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Liu F, Fernie AR, Zhang Y. Can a nitrogen-fixing organelle be engineered within plants? TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00177-8. [PMID: 39054227 DOI: 10.1016/j.tplants.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/27/2024]
Abstract
Given that crop yields are strongly limited by nitrogen, engineering crop plants with self-nitrogen-fertilization capacity holds great promise for sustainable agriculture. Recently, a nitrogen-fixing organelle has been characterized in the unicellular marine microalgae Braarudosphaera bigelowii. Engineering a nitrogen-fixing organelle into the non-nitrogen-fixing crops could benefit both environmental sustainability and global food security.
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Affiliation(s)
- Fang Liu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Youjun Zhang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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2
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Zeng Y, Guo L, Gao Y, Cui L, Wang M, Huang L, Jiang M, Liu Y, Zhu Y, Xiang H, Li DF, Zheng Y. Formation of NifA-P II complex represses ammonium-sensitive nitrogen fixation in diazotrophic proteobacteria lacking NifL. Cell Rep 2024; 43:114476. [PMID: 38985671 DOI: 10.1016/j.celrep.2024.114476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 05/24/2024] [Accepted: 06/25/2024] [Indexed: 07/12/2024] Open
Abstract
Biological nitrogen fixation catalyzed by nitrogenase contributes greatly to the global nitrogen cycle. Nitrogenase expression is subject to regulation in response to nitrogen availability. However, the mechanism through which the transcriptional activator NifA regulates nitrogenase expression by interacting with PII nitrogen regulatory proteins remains unclear in diazotrophic proteobacteria lacking NifL. Here, we demonstrate that in Rhodopseudomonas palustris grown with ammonium, NifA bound deuridylylated PII proteins to form an inactive NifA-PII complex, thereby inhibiting the expression of nitrogenase. Upon nitrogen limitation, the dissociation of uridylylated PII proteins from NifA resulted in the full restoration of NifA activity, and, simultaneously, uridylylation of the significantly up-regulated PII protein GlnK2 led to the increased expression of NifA in R. palustris. This insight into how NifA interacts with PII proteins and controls nitrogenase expression sets the stage for creating highly efficient diazotrophs, reducing the need for energy-intensive chemical fertilizers and helping to diminish carbon emissions.
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Affiliation(s)
- Yan Zeng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lu Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongqiang Gao
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Lingwei Cui
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengmei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingyue Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yaxin Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - De-Feng Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanning Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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3
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Shomar H, Bokinsky G. Harnessing iron‑sulfur enzymes for synthetic biology. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119718. [PMID: 38574823 DOI: 10.1016/j.bbamcr.2024.119718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/13/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
Reactions catalysed by iron-sulfur (Fe-S) enzymes appear in a variety of biosynthetic pathways that produce valuable natural products. Harnessing these biosynthetic pathways by expression in microbial cell factories grown on an industrial scale would yield enormous economic and environmental benefits. However, Fe-S enzymes often become bottlenecks that limits the productivity of engineered pathways. As a consequence, achieving the production metrics required for industrial application remains a distant goal for Fe-S enzyme-dependent pathways. Here, we identify and review three core challenges in harnessing Fe-S enzyme activity, which all stem from the properties of Fe-S clusters: 1) limited Fe-S cluster supply within the host cell, 2) Fe-S cluster instability, and 3) lack of specialized reducing cofactor proteins often required for Fe-S enzyme activity, such as enzyme-specific flavodoxins and ferredoxins. We highlight successful methods developed for a variety of Fe-S enzymes and electron carriers for overcoming these difficulties. We use heterologous nitrogenase expression as a grand case study demonstrating how each of these challenges can be addressed. We predict that recent breakthroughs in protein structure prediction and design will prove well-suited to addressing each of these challenges. A reliable toolkit for harnessing Fe-S enzymes in engineered metabolic pathways will accelerate the development of industry-ready Fe-S enzyme-dependent biosynthesis pathways.
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Affiliation(s)
- Helena Shomar
- Institut Pasteur, université Paris Cité, Inserm U1284, Diversité moléculaire des microbes (Molecular Diversity of Microbes lab), 75015 Paris, France
| | - Gregory Bokinsky
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
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4
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Wang Y, Jia X, An S, Yin W, Huang J, Jiang X. Nanozyme-Based Regulation of Cellular Metabolism and Their Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2301810. [PMID: 37017586 DOI: 10.1002/adma.202301810] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/29/2023] [Indexed: 06/19/2023]
Abstract
Metabolism is the sum of the enzyme-dependent chemical reactions, which produces energy in catabolic process and synthesizes biomass in anabolic process, exhibiting high similarity in mammalian cell, microbial cell, and plant cell. Consequently, the loss or gain of metabolic enzyme activity greatly affects cellular metabolism. Nanozymes, as emerging enzyme mimics with diverse functions and adjustable catalytic activities, have shown attractive potential for metabolic regulation. Although the basic metabolic tasks are highly similar for the cells from different species, the concrete metabolic pathway varies with the intracellular structure of different species. Here, the basic metabolism in living organisms is described and the similarities and differences in the metabolic pathways among mammalian, microbial, and plant cells and the regulation mechanism are discussed. The recent progress on regulation of cellular metabolism mainly including nutrient uptake and utilization, energy production, and the accompanied redox reactions by different kinds of oxidoreductases and their applications in the field of disease therapy, antimicrobial therapy, and sustainable agriculture is systematically reviewed. Furthermore, the prospects and challenges of nanozymes in regulating cell metabolism are also discussed, which broaden their application scenarios.
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Affiliation(s)
- Yue Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xiaodan Jia
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Shangjie An
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China (USTC), Hefei, Anhui, 230026, China
| | - Wenbo Yin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China (USTC), Hefei, Anhui, 230026, China
| | - Jiahao Huang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China (USTC), Hefei, Anhui, 230026, China
| | - Xiue Jiang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China (USTC), Hefei, Anhui, 230026, China
- Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, China
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5
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Dobrzyńska K, Pérez-González A, Echavarri-Erasun C, Coroian D, Salinero-Lanzarote A, Veldhuizen M, Dean DR, Burén S, Rubio LM. Nitrogenase cofactor biosynthesis using proteins produced in mitochondria of Saccharomyces cerevisiae. mBio 2024; 15:e0308823. [PMID: 38126768 PMCID: PMC10865832 DOI: 10.1128/mbio.03088-23] [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: 11/14/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
Biological nitrogen fixation, the conversion of inert N2 to metabolically tractable NH3, is only performed by certain microorganisms called diazotrophs and is catalyzed by the nitrogenases. A [7Fe-9S-C-Mo-R-homocitrate]-cofactor, designated FeMo-co, provides the catalytic site for N2 reduction in the Mo-dependent nitrogenase. Thus, achieving FeMo-co formation in model eukaryotic organisms, such as Saccharomyces cerevisiae, represents an important milestone toward endowing them with a capacity for Mo-dependent biological nitrogen fixation. A central player in FeMo-co assembly is the scaffold protein NifEN upon which processing of NifB-co, an [8Fe-9S-C] precursor produced by NifB, occurs. Prior work established that NifB-co can be produced in S. cerevisiae mitochondria. In the present work, a library of nifEN genes from diverse diazotrophs was expressed in S. cerevisiae, targeted to mitochondria, and surveyed for their ability to produce soluble NifEN protein complexes. Many such NifEN variants supported FeMo-co formation when heterologously produced in the diazotroph A. vinelandii. However, only three of them accumulated in soluble forms in mitochondria of aerobically cultured S. cerevisiae. Of these, two variants were active in the in vitro FeMo-co synthesis assay. NifEN, NifB, and NifH proteins from different species, all of them produced in and purified from S. cerevisiae mitochondria, were combined to establish successful FeMo-co biosynthetic pathways. These findings demonstrate that combining diverse interspecies nitrogenase FeMo-co assembly components could be an effective and, perhaps, the only approach to achieve and optimize nitrogen fixation in a eukaryotic organism.IMPORTANCEBiological nitrogen fixation, the conversion of inert N2 to metabolically usable NH3, is a process exclusive to diazotrophic microorganisms and relies on the activity of nitrogenases. The assembly of the nitrogenase [7Fe-9S-C-Mo-R-homocitrate]-cofactor (FeMo-co) in a eukaryotic cell is a pivotal milestone that will pave the way to engineer cereals with nitrogen fixing capabilities and therefore independent of nitrogen fertilizers. In this study, we identified NifEN protein complexes that were functional in the model eukaryotic organism Saccharomyces cerevisiae. NifEN is an essential component of the FeMo-co biosynthesis pathway. Furthermore, the FeMo-co biosynthetic pathway was recapitulated in vitro using only proteins expressed in S. cerevisiae. FeMo-co biosynthesis was achieved by combining nitrogenase FeMo-co assembly components from different species, a promising strategy to engineer nitrogen fixation in eukaryotic organisms.
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Affiliation(s)
- Katarzyna Dobrzyńska
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | | | - Carlos Echavarri-Erasun
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Diana Coroian
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
| | - Alvaro Salinero-Lanzarote
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
| | - Marcel Veldhuizen
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
| | - Dennis R. Dean
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Stefan Burén
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Luis M. Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
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6
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Wang Y, Li P, Zhu Y, Shang Y, Wu Z, Tao Y, Wang H, Li D, Zhang C. Transcriptome Profiling Reveals the Gene Network Responding to Low Nitrogen Stress in Wheat. PLANTS (BASEL, SWITZERLAND) 2024; 13:371. [PMID: 38337903 PMCID: PMC10856819 DOI: 10.3390/plants13030371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024]
Abstract
As one of the essential nutrients for plants, nitrogen (N) has a major impact on the yield and quality of wheat worldwide. Due to chemical fertilizer pollution, it has become increasingly important to improve crop yield by increasing N use efficiency (NUE). Therefore, understanding the response mechanisms to low N (LN) stress is essential for the regulation of NUE in wheat. In this study, LN stress significantly accelerated wheat root growth, but inhibited shoot growth. Further transcriptome analysis showed that 8468 differentially expressed genes (DEGs) responded to LN stress. The roots and shoots displayed opposite response patterns, of which the majority of DEGs in roots were up-regulated (66.15%; 2955/4467), but the majority of DEGs in shoots were down-regulated (71.62%; 3274/4565). GO and KEGG analyses showed that nitrate reductase activity, nitrate assimilation, and N metabolism were significantly enriched in both the roots and shoots. Transcription factor (TF) and protein kinase analysis showed that genes such as MYB-related (38/38 genes) may function in a tissue-specific manner to respond to LN stress. Moreover, 20 out of 107 N signaling homologous genes were differentially expressed in wheat. A total of 47 transcriptome datasets were used for weighted gene co-expression network analysis (17,840 genes), and five TFs were identified as the potential hub regulatory genes involved in the response to LN stress in wheat. Our findings provide insight into the functional mechanisms in response to LN stress and five candidate regulatory genes in wheat. These results will provide a basis for further research on promoting NUE in wheat.
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Affiliation(s)
- Yiwei Wang
- College of Computer Science and Technology, Taiyuan University of Technology, Taiyuan 030024, China;
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (P.L.); (Y.Z.); (Y.S.); (Z.W.); (Y.T.); (H.W.)
| | - Pengfeng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (P.L.); (Y.Z.); (Y.S.); (Z.W.); (Y.T.); (H.W.)
