
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Affiliation(s)
- Yufang Lu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Herbert J Kronzucker
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Min Yu
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
| | - Sergey Shabala
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China; School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Weiming Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Li Y, Lin Y, Wang F, Wang J, Shoji O, Xu J. Construction of Biocatalysts Using the P450 Scaffold for the Synthesis of Indigo from Indole. Int J Mol Sci 2023; 24:ijms24032395. [PMID: 36768714 PMCID: PMC9917246 DOI: 10.3390/ijms24032395] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023] Open
Abstract
With the increasing demand for blue dyes, it is of vital importance to develop a green and efficient biocatalyst to produce indigo. This study constructed a hydrogen peroxide-dependent catalytic system for the direct conversion of indole to indigo using P450BM3 with the assistance of dual-functional small molecules (DFSM). The arrangements of amino acids at 78, 87, and 268 positions influenced the catalytic activity. F87G/T268V mutant gave the highest catalytic activity with kcat of 1402 min-1 and with a yield of 73%. F87A/T268V mutant was found to produce the indigo product with chemoselectivity as high as 80%. Moreover, F87G/T268A mutant was found to efficiently catalyze indole oxidation with higher activity (kcat/Km = 1388 mM-1 min-1) than other enzymes, such as the NADPH-dependent P450BM3 (2.4-fold), the Ngb (32-fold) and the Mb (117-fold). Computer simulation results indicate that the arrangements of amino acid residues in the active site can significantly affect the catalytic activity of the protein. The DFSM-facilitated P450BM3 peroxygenase system provides an alternative, simple approach for a key step in the bioproduction of indigo.
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Affiliation(s)
- Yanqing Li
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China
| | - Yingwu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Fang Wang
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China
| | - Jinghan Wang
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
- Correspondence: (O.S.); (J.X.)
| | - Jiakun Xu
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China
- Correspondence: (O.S.); (J.X.)
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Maseme MJ, Pennec A, Marwijk J, Opperman DJ, Smit MS. CYP505E3: A Novel Self‐Sufficient ω‐7 In‐Chain Hydroxylase. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Mpeyake Jacob Maseme
- Department of Microbial, Biochemical and Food Biotechnology University of the Free State P.O. Box 339 Bloemfontein 9300 South Africa
- South African DST-NRF Centre of Excellence in Catalysis, c*change University of Cape Town South Africa
| | - Alizé Pennec
- Department of Microbial, Biochemical and Food Biotechnology University of the Free State P.O. Box 339 Bloemfontein 9300 South Africa
- South African DST-NRF Centre of Excellence in Catalysis, c*change University of Cape Town South Africa
| | - Jacqueline Marwijk
- Department of Microbial, Biochemical and Food Biotechnology University of the Free State P.O. Box 339 Bloemfontein 9300 South Africa
- South African DST-NRF Centre of Excellence in Catalysis, c*change University of Cape Town South Africa
| | - Diederik Johannes Opperman
- Department of Microbial, Biochemical and Food Biotechnology University of the Free State P.O. Box 339 Bloemfontein 9300 South Africa
- South African DST-NRF Centre of Excellence in Catalysis, c*change University of Cape Town South Africa
| | - Martha Sophia Smit
- Department of Microbial, Biochemical and Food Biotechnology University of the Free State P.O. Box 339 Bloemfontein 9300 South Africa
- South African DST-NRF Centre of Excellence in Catalysis, c*change University of Cape Town South Africa
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Maseme MJ, Pennec A, Marwijk J, Opperman DJ, Smit MS. CYP505E3: A Novel Self‐Sufficient ω‐7 In‐Chain Hydroxylase. Angew Chem Int Ed Engl 2020; 59:10359-10362. [DOI: 10.1002/anie.202001055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/26/2020] [Indexed: 01/30/2023]
Affiliation(s)
- Mpeyake Jacob Maseme
- Department of Microbial, Biochemical and Food Biotechnology University of the Free State P.O. Box 339 Bloemfontein 9300 South Africa
- South African DST-NRF Centre of Excellence in Catalysis, c*change University of Cape Town South Africa
| | - Alizé Pennec
- Department of Microbial, Biochemical and Food Biotechnology University of the Free State P.O. Box 339 Bloemfontein 9300 South Africa
- South African DST-NRF Centre of Excellence in Catalysis, c*change University of Cape Town South Africa
| | - Jacqueline Marwijk
- Department of Microbial, Biochemical and Food Biotechnology University of the Free State P.O. Box 339 Bloemfontein 9300 South Africa
- South African DST-NRF Centre of Excellence in Catalysis, c*change University of Cape Town South Africa
| | - Diederik Johannes Opperman
- Department of Microbial, Biochemical and Food Biotechnology University of the Free State P.O. Box 339 Bloemfontein 9300 South Africa
- South African DST-NRF Centre of Excellence in Catalysis, c*change University of Cape Town South Africa
| | - Martha Sophia Smit
- Department of Microbial, Biochemical and Food Biotechnology University of the Free State P.O. Box 339 Bloemfontein 9300 South Africa
- South African DST-NRF Centre of Excellence in Catalysis, c*change University of Cape Town South Africa
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Biosynthesis of Medium- to Long-Chain α,ω-Diols from Free Fatty Acids Using CYP153A Monooxygenase, Carboxylic Acid Reductase, and E. coli Endogenous Aldehyde Reductases. Catalysts 2017. [DOI: 10.3390/catal8010004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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