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Yiwang Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (P.L.); (Y.Z.); (Y.S.); (Z.W.); (Y.T.); (H.W.)
| | - Yuping Shang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (P.L.); (Y.Z.); (Y.S.); (Z.W.); (Y.T.); (H.W.)
- College of Agronomy, Shanxi Agricultural University, Jinzhong 030801, China
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (P.L.); (Y.Z.); (Y.S.); (Z.W.); (Y.T.); (H.W.)
| | - Yongfu Tao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (P.L.); (Y.Z.); (Y.S.); (Z.W.); (Y.T.); (H.W.)
| | - Hongru Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (P.L.); (Y.Z.); (Y.S.); (Z.W.); (Y.T.); (H.W.)
| | - Dongxi Li
- College of Computer Science and Technology, Taiyuan University of Technology, Taiyuan 030024, China;
| | - Cuijun Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (P.L.); (Y.Z.); (Y.S.); (Z.W.); (Y.T.); (H.W.)
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7
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Moulin SLY, Frail S, Braukmann T, Doenier J, Steele-Ogus M, Marks JC, Mills MM, Yeh E. The endosymbiont of Epithemia clementina is specialized for nitrogen fixation within a photosynthetic eukaryote. ISME COMMUNICATIONS 2024; 4:ycae055. [PMID: 38707843 PMCID: PMC11070190 DOI: 10.1093/ismeco/ycae055] [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: 02/09/2024] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 05/07/2024]
Abstract
Epithemia spp. diatoms contain obligate, nitrogen-fixing endosymbionts, or diazoplasts, derived from cyanobacteria. These algae are a rare example of photosynthetic eukaryotes that have successfully coupled oxygenic photosynthesis with oxygen-sensitive nitrogenase activity. Here, we report a newly-isolated species, E. clementina, as a model to investigate endosymbiotic acquisition of nitrogen fixation. We demonstrate that the diazoplast, which has lost photosynthesis, provides fixed nitrogen to the diatom host in exchange for fixed carbon. To identify the metabolic changes associated with this endosymbiotic specialization, we compared the Epithemia diazoplast with its close, free-living cyanobacterial relative, Crocosphaera subtropica. Unlike C. subtropica, in which nitrogenase activity is temporally separated from photosynthesis, we show that nitrogenase activity in the diazoplast is continuous through the day (concurrent with host photosynthesis) and night. Host and diazoplast metabolism are tightly coupled to support nitrogenase activity: Inhibition of photosynthesis abolishes daytime nitrogenase activity, while nighttime nitrogenase activity no longer requires cyanobacterial glycogen storage pathways. Instead, import of host-derived carbohydrates supports nitrogenase activity throughout the day-night cycle. Carbohydrate metabolism is streamlined in the diazoplast compared to C. subtropica with retention of the oxidative pentose phosphate pathway and oxidative phosphorylation. Similar to heterocysts, these pathways may be optimized to support nitrogenase activity, providing reducing equivalents and ATP and consuming oxygen. Our results demonstrate that the diazoplast is specialized for endosymbiotic nitrogen fixation. Altogether, we establish a new model for studying endosymbiosis, perform a functional characterization of this diazotroph endosymbiosis, and identify metabolic adaptations for endosymbiotic acquisition of a critical biological function.
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Affiliation(s)
- Solène L Y Moulin
- Department of Pathology, Stanford School of Medicine, Stanford, CA 94305, United States
| | - Sarah Frail
- Department of Biochemistry, Stanford School of Medicine, Stanford, CA 94305, United States
| | - Thomas Braukmann
- Department of Pathology, Stanford School of Medicine, Stanford, CA 94305, United States
- Department of Biochemistry, Stanford School of Medicine, Stanford, CA 94305, United States
| | - Jon Doenier
- Department of Biochemistry, Stanford School of Medicine, Stanford, CA 94305, United States
| | - Melissa Steele-Ogus
- Department of Pathology, Stanford School of Medicine, Stanford, CA 94305, United States
| | - Jane C Marks
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AR 86011, United States
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011, United States
| | - Matthew M Mills
- Department of Earth System Science, Stanford Doerr School of Sustainability, Stanford, CA 94305, United States
| | - Ellen Yeh
- Department of Pathology, Stanford School of Medicine, Stanford, CA 94305, United States
- Department of Microbiology & Immunology, Stanford School of Medicine, Stanford, CA 94305, United States
- Chan Zuckerberg Biohub, San Francisco, CA 94158, United States
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8
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Gao J, Feng P, Zhang J, Dong C, Wang Z, Chen M, Yu Z, Zhao B, Hou X, Wang H, Wu Z, Jemim RS, Yu H, Sun D, Jing P, Chen J, Song W, Zhang X, Zhou Z, Wu J. Enhancing maize's nitrogen-fixing potential through ZmSBT3, a gene suppressing mucilage secretion. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2645-2659. [PMID: 37929676 DOI: 10.1111/jipb.13581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 11/04/2023] [Indexed: 11/07/2023]
Abstract
Maize (Zea mays) requires substantial amounts of nitrogen, posing a challenge for its cultivation. Recent work discovered that some ancient Mexican maize landraces harbored diazotrophic bacteria in mucilage secreted by their aerial roots. To see if this trait is retained in modern maize, we conducted a field study of aerial root mucilage (ARM) in 258 inbred lines. We observed that ARM secretion is common in modern maize, but the amount significantly varies, and only a few lines have retained the nitrogen-fixing traits found in ancient landraces. The mucilage of the high-ARM inbred line HN5-724 had high nitrogen-fixing enzyme activity and abundant diazotrophic bacteria. Our genome-wide association study identified 17 candidate genes associated with ARM across three environments. Knockouts of one candidate gene, the subtilase family gene ZmSBT3, confirmed that it negatively regulates ARM secretion. Notably, the ZmSBT3 knockout lines had increased biomass and total nitrogen accumulation under nitrogen-free culture conditions. High ARM was associated with three ZmSBT3 haplotypes that were gradually lost during maize domestication, being retained in only a few modern inbred lines such as HN5-724. In summary, our results identify ZmSBT3 as a potential tool for enhancing ARM, and thus nitrogen fixation, in maize.
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Affiliation(s)
- Jingyang Gao
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Peijiang Feng
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jingli Zhang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Chaopei Dong
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhao Wang
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Mingxiang Chen
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhongliang Yu
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Bowen Zhao
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xin Hou
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Huijuan Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhaokun Wu
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Razia Sultana Jemim
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Haidong Yu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Doudou Sun
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Pei Jing
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jiafa Chen
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Weibin Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, 56237, Mexico
| | - Zijian Zhou
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jianyu Wu
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
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9
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Tang Y, Qin D, Tian Z, Chen W, Ma Y, Wang J, Yang J, Yan D, Dixon R, Wang YP. Diurnal switches in diazotrophic lifestyle increase nitrogen contribution to cereals. Nat Commun 2023; 14:7516. [PMID: 37980355 PMCID: PMC10657418 DOI: 10.1038/s41467-023-43370-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/07/2023] [Indexed: 11/20/2023] Open
Abstract
Uncoupling of biological nitrogen fixation from ammonia assimilation is a prerequisite step for engineering ammonia excretion and improvement of plant-associative nitrogen fixation. In this study, we have identified an amino acid substitution in glutamine synthetase, which provides temperature sensitive biosynthesis of glutamine, the intracellular metabolic signal of the nitrogen status. As a consequence, negative feedback regulation of genes and enzymes subject to nitrogen regulation, including nitrogenase is thermally controlled, enabling ammonia excretion in engineered Escherichia coli and the plant-associated diazotroph Klebsiella oxytoca at 23 °C, but not at 30 °C. We demonstrate that this temperature profile can be exploited to provide diurnal oscillation of ammonia excretion when variant bacteria are used to inoculate cereal crops. We provide evidence that diurnal temperature variation improves nitrogen donation to the plant because the inoculant bacteria have the ability to recover and proliferate at higher temperatures during the daytime.
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Affiliation(s)
- Yuqian Tang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Debin Qin
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Zhexian Tian
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Wenxi Chen
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Yuanxi Ma
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Jilong Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Jianguo Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Dalai Yan
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK.
| | - Yi-Ping Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China.
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10
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Libourel C, Keller J, Brichet L, Cazalé AC, Carrère S, Vernié T, Couzigou JM, Callot C, Dufau I, Cauet S, Marande W, Bulach T, Suin A, Masson-Boivin C, Remigi P, Delaux PM, Capela D. Comparative phylotranscriptomics reveals ancestral and derived root nodule symbiosis programmes. NATURE PLANTS 2023:10.1038/s41477-023-01441-w. [PMID: 37322127 PMCID: PMC10356618 DOI: 10.1038/s41477-023-01441-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023]
Abstract
Symbiotic interactions such as the nitrogen-fixing root nodule symbiosis (RNS) have structured ecosystems during the evolution of life. Here we aimed at reconstructing ancestral and intermediate steps that shaped RNS observed in extant flowering plants. We compared the symbiotic transcriptomic responses of nine host plants, including the mimosoid legume Mimosa pudica for which we assembled a chromosome-level genome. We reconstructed the ancestral RNS transcriptome composed of most known symbiotic genes together with hundreds of novel candidates. Cross-referencing with transcriptomic data in response to experimentally evolved bacterial strains with gradual symbiotic proficiencies, we found the response to bacterial signals, nodule infection, nodule organogenesis and nitrogen fixation to be ancestral. By contrast, the release of symbiosomes was associated with recently evolved genes encoding small proteins in each lineage. We demonstrate that the symbiotic response was mostly in place in the most recent common ancestor of the RNS-forming species more than 90 million years ago.
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Affiliation(s)
- Cyril Libourel
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Lukas Brichet
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | | | - Sébastien Carrère
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Tatiana Vernié
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Jean-Malo Couzigou
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Caroline Callot
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - Isabelle Dufau
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - Stéphane Cauet
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - William Marande
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - Tabatha Bulach
- INRAE, US1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Amandine Suin
- INRAE, US1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | | | - Philippe Remigi
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France.
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France.
| | - Delphine Capela
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France.
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11
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Pang Z, Mao X, Zhou S, Yu S, Liu G, Lu C, Wan J, Hu L, Xu P. Microbiota-mediated nitrogen fixation and microhabitat homeostasis in aerial root-mucilage. MICROBIOME 2023; 11:85. [PMID: 37085934 PMCID: PMC10120241 DOI: 10.1186/s40168-023-01525-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Plants sustain intimate relationships with diverse microbes. It is well-recognized that these plant-associated microbiota shape individual performance and fitness of host plants, but much remains to be explored regarding how they exert their function and maintain their homeostasis. RESULTS Here, using pink lady (Heterotis rotundifolia) as a study plant, we investigated the phenomenon of microbiota-mediated nitrogen fixation and elucidated how this process is steadily maintained in the root mucilage microhabitat. Metabolite and microbiota profiling showed that the aerial root mucilage is enriched in carbohydrates and diazotrophic bacteria. Nitrogen isotope-labeling experiments, 15N natural abundance, and gene expression analysis indicated that the aerial root-mucilage microbiota could fix atmospheric nitrogen to support plant growth. While the aerial root mucilage is a hotspot of nutrients, we did not observe high abundance of other environmental and pathogenic microbes inside. We further identified a fungus isolate in mucilage that has shown broad-spectrum antimicrobial activities, but solely allows the growth of diazotrophic bacteria. This "friendly" fungus may be the key driver to maintain nitrogen fixation function in the mucilage microhabitat. Video Abstract CONCLUSION: The discovery of new biological function and mucilage-habitat friendly fungi provides insights into microbial homeostasis maintenance of microenvironmental function and rhizosphere ecology.
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Affiliation(s)
- Zhiqiang Pang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xinyu Mao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shaoqun Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Sheng Yu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Guizhou Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Chengkai Lu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Jinpeng Wan
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Lingfei Hu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Peng Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
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12
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CNN_FunBar: Advanced Learning Technique for Fungi ITS Region Classification. Genes (Basel) 2023; 14:genes14030634. [PMID: 36980906 PMCID: PMC10048311 DOI: 10.3390/genes14030634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/28/2022] [Accepted: 01/09/2023] [Indexed: 03/06/2023] Open
Abstract
Fungal species identification from metagenomic data is a highly challenging task. Internal Transcribed Spacer (ITS) region is a potential DNA marker for fungi taxonomy prediction. Computational approaches, especially deep learning algorithms, are highly efficient for better pattern recognition and classification of large datasets compared to in silico techniques such as BLAST and machine learning methods. Here in this study, we present CNN_FunBar, a convolutional neural network-based approach for the classification of fungi ITS sequences from UNITE+INSDC reference datasets. Effects of convolution kernel size, filter numbers, k-mer size, degree of diversity and category-wise frequency of ITS sequences on classification performances of CNN models have been assessed at all taxonomic levels (species, genus, family, order, class and phylum). It is observed that CNN models can produce >93% average accuracy for classifying ITS sequences from balanced datasets with 500 sequences per category and 6-mer frequency features at all levels. The comparative study has revealed that CNN_FunBar can outperform machine learning-based algorithms (SVM, KNN, Naïve-Bayes and Random Forest) as well as existing fungal taxonomy prediction software (funbarRF, Mothur, RDP Classifier and SINTAX). The present study will be helpful for fungal taxonomy classification using large metagenomic datasets.
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13
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Lace B, Su C, Invernot Perez D, Rodriguez-Franco M, Vernié T, Batzenschlager M, Egli S, Liu CW, Ott T. RPG acts as a central determinant for infectosome formation and cellular polarization during intracellular rhizobial infections. eLife 2023; 12:80741. [PMID: 36856086 PMCID: PMC9991063 DOI: 10.7554/elife.80741] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 02/21/2023] [Indexed: 03/02/2023] Open
Abstract
Host-controlled intracellular accommodation of nitrogen-fixing bacteria is essential for the establishment of a functional Root Nodule Symbiosis (RNS). In many host plants, this occurs via transcellular tubular structures (infection threads - ITs) that extend across cell layers via polar tip-growth. Comparative phylogenomic studies have identified RPG (RHIZOBIUM-DIRECTED POLAR GROWTH) among the critical genetic determinants for bacterial infection. In Medicago truncatula, RPG is required for effective IT progression within root hairs but the cellular and molecular function of the encoded protein remains elusive. Here, we show that RPG resides in the protein complex formed by the core endosymbiotic components VAPYRIN (VPY) and LUMPY INFECTION (LIN) required for IT polar growth, co-localizes with both VPY and LIN in IT tip- and perinuclear-associated puncta of M. truncatula root hairs undergoing infection and is necessary for VPY recruitment into these structures. Fluorescence Lifetime Imaging Microscopy (FLIM) of phosphoinositide species during bacterial infection revealed that functional RPG is required to sustain strong membrane polarization at the advancing tip of the IT. In addition, loss of RPG functionality alters the cytoskeleton-mediated connectivity between the IT tip and the nucleus and affects the polar secretion of the cell wall modifying enzyme NODULE PECTATE LYASE (NPL). Our results integrate RPG into a core host machinery required to support symbiont accommodation, suggesting that its occurrence in plant host genomes is essential to co-opt a multimeric protein module committed to endosymbiosis to sustain IT-mediated bacterial infection.
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Affiliation(s)
- Beatrice Lace
- University of Freiburg, Faculty of BiologyFreiburgGermany
| | - Chao Su
- University of Freiburg, Faculty of BiologyFreiburgGermany
| | | | | | - Tatiana Vernié
- LRSV, Université de Toulouse, CNRS, UPS, INP ToulouseCastanet-TolosanFrance
| | | | - Sabrina Egli
- University of Freiburg, Faculty of BiologyFreiburgGermany
| | - Cheng-Wu Liu
- School of Life Sciences, Division of Life Sciences and Medicine, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of ChinaHefeiChina
| | - Thomas Ott
- University of Freiburg, Faculty of BiologyFreiburgGermany
- CIBSS – Centre of Integrative Biological Signalling Studies, University of FreiburgFreiburgGermany
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14
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Liu Y, Hu B, Chu C. Toward improving nitrogen use efficiency in rice: Utilization, coordination, and availability. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102327. [PMID: 36525788 DOI: 10.1016/j.pbi.2022.102327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 11/13/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Nitrogen (N) fertilizer drives crop productivity and underlies intensive agriculture, but overuse of fertilizers also causes detrimental effects to ecosystem. To cope with this challenge while meeting the ever-growing demand for food, it is critical and urgent to improve nitrogen use efficiency (NUE) of crops. To date, numerous efforts have been made in developing strategies for NUE improvement with different disciplines. Given the intricate and interconnected route of N for delivering its effect, it is necessary to comprehensively understand various procedures and their interplays in determining NUE. In this review, we expand the scope of NUE improvement, not only the N utilization by plants, but also the N coordination with other resources as well as the N availability in the soil, which represent the major dimensions in manipulating NUE. Moreover, both agronomic practices and genetic improvement in facilitating NUE are also included and discussed. Lastly, we provide our perspective in improving the NUE in the future, particularly highlighting the integration of various agronomic and genetic approaches for NUE improvement underlying the sustainable agriculture.
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Affiliation(s)
- Yongqiang Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Bin Hu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Agriculture, South China Agricultural University, Guangzhou, China; Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China.
| | - Chengcai Chu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Agriculture, South China Agricultural University, Guangzhou, China; Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China.
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15
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Borzouei A, Karimzadeh H, Müller C, Sanz-Cobena A, Zaman M, Kim DG, Ding W. Relationship between nitrapyrin and varying nitrogen application rates with nitrous oxide emissions and nitrogen use efficiency in a maize filed. Sci Rep 2022; 12:18424. [PMID: 36319739 PMCID: PMC9626639 DOI: 10.1038/s41598-022-23030-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 10/25/2022] [Indexed: 11/05/2022] Open
Abstract
Reducing nitrogen losses can be accomplished by mixing fertilizers with nitrification inhibitors (NI). In some agricultural systems, increasing soil N supply capacity by the use of NI could lead to improved N use efficiency (NUE) and increased crop yields. This study examined the effect of different N rates and NI in maize in the north of Iran. The maize was fertilized with urea at three levels (69, 115 and 161 kg N.ha-1) alone or with nitrapyrin as NI. Increasing the N application rate resulted in a considerable rise in growing-season N2O emissions. When nitrapyrin was used, N2O emissions were dramatically reduced. NI treatment reduced N2O emissions in the growth season by 88%, 88%, and 69% in 69, 115, and 161 kg of N.ha-1, respectively. NI treatment reduced yield-scaled N2O emissions; the lowest quantity of yield-scaled N2O was found in 69 N + NI (0.09 g N2O-N kg-1 N uptake). Additionally, grain yield increased by 19%, 31% and 18.4% after applying NI to 69 N, 115 N, and N69, N115 and N161. Results showed that 115 N + NI and N69 treatments showed the highest (65%) and lowest (29%) NUEs, respectively. Finally, our findings show that NI can reduce N2O emissions while increasing NUE and yield, but that the application method and rate of nitrapyrin application need to be improved in order to maximize its mitigation potential.
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Affiliation(s)
- Azam Borzouei
- grid.459846.20000 0004 0611 7306Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), P. O. Box: 31485-498, Karaj, Iran
| | - Hedayat Karimzadeh
- grid.459846.20000 0004 0611 7306Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), P. O. Box: 31485-498, Karaj, Iran
| | - Christoph Müller
- grid.8664.c0000 0001 2165 8627Justus Liebig University Giessen, Giessen, Germany ,grid.7886.10000 0001 0768 2743University College Dublin, Belfield, Ireland
| | - Alberto Sanz-Cobena
- grid.5690.a0000 0001 2151 2978ETSI Agrónomos, Technical University of Madrid, Ciudad Universitaria, 28040 Madrid, Spain
| | - Mohammad Zaman
- Soil and Water Management and Crop Nutrition, Joint FAO, IAEA Division of Nuclear Techniques in Food and Agriculture, P.O. Box 100, 1400 Vienna, Austria
| | - Dong-Gill Kim
- grid.192268.60000 0000 8953 2273Wondo Genet College of Forestry and Natural Resources, Hawassa University, PO Box 128, Shashemene, Ethiopia
| | - Weixin Ding
- grid.9227.e0000000119573309Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 China
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16
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He W, Burén S, Baysal C, Jiang X, Capell T, Christou P, Rubio LM. Nitrogenase Cofactor Maturase NifB Isolated from Transgenic Rice is Active in FeMo-co Synthesis. ACS Synth Biol 2022; 11:3028-3036. [PMID: 35998307 PMCID: PMC9486962 DOI: 10.1021/acssynbio.2c00194] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The engineering of nitrogen fixation in plants requires assembly of an active prokaryotic nitrogenase complex, which is yet to be achieved. Nitrogenase biogenesis relies on NifB, which catalyzes the formation of the [8Fe-9S-C] metal cluster NifB-co. This is the first committed step in the biosynthesis of the iron-molybdenum cofactor (FeMo-co) found at the nitrogenase active site. The production of NifB in plants is challenging because this protein is often insoluble in eukaryotic cells, and its [Fe-S] clusters are extremely unstable and sensitive to O2. As a first step to address this challenge, we generated transgenic rice plants expressing NifB from the Archaea Methanocaldococcus infernus and Methanothermobacter thermautotrophicus. The recombinant proteins were targeted to the mitochondria to limit exposure to O2 and to have access to essential [4Fe-4S] clusters required for NifB-co biosynthesis. M. infernus and M. thermautotrophicus NifB accumulated as soluble proteins in planta, and the purified proteins were functional in the in vitro FeMo-co synthesis assay. We thus report NifB protein expression and purification from an engineered staple crop, representing a first step in the biosynthesis of a functional NifDK complex, as required for independent biological nitrogen fixation in cereals.
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Affiliation(s)
- Wenshu He
- Department
of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Av. Alcalde Rovira Roure, 191, 25198 Lleida, Spain
| | - Stefan Burén
- Centro
de Biotecnología y Genómica de Plantas, Universidad
Politécnica de Madrid (UPM), Instituto
Nacional de Investigación y Tecnología Agraria y Alimentaria
(INIA), Campus Montegancedo
UPM, Pozuelo de Alarcón, 28223 , Madrid, Spain,Departamento
de Biotecnología-Biología Vegetal, Escuela Técnica
Superior de Ingeniería Agronómica, Alimentaria y de
Biosistemas, Universidad Politécnica
de Madrid, 28040 Madrid, Spain
| | - Can Baysal
- Department
of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Av. Alcalde Rovira Roure, 191, 25198 Lleida, Spain
| | - Xi Jiang
- Centro
de Biotecnología y Genómica de Plantas, Universidad
Politécnica de Madrid (UPM), Instituto
Nacional de Investigación y Tecnología Agraria y Alimentaria
(INIA), Campus Montegancedo
UPM, Pozuelo de Alarcón, 28223 , Madrid, Spain,Departamento
de Biotecnología-Biología Vegetal, Escuela Técnica
Superior de Ingeniería Agronómica, Alimentaria y de
Biosistemas, Universidad Politécnica
de Madrid, 28040 Madrid, Spain
| | - Teresa Capell
- Department
of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Av. Alcalde Rovira Roure, 191, 25198 Lleida, Spain
| | - Paul Christou
- Department
of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Av. Alcalde Rovira Roure, 191, 25198 Lleida, Spain,ICREA,
Catalan Institute for Research and Advanced Studies, Passeig Lluís Companys 23, 08010 Barcelona, Spain,
| | - Luis M. Rubio
- Centro
de Biotecnología y Genómica de Plantas, Universidad
Politécnica de Madrid (UPM), Instituto
Nacional de Investigación y Tecnología Agraria y Alimentaria
(INIA), Campus Montegancedo
UPM, Pozuelo de Alarcón, 28223 , Madrid, Spain,Departamento
de Biotecnología-Biología Vegetal, Escuela Técnica
Superior de Ingeniería Agronómica, Alimentaria y de
Biosistemas, Universidad Politécnica
de Madrid, 28040 Madrid, Spain,
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17
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Usowicz B, Lipiec J. Assessment of the spatial distribution of cereal yields on sandy soil related to the application of soil-improving cropping systems (SICS). THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154791. [PMID: 35351506 DOI: 10.1016/j.scitotenv.2022.154791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/10/2022] [Accepted: 03/20/2022] [Indexed: 06/14/2023]
Abstract
Sandy soils occur in different regions throughout the world. In spite of poor quality, they are being used in crop production. The use of sandy soils for crop production requires soil-improving cropping systems (SICS). The aim of this study was to determine the spatial relationships of soil properties including intrinsic texture and relatively stable organic carbon, pH(KCl), cation exchange capacity, and cereal yield (grain and straw yields and plant height) in response to random application of SICS using geostatistics and maps. A 4-year field experiment included the following crop rotation: oat, wheat, wheat and oat and SICS: the control (C) and SICS: liming (L), leguminous catch crops for green manure (LU), farmyard manure (M), and farmyard manure+liming+leguminous catch crops together (M + L + LU). The use of the soil properties as auxiliary variables in the cross-semivariograms improved the prediction of the spatial distribution of the cereal yield, compared to the semi-variograms. The cokriging maps showed positional similarity between the cereal yield, the application of some SICS, and soil textural fractions. The application of M and M + L + LU providing the greatest amounts of organic matter and nitrogen was an effective measure in increasing cereal yields in sub-areas with low contents of sand, compared with the C, L, and LU variants. This increase in the yield was most pronounced in the last study year with an adequate rainfall amount and distribution during the growing season. The similar spatial effects of the SICS M and M + L + LU suggest that the application of M can be in part replaced by incorporation of atmospheric nitrogen-fixing legume catch crops and liming with maintenance of the same productivity and nitrogen supply. The spatial interrelations of the yield response, soil texture, and SICS type will help in selection of the most effective SICS in terms of cereal productivity, depending on local soil conditions.
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Affiliation(s)
- Boguslaw Usowicz
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland; Faculty of Civil Engineering and Environmental Sciences, Bialystok University of Technology, Wiejska 45 E, 15-351 Białystok, Poland.
| | - Jerzy Lipiec
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland
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18
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Jiang X, Coroian D, Barahona E, Echavarri-Erasun C, Castellanos-Rueda R, Eseverri Á, Aznar-Moreno JA, Burén S, Rubio LM. Functional Nitrogenase Cofactor Maturase NifB in Mitochondria and Chloroplasts of Nicotiana benthamiana. mBio 2022; 13:e0026822. [PMID: 35695456 PMCID: PMC9239050 DOI: 10.1128/mbio.00268-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/16/2022] [Indexed: 11/20/2022] Open
Abstract
Engineering plants to synthesize nitrogenase and assimilate atmospheric N2 will reduce crop dependency on industrial N fertilizers. This technology can be achieved by expressing prokaryotic nitrogen fixation gene products for the assembly of a functional nitrogenase in plants. NifB is a critical nitrogenase component since it catalyzes the first committed step in the biosynthesis of all types of nitrogenase active-site cofactors. Here, we used a library of 30 distinct nifB sequences originating from different phyla and ecological niches to restore diazotrophic growth of an Azotobacter vinelandii nifB mutant. Twenty of these variants rescued the nifB mutant phenotype despite their phylogenetic distance to A. vinelandii. Because multiple protein interactions are required in the iron-molybdenum cofactor (FeMo-co) biosynthetic pathway, the maturation of nitrogenase in a heterologous host can be divided in independent modules containing interacting proteins that function together to produce a specific intermediate. Therefore, nifB functional modules composed of a nifB variant, together with the A. vinelandii NifS and NifU proteins (for biosynthesis of NifB [Fe4S4] clusters) and the FdxN ferredoxin (for NifB function), were expressed in Nicotiana benthamiana chloroplasts and mitochondria. Three archaeal NifB proteins accumulated at high levels in soluble fractions of chloroplasts (Methanosarcina acetivorans and Methanocaldococcus infernus) or mitochondria (M. infernus and Methanothermobacter thermautotrophicus). These NifB proteins were shown to accept [Fe4S4] clusters from NifU and were functional in FeMo-co synthesis in vitro. The accumulation of significant levels of soluble and functional NifB proteins in chloroplasts and mitochondria is critical to engineering biological nitrogen fixation in plants. IMPORTANCE Biological nitrogen fixation is the conversion of inert atmospheric dinitrogen gas into nitrogen-reactive ammonia, a reaction catalyzed by the nitrogenase enzyme of diazotrophic bacteria and archaea. Because plants cannot fix their own nitrogen, introducing functional nitrogenase in cereals and other crop plants would reduce our strong dependency on N fertilizers. NifB is required for the biosynthesis of the active site cofactors of all nitrogenases, which arguably makes it the most important protein in global nitrogen fixation. NifB functionality is therefore a requisite to engineer a plant nitrogenase. The expression of nifB genes from a wide range of prokaryotes into the model diazotroph Azotobacter vinelandii shows a surprising level of genetic complementation suggestive of plasticity in the nitrogenase biosynthetic pathway. In addition, we obtained NifB proteins from both mitochondria and chloroplasts of tobacco that are functional in vitro after reconstitution by providing [Fe4S4] clusters from NifU, paving the way to nitrogenase cofactor biosynthesis in plants.
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Affiliation(s)
- Xi Jiang
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Diana Coroian
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain
| | - Emma Barahona
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain
| | - Carlos Echavarri-Erasun
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Rocío Castellanos-Rueda
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain
| | - Álvaro Eseverri
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain
| | - Jose A. Aznar-Moreno
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain
| | - Stefan Burén
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Luis M. Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
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19
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Oburger E, Schmidt H, Staudinger C. Harnessing belowground processes for sustainable intensification of agricultural systems. PLANT AND SOIL 2022; 478:177-209. [PMID: 36277079 PMCID: PMC9579094 DOI: 10.1007/s11104-022-05508-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/18/2022] [Indexed: 06/16/2023]
Abstract
Increasing food demand coupled with climate change pose a great challenge to agricultural systems. In this review we summarize recent advances in our knowledge of how plants, together with their associated microbiota, shape rhizosphere processes. We address (molecular) mechanisms operating at the plant-microbe-soil interface and aim to link this knowledge with actual and potential avenues for intensifying agricultural systems, while at the same time reducing irrigation water, fertilizer inputs and pesticide use. Combining in-depth knowledge about above and belowground plant traits will not only significantly advance our mechanistic understanding of involved processes but also allow for more informed decisions regarding agricultural practices and plant breeding. Including belowground plant-soil-microbe interactions in our breeding efforts will help to select crops resilient to abiotic and biotic environmental stresses and ultimately enable us to produce sufficient food in a more sustainable agriculture in the upcoming decades.
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Affiliation(s)
- Eva Oburger
- Department of Forest and Soil Science, Institute of Soil Research, University of Natural Resources and Life Sciences, Konrad Lorenzstrasse 24, 3430 Tulln an der Donau, Austria
| | - Hannes Schmidt
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Christiana Staudinger
- Department of Forest and Soil Science, Institute of Soil Research, University of Natural Resources and Life Sciences, Konrad Lorenzstrasse 24, 3430 Tulln an der Donau, Austria
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-7-1, Higashi-Hiroshima, Japan
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20
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Abstract
Inoculation of cereals with diazotrophic (N2-fixing) bacteria offers a sustainable alternative to the application of nitrogen fertilizers in agriculture. While natural diazotrophs have evolved multilayered regulatory mechanisms that couple N2 fixation with assimilation of the product NH3 and prevent release to plants, genetic modifications can permit excess production and excretion of NH3. However, a lack of stringent host-specificity for root colonization by the bacteria would allow growth promotion of target and nontarget plants species alike. Here, we exploit synthetic transkingdom signaling to establish plant host-specific control of the N2-fixation catalyst nitrogenase in Azorhizobium caulinodans occupying barley roots. This work demonstrates how partner-specific interactions can be established to avoid potential growth promotion of nontarget plants. Engineering N2-fixing symbioses between cereals and diazotrophic bacteria represents a promising strategy to sustainably deliver biologically fixed nitrogen (N) in agriculture. We previously developed novel transkingdom signaling between plants and bacteria, through plant production of the bacterial signal rhizopine, allowing control of bacterial gene expression in association with the plant. Here, we have developed both a homozygous rhizopine producing (RhiP) barley line and a hybrid rhizopine uptake system that conveys upon our model bacterium Azorhizobium caulinodans ORS571 (Ac) 103-fold improved sensitivity for rhizopine perception. Using this improved genetic circuitry, we established tight rhizopine-dependent transcriptional control of the nitrogenase master regulator nifA and the N metabolism σ-factor rpoN, which drove nitrogenase expression and activity in vitro and in situ by bacteria colonizing RhiP barley roots. Although in situ nitrogenase activity was suboptimally effective relative to the wild-type strain, activation was specific to RhiP barley and was not observed on the roots of wild-type plants. This work represents a key milestone toward the development of a synthetic plant-controlled symbiosis in which the bacteria fix N2 only when in contact with the desired host plant and are prevented from interaction with nontarget plant species.
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21
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Battenberg K, Hayashi M. Evolution of root nodule symbiosis: Focusing on the transcriptional regulation from the genomic point of view. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2022; 39:79-83. [PMID: 35800960 PMCID: PMC9200091 DOI: 10.5511/plantbiotechnology.22.0127a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/27/2022] [Indexed: 05/04/2023]
Abstract
Since molecular phylogenetics recognized root nodule symbiosis (RNS) of all lineages as potentially homologous, scientists have tried to understand the "when" and the "how" of RNS evolution. Initial progress was made on understanding the timing of RNS evolution, facilitating our progress on understanding the underlying genomic changes leading to RNS. Here, we will first cover the different hypotheses on the timings of gains/losses of RNS and show how this has helped us understand how RNS has evolved. Finally, we will discuss how our improved understanding of the genetic changes that led to RNS is now helping us refine our understanding on when RNS has evolved.
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Affiliation(s)
- Kai Battenberg
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Makoto Hayashi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- E-mail: Tel: +81-45-503-9493 Fax: +81-45-503-9492
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22
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Wen A, Havens KL, Bloch SE, Shah N, Higgins DA, Davis-Richardson AG, Sharon J, Rezaei F, Mohiti-Asli M, Johnson A, Abud G, Ane JM, Maeda J, Infante V, Gottlieb SS, Lorigan JG, Williams L, Horton A, McKellar M, Soriano D, Caron Z, Elzinga H, Graham A, Clark R, Mak SM, Stupin L, Robinson A, Hubbard N, Broglie R, Tamsir A, Temme K. Enabling Biological Nitrogen Fixation for Cereal Crops in Fertilized Fields. ACS Synth Biol 2021; 10:3264-3277. [PMID: 34851109 DOI: 10.1021/acssynbio.1c00049] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Agricultural productivity relies on synthetic nitrogen fertilizers, yet half of that reactive nitrogen is lost to the environment. There is an urgent need for alternative nitrogen solutions to reduce the water pollution, ozone depletion, atmospheric particulate formation, and global greenhouse gas emissions associated with synthetic nitrogen fertilizer use. One such solution is biological nitrogen fixation (BNF), a component of the complex natural nitrogen cycle. BNF application to commercial agriculture is currently limited by fertilizer use and plant type. This paper describes the identification, development, and deployment of the first microbial product optimized using synthetic biology tools to enable BNF for corn (Zea mays) in fertilized fields, demonstrating the successful, safe commercialization of root-associated diazotrophs and realizing the potential of BNF to replace and reduce synthetic nitrogen fertilizer use in production agriculture. Derived from a wild nitrogen-fixing microbe isolated from agricultural soils, Klebsiella variicola 137-1036 ("Kv137-1036") retains the capacity of the parent strain to colonize corn roots while increasing nitrogen fixation activity 122-fold in nitrogen-rich environments. This technical milestone was then commercialized in less than half of the time of a traditional biological product, with robust biosafety evaluations and product formulations contributing to consumer confidence and ease of use. Tested in multi-year, multi-site field trial experiments throughout the U.S. Corn Belt, fields grown with Kv137-1036 exhibited both higher yields (0.35 ± 0.092 t/ha ± SE or 5.2 ± 1.4 bushels/acre ± SE) and reduced within-field yield variance by 25% in 2018 and 8% in 2019 compared to fields fertilized with synthetic nitrogen fertilizers alone. These results demonstrate the capacity of a broad-acre BNF product to fix nitrogen for corn in field conditions with reliable agronomic benefits.
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Affiliation(s)
- Amy Wen
- Pivot Bio, Berkeley, California 94710, United States
| | | | - Sarah E. Bloch
- Morrison & Foerster LLP, San Francisco, California 94105, United States
| | - Neal Shah
- Pivot Bio, Berkeley, California 94710, United States
| | | | | | - Judee Sharon
- University of Minnesota─Twin Cities, Minneapolis, Minnesota 55401, United States
| | | | | | | | - Gabriel Abud
- Tempo Automation, San Francisco, California 94103, United States
| | - Jean-Michel Ane
- University of Minnesota─Twin Cities, Minneapolis, Minnesota 55401, United States
| | - Junko Maeda
- University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Valentina Infante
- University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | | | | | | | - Alana Horton
- Pivot Bio, Berkeley, California 94710, United States
| | | | | | - Zoe Caron
- Pivot Bio, Berkeley, California 94710, United States
| | | | - Ashley Graham
- Olema Oncology, San Francisco, California 94107, United States
| | | | - San-Ming Mak
- Pivot Bio, Berkeley, California 94710, United States
| | - Laura Stupin
- Pivot Bio, Berkeley, California 94710, United States
| | | | | | | | - Alvin Tamsir
- Pivot Bio, Berkeley, California 94710, United States
| | - Karsten Temme
- Pivot Bio, Berkeley, California 94710, United States
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23
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Abstract
Schism is the new normal for the bioeconomy concept. Since its proliferation in governments, the concept has been adapted to fit national or regional exigencies. Earlier this century the knowledge-based bioeconomy (KBBE) in Europe was seen as a technical and knowledge fix in the evolving sustainability landscape. At the OECD, the concept was further honed by imagining a future where biotechnologies contribute significantly to economic growth and development. Countries started to make national bioeconomy strategies. Some countries have diverged and made the bioeconomy both much larger and more general, involving a wide variety of sectors, such as industry, energy, healthcare, agriculture, aquaculture, forestry and fishing. Whatever the approach, what seems to be consistent is the need to reconcile environmental, social and economic sustainability. This paper attempts to establish one schism that could have ramifications for the future development of the bioeconomy. Some countries, including some of the largest economies but not exclusively so, are clearly following a biotechnology model, whereas others are clearly not. In the wake of the COVID-19 pandemic, biotechnologies offer outstanding potential in healthcare, although this sector is by no means included in all bioeconomy strategies. The paper also attempts to clarify how biotechnologies can address the grand challenges and the United Nations Sustainable Development Goals. The communities of scientists seem to have no difficulty with this, but citizens and governments find it more difficult. In fact, some biotechnologies are already well established, whereas others are emerging and more controversial.
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24
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Wani SH, Vijayan R, Choudhary M, Kumar A, Zaid A, Singh V, Kumar P, Yasin JK. Nitrogen use efficiency (NUE): elucidated mechanisms, mapped genes and gene networks in maize ( Zea mays L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2875-2891. [PMID: 35035142 PMCID: PMC8720126 DOI: 10.1007/s12298-021-01113-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 11/22/2021] [Accepted: 12/07/2021] [Indexed: 05/22/2023]
Abstract
UNLABELLED Nitrogen, the vital primary plant growth nutrient at deficit soil conditions, drastically affects the growth and yield of a crop. Over the years, excess use of inorganic nitrogenous fertilizers resulted in pollution, eutrophication and thereby demanding the reduction in the use of chemical fertilizers. Being a C4 plant with fibrous root system and high NUE, maize can be deployed to be the best candidate for better N uptake and utilization in nitrogen deficient soils. The maize germplasm sources has enormous genetic variation for better nitrogen uptake contributing traits. Adoption of single cross maize hybrids as well as inherent property of high NUE has helped maize cultivars to achieve the highest growth rate among the cereals during last decade. Further, considering the high cost of nitrogenous fertilizers, adverse effects on soil health and environmental impact, maize improvement demands better utilization of existing genetic variation for NUE via introgression of novel allelic combinations in existing cultivars. Marker assisted breeding efforts need to be supplemented with introgression of genes/QTLs related to NUE in ruling varieties and thereby enhancing the overall productivity of maize in a sustainable manner. To achieve this, we need mapped genes and network of interacting genes and proteins to be elucidated. Identified genes may be used in screening ideal maize genotypes in terms of better physiological functionality exhibiting high NUE. Future genome editing may help in developing lines with increased productivity under low N conditions in an environment of optimum agronomic practices. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01113-z.
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Affiliation(s)
- Shabir H. Wani
- Genetics and Plant Breeding, Mountain Research Centre For Field Crops, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani Anantnag, J&K 192101 India
| | - Roshni Vijayan
- Regional Agricultural Research Station-Central Zone, Kerala Agricultural University, MelePattambi, Palakkad, Kerala 679306 India
| | | | - Anuj Kumar
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - Abbu Zaid
- Plant Physiology and Biochemistry Section, Department of Botany, Aligarh Muslim University, Aligarh, 202002 India
| | - Vishal Singh
- Department of Plants, Soils and Climate, Utah State University, 4820 Old Main Hill, Logan, UT 84322 USA
| | - Pardeep Kumar
- ICAR-Indian Institute of Maize Research, Ludhiana, 141001 India
| | - Jeshima Khan Yasin
- Division of Genomic Resources, ICAR-National Bureau Plant Genetic Resources, PUSA Campus, New Delhi, 110012 India
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25
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Shomar H, Bokinsky G. Towards a Synthetic Biology Toolset for Metallocluster Enzymes in Biosynthetic Pathways: What We Know and What We Need. Molecules 2021; 26:molecules26226930. [PMID: 34834021 PMCID: PMC8617995 DOI: 10.3390/molecules26226930] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 11/16/2022] Open
Abstract
Microbes are routinely engineered to synthesize high-value chemicals from renewable materials through synthetic biology and metabolic engineering. Microbial biosynthesis often relies on expression of heterologous biosynthetic pathways, i.e., enzymes transplanted from foreign organisms. Metallocluster enzymes are one of the most ubiquitous family of enzymes involved in natural product biosynthesis and are of great biotechnological importance. However, the functional expression of recombinant metallocluster enzymes in live cells is often challenging and represents a major bottleneck. The activity of metallocluster enzymes requires essential supporting pathways, involved in protein maturation, electron supply, and/or enzyme stability. Proper function of these supporting pathways involves specific protein-protein interactions that remain poorly characterized and are often overlooked by traditional synthetic biology approaches. Consequently, engineering approaches that focus on enzymatic expression and carbon flux alone often overlook the particular needs of metallocluster enzymes. This review highlights the biotechnological relevance of metallocluster enzymes and discusses novel synthetic biology strategies to advance their industrial application, with a particular focus on iron-sulfur cluster enzymes. Strategies to enable functional heterologous expression and enhance recombinant metallocluster enzyme activity in industrial hosts include: (1) optimizing specific maturation pathways; (2) improving catalytic stability; and (3) enhancing electron transfer. In addition, we suggest future directions for developing microbial cell factories that rely on metallocluster enzyme catalysis.
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Affiliation(s)
- Helena Shomar
- INSERM U722, Faculté de Médecine, Université de Paris, Site Xavier Bichat, 75018 Paris, France
- Correspondence: (H.S.); (G.B.)
| | - Gregory Bokinsky
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
- Correspondence: (H.S.); (G.B.)
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26
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Priyadarshini P, Choudhury S, Tilgam J, Bharati A, Sreeshma N. Nitrogen fixing cereal: A rising hero towards meeting food security. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:912-920. [PMID: 34547550 DOI: 10.1016/j.plaphy.2021.09.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 09/05/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
Nitrogen serves as one of the primary components of major biomolecules and thus extends a significant contribution to crop growth and yield. But the inability of plants to utilize freely available atmospheric N2 makes the whole agricultural system dependent on chemical fertilizers, which incur significant input cost to supplement required quantities of nitrogen to crops. Only bacteria and archaea have been gifted with the power of drawing free N2 from air to convert them into NH3, which is one of the two utilizable forms of nitrogen taken up by plants. Legumes, the only family of crops, can engage themselves in symbiotic nitrogen fixation where they establish a mutualistic relationship with nitrogen-fixing bacteria and in turn, can waive off the necessity of adding nitrogen fertilizers. Sincere effort, therefore, has been undertaken to incorporate this capability of nitrogen-fixation into non-legume crops, especially cereals which make up a vital portion in the food basket. Biotechnological interventions have also played important role in providing nitrogen fixing trait to non-legumes. This review takes up an effort to look into and accumulate all the important updates to date regarding nitrogen-fixing non-legumes with a special focus on cereals, which is one of the most important future goals in the field of science in the present era.
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Affiliation(s)
- Parichita Priyadarshini
- ICAR-Crop Improvement Division, Indian Grassland and Fodder Research Institute, Jhansi, U.P., 284003, India
| | - Sharani Choudhury
- ICAR - National Institute for Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Jyotsana Tilgam
- ICAR- National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, U.P., 274103, India.
| | - Alka Bharati
- ICAR-Central Agroforestry Research Institute, Jhansi, U.P., 284003, India
| | - N Sreeshma
- ICAR - National Institute for Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
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27
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Stepanova AN. Plant Biology Research: What Is Next? FRONTIERS IN PLANT SCIENCE 2021; 12:749104. [PMID: 34659319 PMCID: PMC8514653 DOI: 10.3389/fpls.2021.749104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Anna N. Stepanova
- Department of Plant and Microbial Biology, Program in Genetics, North Carolina State University, Raleigh, NC, United States
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28
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Waite CJ, Lindström Battle A, Bennett MH, Carey MR, Hong CK, Kotta-Loizou I, Buck M, Schumacher J. Resource Allocation During the Transition to Diazotrophy in Klebsiella oxytoca. Front Microbiol 2021; 12:718487. [PMID: 34434180 PMCID: PMC8381380 DOI: 10.3389/fmicb.2021.718487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Free-living nitrogen-fixing bacteria can improve growth yields of some non-leguminous plants and, if enhanced through bioengineering approaches, have the potential to address major nutrient imbalances in global crop production by supplementing inorganic nitrogen fertilisers. However, nitrogen fixation is a highly resource-costly adaptation and is de-repressed only in environments in which sources of reduced nitrogen are scarce. Here we investigate nitrogen fixation (nif) gene expression and nitrogen starvation response signaling in the model diazotroph Klebsiella oxytoca (Ko) M5a1 during ammonium depletion and the transition to growth on atmospheric N2. Exploratory RNA-sequencing revealed that over 50% of genes were differentially expressed under diazotrophic conditions, among which the nif genes are among the most highly expressed and highly upregulated. Isotopically labelled QconCAT standards were designed for multiplexed, absolute quantification of Nif and nitrogen-stress proteins via multiple reaction monitoring mass spectrometry (MRM-MS). Time-resolved Nif protein concentrations were indicative of bifurcation in the accumulation rates of nitrogenase subunits (NifHDK) and accessory proteins. We estimate that the nitrogenase may account for more than 40% of cell protein during diazotrophic growth and occupy approximately half the active ribosome complement. The concentrations of free amino acids in nitrogen-starved cells were insufficient to support the observed rates of Nif protein expression. Total Nif protein accumulation was reduced 10-fold when the NifK protein was truncated and nitrogenase catalysis lost (nifK1–1203), implying that reinvestment of de novo fixed nitrogen is essential for further nif expression and a complete diazotrophy transition. Several amino acids accumulated in non-fixing ΔnifLA and nifK1–1203 mutants, while the rest remained highly stable despite prolonged N starvation. Monitoring post-translational uridylylation of the PII-type signaling proteins GlnB and GlnK revealed distinct nitrogen regulatory roles in Ko M5a1. GlnK uridylylation was persistent throughout the diazotrophy transition while a ΔglnK mutant exhibited significantly reduced Nif expression and nitrogen fixation activity. Altogether, these findings highlight quantitatively the scale of resource allocation required to enable the nitrogen fixation adaptation to take place once underlying signaling processes are fulfilled. Our work also provides an omics-level framework with which to model nitrogen fixation in free-living diazotrophs and inform rational engineering strategies.
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Affiliation(s)
- Christopher J Waite
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | | | - Mark H Bennett
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Matthew R Carey
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Chun K Hong
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Ioly Kotta-Loizou
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Martin Buck
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Jörg Schumacher
- Department of Life Sciences, Imperial College London, London, United Kingdom
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29
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Buzdin AV, Patrushev MV, Sverdlov ED. Will Plant Genome Editing Play a Decisive Role in "Quantum-Leap" Improvements in Crop Yield to Feed an Increasing Global Human Population? PLANTS (BASEL, SWITZERLAND) 2021; 10:1667. [PMID: 34451712 PMCID: PMC8398637 DOI: 10.3390/plants10081667] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/04/2021] [Accepted: 08/07/2021] [Indexed: 02/08/2023]
Abstract
Growing scientific evidence demonstrates unprecedented planetary-scale human impacts on the Earth's system with a predicted threat to the existence of the terrestrial biosphere due to population increase, resource depletion, and pollution. Food systems account for 21-34% of global carbon dioxide (CO2) emissions. Over the past half-century, water and land-use changes have significantly impacted ecosystems, biogeochemical cycles, biodiversity, and climate. At the same time, food production is falling behind consumption, and global grain reserves are shrinking. Some predictions suggest that crop yields must approximately double by 2050 to adequately feed an increasing global population without a large expansion of crop area. To achieve this, "quantum-leap" improvements in crop cultivar productivity are needed within very narrow planetary boundaries of permissible environmental perturbations. Strategies for such a "quantum-leap" include mutation breeding and genetic engineering of known crop genome sequences. Synthetic biology makes it possible to synthesize DNA fragments of any desired sequence, and modern bioinformatics tools may hopefully provide an efficient way to identify targets for directed modification of selected genes responsible for known important agronomic traits. CRISPR/Cas9 is a new technology for incorporating seamless directed modifications into genomes; it is being widely investigated for its potential to enhance the efficiency of crop production. We consider the optimism associated with the new genetic technologies in terms of the complexity of most agronomic traits, especially crop yield potential (Yp) limits. We also discuss the possible directions of overcoming these limits and alternative ways of providing humanity with food without transgressing planetary boundaries. In conclusion, we support the long-debated idea that new technologies are unlikely to provide a rapidly growing population with significantly increased crop yield. Instead, we suggest that delicately balanced humane measures to limit its growth and the amount of food consumed per capita are highly desirable for the foreseeable future.
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Affiliation(s)
- Anton V Buzdin
- The Laboratory of Clinical and Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Maxim V Patrushev
- Kurchatov Center for Genome Research, National Research Center Kurchatov Institute, 123182 Moscow, Russia
| | - Eugene D Sverdlov
- Kurchatov Center for Genome Research, National Research Center Kurchatov Institute, 123182 Moscow, Russia
- Institute of Molecular Genetics, National Research Center Kurchatov Institute, 123182 Moscow, Russia
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Haskett TL, Knights HE, Jorrin B, Mendes MD, Poole PS. A Simple in situ Assay to Assess Plant-Associative Bacterial Nitrogenase Activity. Front Microbiol 2021; 12:690439. [PMID: 34248916 PMCID: PMC8261070 DOI: 10.3389/fmicb.2021.690439] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/25/2021] [Indexed: 11/23/2022] Open
Abstract
Assessment of plant-associative bacterial nitrogen (N) fixation is crucial for selection and development of elite diazotrophic inoculants that could be used to supply cereal crops with nitrogen in a sustainable manner. Although diazotrophic bacteria possess diverse oxygen tolerance mechanisms, most require a sub 21% oxygen environment to achieve optimal stability and function of the N-fixing catalyst nitrogenase. Consequently, assessment of N fixation is routinely carried out on “free-living” bacteria grown in the absence of a host plant and such experiments may not accurately divulge activity in the rhizosphere where the availability and forms of nutrients such as carbon and N, which are key regulators of N fixation, may vary widely. Here, we present a modified in situ acetylene reduction assay (ARA), utilizing the model cereal barley as a host to comparatively assess nitrogenase activity in diazotrophic bacteria. The assay is rapid, highly reproducible, applicable to a broad range of diazotrophs, and can be performed with simple equipment commonly found in most laboratories that investigate plant-microbe interactions. Thus, the assay could serve as a first point of order for high-throughput identification of elite plant-associative diazotrophs.
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Affiliation(s)
- Timothy L Haskett
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Hayley E Knights
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Beatriz Jorrin
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Marta D Mendes
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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31
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Udvardi M, Below FE, Castellano MJ, Eagle AJ, Giller KE, Ladha JK, Liu X, Maaz TM, Nova-Franco B, Raghuram N, Robertson GP, Roy S, Saha M, Schmidt S, Tegeder M, York LM, Peters JW. A Research Road Map for Responsible Use of Agricultural Nitrogen. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.660155] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Nitrogen (N) is an essential but generally limiting nutrient for biological systems. Development of the Haber-Bosch industrial process for ammonia synthesis helped to relieve N limitation of agricultural production, fueling the Green Revolution and reducing hunger. However, the massive use of industrial N fertilizer has doubled the N moving through the global N cycle with dramatic environmental consequences that threaten planetary health. Thus, there is an urgent need to reduce losses of reactive N from agriculture, while ensuring sufficient N inputs for food security. Here we review current knowledge related to N use efficiency (NUE) in agriculture and identify research opportunities in the areas of agronomy, plant breeding, biological N fixation (BNF), soil N cycling, and modeling to achieve responsible, sustainable use of N in agriculture. Amongst these opportunities, improved agricultural practices that synchronize crop N demand with soil N availability are low-hanging fruit. Crop breeding that targets root and shoot physiological processes will likely increase N uptake and utilization of soil N, while breeding for BNF effectiveness in legumes will enhance overall system NUE. Likewise, engineering of novel N-fixing symbioses in non-legumes could reduce the need for chemical fertilizers in agroecosystems but is a much longer-term goal. The use of simulation modeling to conceptualize the complex, interwoven processes that affect agroecosystem NUE, along with multi-objective optimization, will also accelerate NUE gains.
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32
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Sheoran S, Kumar S, Kumar P, Meena RS, Rakshit S. Nitrogen fixation in maize: breeding opportunities. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1263-1280. [PMID: 33677701 DOI: 10.1007/s00122-021-03791-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/06/2021] [Indexed: 06/12/2023]
Abstract
Maize (Zea mays L.) is a highly versatile crop with huge demand of nitrogen (N) for its growth and development. N is the most essential macronutrient for crop production. Despite being the highest abundant element in the atmosphere (~ 78%), it is scarcely available for plant growth. To fulfil the N demand, commercial agriculture is largely dependent on synthetic fertilizers. Excessive dependence on inorganic fertilizers has created extensive ecological as well as economic problems worldwide. Hence, for a sustainable solution to nitrogenous fertilizer use, development of biological nitrogen fixation (BNF) in cereals will be the best alternative. BNF is a well-known mechanism in legumes where diazotrophs convert atmospheric nitrogen (N≡N) to plant-available form, ammonium (NH4+). From many decades, researchers have dreamt to develop a similar symbiotic partnership as in legumes to the cereal crops. A large number of endophytic diazotrophs have been found associated with maize. Elucidation of the genetic and molecular aspects of their interaction will open up new avenues to introgress BNF in maize breeding. With the advanced understanding of N-fixation process, researchers are at a juncture of breeding and engineering this symbiotic relationships in cereals. Different breeding, genetic engineering, omics, gene editing, and synthetic biology approaches will be discussed in this review to make BNF a reality in cereals. It will help to provide a road map to develop/improve the BNF in maize to an advance step for the sustainable production system to achieve the food and nutritional security.
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Affiliation(s)
- Seema Sheoran
- ICAR-Indian Institute of Maize Research, PAU Campus, Ludhiana, 1410 04, India
| | - Sandeep Kumar
- ICAR-Indian Institute of Pulses Research, Regional Station, Phanda, Bhopal, 462 030, India
| | - Pradeep Kumar
- ICAR-Indian Institute of Maize Research, PAU Campus, Ludhiana, 1410 04, India
| | - Ram Swaroop Meena
- Department of Agronomy, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221 005, India
| | - Sujay Rakshit
- ICAR-Indian Institute of Maize Research, PAU Campus, Ludhiana, 1410 04, India.
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Smercina DN, Evans SE, Friesen ML, Tiemann LK. Impacts of nitrogen addition on switchgrass root-associated diazotrophic community structure and function. FEMS Microbiol Ecol 2021; 96:5920613. [PMID: 33038234 DOI: 10.1093/femsec/fiaa208] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/08/2020] [Indexed: 02/02/2023] Open
Abstract
Cellulosic bioenergy crops, like switchgrass (Panicum virgatum), have potential for growth on lands unsuitable for food production coupled with potential for climate mitigation. Sustainability of these systems lies in identifying conditions that promote high biomass yields on marginal lands under low-input agricultural practices. Associative nitrogen fixation (ANF) is a potentially important nitrogen (N) source for these crops, yet ANF contributions to plant N, especially under fertilizer N addition are unclear. In this study, we assess structure (nifH) and function (ANF) of switchgrass root-associated diazotrophic communities to long-term and short-term N additions using soil from three marginal land sites. ANF rates were variable and often unexpectedly high, sometimes 10× greater than reported in the literature, and did not respond in repeatable ways to long-term or short-term N. We found few impacts of N addition on root-associated diazotrophic community structure or membership. Instead, we found a very consistent root-associated diazotrophic community even though switchgrass seeds were germinated in soil from field sites with distinct diazotrophic communities. Ultimately, this work demonstrates that root-associated diazotrophic communities have the potential to contribute to switchgrass N demands, independent of N addition, and this may be driven by selection of the diazotrophic community by switchgrass roots.
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Affiliation(s)
- Darian N Smercina
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Sarah E Evans
- W.K. Kellogg Biological Station, Department of Integrative Biology, Michigan State University, Hickory Corners, MI 49060, USA
| | - Maren L Friesen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA.,Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
| | - Lisa K Tiemann
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
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Computational characterizations of GDP-mannose 4,6-dehydratase (NoeL) Rhizobial proteins. Curr Genet 2021; 67:769-784. [PMID: 33837815 DOI: 10.1007/s00294-021-01184-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/19/2021] [Accepted: 03/29/2021] [Indexed: 10/21/2022]
Abstract
A growing body of evidence suggests that Nod Factors molecules are the critical structural components in nitrogen fixation. These molecules have been implicated in plant-microbe signaling. Many enzymes involved in Nod factors biosynthesis; however, the enzymes that decorate (modify) nod factor main structure play a vital role. Here, the computational analysis of GDP-mannose 4,6-dehydratase (NoeL) proteins with great impact in modification of nod factor structure in four genomes of agriculturally important rhizobia (Bradyrhizobium, Mesorhizobium, Rhizobium, Sinorhizobium) presented. The NoeL number of amino acids was in the range of 147 (M5AMF5) to 372 (A0A023XWX0, Q89TZ1). The molecular weights were around 41 KDa. The results showed that the strain-specific purification strategy should apply as the pI of the sequences varied significantly (in the range of 5.59 to 9.12). The enzyme sequences and eight 3-dimensional structures predicted with homology modeling and machine learning representing the phylogenetic tree revealed the stability of enzymes in different conditions (Instability and Aliphatic index); however, this stability is also strain-specific. Disulphide bonds were observed in some species; however, the pattern was not detected in all members of the same species. Alpha helix was the dominant secondary structure predicted in all cytoplasmic NoeL. All models were homo-tetramer with acceptable sequence identity, GMEAN and coverage (60, - 1.80, 88, respectively). Additionally, Ramachandran maps showed that more than 94% of residues are in favored regions. We also highlight several key characterizations of NoeL from four rhizobia genomes annotation. These findings provide novel insights into the complexity and diversity of NoeL enzymes among important rhizobia and suggest considering a broader framework of biofilm for future research.
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Deferred control of ammonium cross-feeding in a N 2-fixing bacterium-microalga artificial consortium. Appl Microbiol Biotechnol 2021; 105:2937-2950. [PMID: 33687504 DOI: 10.1007/s00253-021-11210-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 02/22/2021] [Accepted: 02/28/2021] [Indexed: 10/22/2022]
Abstract
There is an increasing interest in the use of N2-fixing bacteria for the sustainable biofertilization of crops. Genetically-optimized bacteria for ammonium release have an improved biofertilization capacity. Some of these strains also cross-feed ammonium into microalgae raising additional concerns on their sustainable use in agriculture due to the potential risk of producing a higher and longer-lasting eutrophication problem than synthetic N-fertilizers. Here we studied the dynamic algal cross-feeding properties of a genetically-modified Azotobacter vinelandii strain which can be tuned to over-accumulate different levels of glutamine synthetase (GS, EC 6.3.1.20) under the control of an exogenous inducer. After switching cells overaccumulating GS into a noninducing medium, they proliferated for several generations at the expense of the previously accumulated GS. Further dilution of GS by cell division slowed-down growth, promoted ammonium-excretion and cross-fed algae. The final bacterial population, and timing and magnitude of algal N-biofertlization was finely tuned in a deferred manner. This tuning was in accordance with the intensity of the previous induction of GS accumulation in the cells. This bacterial population behavior could be maintained up to about 15 bacterial cell generations, until faster-growing and nonammonium excreting cells arose at an apparent high frequency. Further improvements of this genetic engineering strategy might help to align efficiency of N-biofertilizers and safe use in an open environment. KEY POINTS: • Ammonium-excreting bacteria are potential eutrophication agents • GS-dependent deferred control of bacterial growth and ammonium release • Strong but transient ammonium cross-feeding of microalgae.
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Mao N, Aggarwal N, Poh CL, Cho BK, Kondo A, Liu C, Yew WS, Chang MW. Future trends in synthetic biology in Asia. ADVANCED GENETICS (HOBOKEN, N.J.) 2021; 2:e10038. [PMID: 36618442 PMCID: PMC9744534 DOI: 10.1002/ggn2.10038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/10/2021] [Accepted: 01/21/2021] [Indexed: 05/06/2023]
Abstract
Synthetic biology research and technology translation has garnered increasing interest from the governments and private investors in Asia, where the technology has great potential in driving a sustainable bio-based economy. This Perspective reviews the latest developments in the key enabling technologies of synthetic biology and its application in bio-manufacturing, medicine, food and agriculture in Asia. Asia-centric strengths in synthetic biology to grow the bio-based economy, such as advances in genome editing and the presence of biofoundries combined with the availability of natural resources and vast markets, are also highlighted. The potential barriers to the sustainable development of the field, including inadequate infrastructure and policies, with suggestions to overcome these by building public-private partnerships, more effective multi-lateral collaborations and well-developed governance framework, are presented. Finally, the roles of technology, education and regulation in mitigating potential biosecurity risks are examined. Through these discussions, stakeholders from different groups, including academia, industry and government, are expectantly better positioned to contribute towards the establishment of innovation and bio-economy hubs in Asia.
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Affiliation(s)
- Ning Mao
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)National University of SingaporeSingaporeSingapore
| | - Nikhil Aggarwal
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)National University of SingaporeSingaporeSingapore
- Synthetic Biology Translational Research Program and Department of Biochemistry, Yong Loo Ling School of MedicineNational University of SingaporeSingaporeSingapore
| | - Chueh Loo Poh
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)National University of SingaporeSingaporeSingapore
- Department of Biomedical EngineeringNational University of SingaporeSingaporeSingapore
| | - Byung Kwan Cho
- Department of Biological Sciences, and KI for the BioCenturyKorea Advanced Institute of Science and TechnologyDaejeonSouth Korea
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, and Engineering Biology Research CenterKobe UniversityKobeJapan
| | - Chenli Liu
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenChina
| | - Wen Shan Yew
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)National University of SingaporeSingaporeSingapore
- Synthetic Biology Translational Research Program and Department of Biochemistry, Yong Loo Ling School of MedicineNational University of SingaporeSingaporeSingapore
| | - Matthew Wook Chang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)National University of SingaporeSingaporeSingapore
- Synthetic Biology Translational Research Program and Department of Biochemistry, Yong Loo Ling School of MedicineNational University of SingaporeSingaporeSingapore
- Department of Biomedical EngineeringNational University of SingaporeSingaporeSingapore
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37
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Nitrogen Losses and Potential Mitigation Strategies for a Sustainable Agroecosystem. SUSTAINABILITY 2021. [DOI: 10.3390/su13042400] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nitrogen (N) in the agricultural production system influences many aspects of agroecosystems and several critical ecosystem services widely depend on the N availability in the soil. Cumulative changes in regional ecosystem services may lead to global environmental changes. Thus, the soil N status in agriculture is of critical importance to strategize its most efficient use. Nitrogen is also one of the most susceptible macronutrients to environmental loss, such as ammonia volatilization (NH3), nitrous oxide (N2O) emissions, nitrate leaching (NO3), etc. Any form of N losses from agricultural systems can be major limitations for crop production, soil sustainability, and environmental safeguard. There is a need to focus on mitigation strategies to minimize global N pollution and implement agricultural management practices that encourage regenerative and sustainable agriculture. In this review, we identified the avenues of N loss into the environment caused by current agronomic practices and discussed the potential practices that can be adapted to prevent this N loss in production agriculture. This review also explored the N status in agriculture during the COVID-19 pandemic and the existing knowledge gaps and questions that need to be addressed.
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38
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Jiang X, Payá-Tormo L, Coroian D, García-Rubio I, Castellanos-Rueda R, Eseverri Á, López-Torrejón G, Burén S, Rubio LM. Exploiting genetic diversity and gene synthesis to identify superior nitrogenase NifH protein variants to engineer N 2-fixation in plants. Commun Biol 2021; 4:4. [PMID: 33398015 PMCID: PMC7782807 DOI: 10.1038/s42003-020-01536-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 11/25/2020] [Indexed: 01/01/2023] Open
Abstract
Engineering nitrogen fixation in eukaryotes requires high expression of functional nitrogenase structural proteins, a goal that has not yet been achieved. Here we build a knowledge-based library containing 32 nitrogenase nifH sequences from prokaryotes of diverse ecological niches and metabolic features and combine with rapid screening in tobacco to identify superior NifH variants for plant mitochondria expression. Three NifH variants outperform in tobacco mitochondria and are further tested in yeast. Hydrogenobacter thermophilus (Aquificae) NifH is isolated in large quantities from yeast mitochondria and fulfills NifH protein requirements for efficient N2 fixation, including electron transfer for substrate reduction, P-cluster maturation, and FeMo-co biosynthesis. H. thermophilus NifH expressed in tobacco leaves shows lower nitrogenase activity than that from yeast. However, transfer of [Fe4S4] clusters from NifU to NifH in vitro increases 10-fold the activity of the tobacco-isolated NifH, revealing that plant mitochondria [Fe-S] cluster availability constitutes a bottleneck to engineer plant nitrogenases.
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Affiliation(s)
- Xi Jiang
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - Lucía Payá-Tormo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - Diana Coroian
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Inés García-Rubio
- Centro Universitario de la Defensa, Ctra. de Huesca s/n, 50090, Zaragoza, Spain
| | - Rocío Castellanos-Rueda
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain
- Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland
| | - Álvaro Eseverri
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - Gema López-Torrejón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - Stefan Burén
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain.
| | - Luis Manuel Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain.
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain.
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Herrero M, Thornton PK, Mason-D'Croz D, Palmer J, Bodirsky BL, Pradhan P, Barrett CB, Benton TG, Hall A, Pikaar I, Bogard JR, Bonnett GD, Bryan BA, Campbell BM, Christensen S, Clark M, Fanzo J, Godde CM, Jarvis A, Loboguerrero AM, Mathys A, McIntyre CL, Naylor RL, Nelson R, Obersteiner M, Parodi A, Popp A, Ricketts K, Smith P, Valin H, Vermeulen SJ, Vervoort J, van Wijk M, van Zanten HH, West PC, Wood SA, Rockström J. Articulating the effect of food systems innovation on the Sustainable Development Goals. Lancet Planet Health 2021; 5:e50-e62. [PMID: 33306994 DOI: 10.1016/s2542-5196(20)30277-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/18/2020] [Accepted: 11/18/2020] [Indexed: 05/15/2023]
Abstract
Food system innovations will be instrumental to achieving multiple Sustainable Development Goals (SDGs). However, major innovation breakthroughs can trigger profound and disruptive changes, leading to simultaneous and interlinked reconfigurations of multiple parts of the global food system. The emergence of new technologies or social solutions, therefore, have very different impact profiles, with favourable consequences for some SDGs and unintended adverse side-effects for others. Stand-alone innovations seldom achieve positive outcomes over multiple sustainability dimensions. Instead, they should be embedded as part of systemic changes that facilitate the implementation of the SDGs. Emerging trade-offs need to be intentionally addressed to achieve true sustainability, particularly those involving social aspects like inequality in its many forms, social justice, and strong institutions, which remain challenging. Trade-offs with undesirable consequences are manageable through the development of well planned transition pathways, careful monitoring of key indicators, and through the implementation of transparent science targets at the local level.
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Affiliation(s)
- Mario Herrero
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, QLD, Australia.
| | - Philip K Thornton
- CGIAR Research Programme on Climate Change, Agriculture and Food Security, International Livestock Research Institute, Nairobi, Kenya
| | - Daniel Mason-D'Croz
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, QLD, Australia
| | - Jeda Palmer
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, QLD, Australia
| | | | - Prajal Pradhan
- Potsdam Institute for Climate Impact Research (PIK), Potsdam, Germany
| | - Christopher B Barrett
- Dyson School of Applied Economics and Management, Cornell University, New York, NY, USA
| | - Tim G Benton
- The Royal Institute for International Affairs, Chatham House, London, UK
| | - Andrew Hall
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT, Australia
| | - Ilje Pikaar
- The University of Queensland, St Lucia, QLD, Australia
| | - Jessica R Bogard
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, QLD, Australia
| | - Graham D Bonnett
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, QLD, Australia
| | - Brett A Bryan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Burwood, VIC, Australia
| | - Bruce M Campbell
- CGIAR Research Program on Climate Change, Agriculture and Food Security and International Center for Tropical Agriculture, Valle del Cauca, Colombia; Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Svend Christensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Clark
- Nuffield Department of Population Health, University of Oxford, Oxford, UK; Oxford Martin School, University of Oxford, Oxford, UK
| | - Jessica Fanzo
- School of Advanced International Studies, Berman Institute of Bioethics, Johns Hopkins University, Washington, DC, USA; Bloomberg School of Public Health, Johns Hopkins University, Washington, DC, USA
| | - Cecile M Godde
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, QLD, Australia
| | - Andy Jarvis
- CGIAR Research Program on Climate Change, Agriculture and Food Security and International Center for Tropical Agriculture, Valle del Cauca, Colombia
| | - Ana Maria Loboguerrero
- CGIAR Research Program on Climate Change, Agriculture and Food Security and International Center for Tropical Agriculture, Valle del Cauca, Colombia
| | - Alexander Mathys
- Sustainable Food Processing Laboratory, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - C Lynne McIntyre
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, QLD, Australia
| | - Rosamond L Naylor
- Center on Food Security and the Environment, Stanford University, Stanford, CA, USA
| | - Rebecca Nelson
- Dyson School of Applied Economics and Management, Cornell University, New York, NY, USA
| | - Michael Obersteiner
- International Institute for Applied Systems Analysis (IIASA), Laxenburg, Austria; Environmental Change Institute, University of Oxford, Oxford, UK
| | - Alejandro Parodi
- Animal Production Systems group, Wageningen University & Research, Wageningen, Netherlands
| | - Alexander Popp
- Potsdam Institute for Climate Impact Research (PIK), Potsdam, Germany
| | - Katie Ricketts
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT, Australia
| | - Pete Smith
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK
| | - Hugo Valin
- International Institute for Applied Systems Analysis (IIASA), Laxenburg, Austria
| | | | - Joost Vervoort
- Copernicus Institute of Sustainable Development, Utrecht University, Utrecht, Netherlands
| | - Mark van Wijk
- International Livestock Research Institute, Nairobi, Kenya
| | - Hannah He van Zanten
- Farming Systems Ecology Group, Wageningen University & Research, Wageningen, Netherlands
| | - Paul C West
- Institute on the Environment, University of Minnesota, Minneapolis, MN, USA
| | - Stephen A Wood
- The Nature Conservancy, Arlington, VA, USA; Yale School of the Environment, New Haven, CT, USA
| | - Johan Rockström
- Potsdam Institute for Climate Impact Research (PIK), Potsdam, Germany; Institute of Environmental Science and Geography, Universität Potsdam, Potsdam-Golm, Germany
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40
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Biz A, Mahadevan R. Overcoming Challenges in Expressing Iron-Sulfur Enzymes in Yeast. Trends Biotechnol 2020; 39:665-677. [PMID: 33339619 DOI: 10.1016/j.tibtech.2020.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/03/2020] [Accepted: 11/09/2020] [Indexed: 01/07/2023]
Abstract
Iron-sulfur clusters are metal cofactors that are present in all domains of life. Many enzymes that require these cofactors have biotechnological importance, because they can be used to uncover catabolic routes to new sugar substrates or can be a critical part of pathways to produce chemicals and biofuels. However, the expression of these iron-sulfur enzymes of bacterial origin in yeast at high levels is a significant bottleneck. Intermediates upstream of the enzyme accumulate, because the activity of these enzymes is either low or completely absent. In this review, we examine possible explanations for this limitation, discuss potential genetic interventions in the yeast host that can increase iron-sulfur enzyme activity, and suggest future directions for creating more efficient yeast hosts capable of high iron-sulfur enzyme expression.
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Affiliation(s)
- Alessandra Biz
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ONT, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ONT, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ONT, Canada.
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41
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Landazuri CFG, Gomez JS, Raaijmakers JM, Oyserman BO. Restoring degraded microbiome function with self-assembled communities. FEMS Microbiol Ecol 2020; 96:5956484. [PMID: 33150935 DOI: 10.1093/femsec/fiaa225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 11/03/2020] [Indexed: 01/04/2023] Open
Abstract
The natural microbial functions of many soils are severely degraded. Current state-of-the-art technology to restore these functions is through the isolation, screening, formulation and application of microbial inoculants and synthetic consortia. These approaches have inconsistent success, in part due to the incompatibility between the biofertilizer, crop, climate, existing soil microbiome and physicochemical characteristics of the soils. Here, we review the current state of the art in biofertilization and identify two key deficiencies in current strategies: the difficulty in designing complex multispecies biofertilizers and the bottleneck in scaling the production of complex multispecies biofertilizers. To address the challenge of producing scalable, multispecies biofertilizers, we propose to merge ecological theory with bioprocess engineering to produce 'self-assembled communities' enriched for particular functional guilds and adapted to a target soil and host plant. Using the nitrogen problem as an anchor, we review relevant ecology (microbial, plant and environmental), as well as reactor design strategies and operational parameters for the production of functionally enriched self-assembled communities. The use of self-assembled communities for biofertilization addresses two major hurdles in microbiome engineering: the importance of enriching microbes indigenous to (and targeted for) a specific environment and the recognized potential benefits of microbial consortia over isolates (e.g. functional redundancy). The proposed community enrichment model could also be instrumental for other microbial functions such as phosphorus solubilization, plant growth promotion or disease suppression.
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Affiliation(s)
- Carlos Fernando Gutierrez Landazuri
- Environmental Microbiology and Biotechnology Laboratory, Engineering School of Environmental and Natural Resources, Engineering Faculty, Universidad del Valle, 760032, Cali, Colombia
| | - Janeth Sanabria Gomez
- Environmental Microbiology and Biotechnology Laboratory, Engineering School of Environmental and Natural Resources, Engineering Faculty, Universidad del Valle, 760032, Cali, Colombia
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.,Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Ben O Oyserman
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.,Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1,6708 PB, Wageningen, The Netherlands
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42
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Higdon SM, Pozzo T, Tibbett EJ, Chiu C, Jeannotte R, Weimer BC, Bennett AB. Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts. PLoS One 2020; 15:e0239081. [PMID: 32925972 PMCID: PMC7489573 DOI: 10.1371/journal.pone.0239081] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/28/2020] [Indexed: 11/18/2022] Open
Abstract
Sierra Mixe maize is a geographically remote landrace variety grown on nitrogen-deficient fields in Oaxaca, Mexico that meets its nutritional requirements without synthetic fertilizer by associating with free-living diazotrophs comprising the microbiota of its aerial root mucilage. We selected nearly 500 diazotrophic (N2-fixing) bacteria isolated from Sierra Mixe maize mucilage and sequenced their genomes. Comparative genomic analysis demonstrated that isolates represented diverse genera and composed three major diazotrophic groups based on nitrogen fixation gene content. In addition to nitrogen fixation, we examined deamination of 1-amino-1-cyclopropanecarboxylic acid, biosynthesis of indole-3-acetic acid, and phosphate solubilization as alternative mechanisms of direct plant growth promotion (PGP). Genome mining showed that isolates of all diazotrophic groups possessed marker genes for multiple mechanisms of direct plant growth promotion (PGP). Implementing in vitro assays corroborated isolate genotypes by measuring each isolate's potential to confer the targeted PGP traits and revealed phenotypic variation among isolates based on diazotrophic group assignment. Investigating the ability of mucilage diazotrophs to confer PGP by direct inoculation of clonally propagated potato plants in planta led to the identification of 16 bio-stimulant candidates. Conducting nitrogen-stress greenhouse experiments demonstrated that potato inoculation with a synthetic community of bio-stimulant candidates, as well as with its individual components, resulted in PGP phenotypes. We further demonstrated that one diazotrophic isolate conferred PGP to a conventional maize variety under nitrogen-stress in the greenhouse. These results indicate that, while many diazotrophic isolates from Sierra Mixe maize possessed genotypes and in vitro phenotypes for targeted PGP traits, a subset of these organisms promoted the growth of potato and conventional maize, potentially through the use of multiple promotion mechanisms.
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Affiliation(s)
- Shawn M. Higdon
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Tania Pozzo
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Emily J. Tibbett
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Colleen Chiu
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Richard Jeannotte
- Department of Population Health and Reproduction, University of California, Davis, California, United States of America
| | - Bart C. Weimer
- Department of Population Health and Reproduction, University of California, Davis, California, United States of America
| | - Alan B. Bennett
- Department of Plant Sciences, University of California, Davis, California, United States of America
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43
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Bloch SE, Clark R, Gottlieb SS, Wood LK, Shah N, Mak SM, Lorigan JG, Johnson J, Davis-Richardson AG, Williams L, McKellar M, Soriano D, Petersen M, Horton A, Smith O, Wu L, Tung E, Broglie R, Tamsir A, Temme K. Biological nitrogen fixation in maize: optimizing nitrogenase expression in a root-associated diazotroph. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4591-4603. [PMID: 32267497 PMCID: PMC7382387 DOI: 10.1093/jxb/eraa176] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 04/09/2020] [Indexed: 05/04/2023]
Abstract
Plants depend upon beneficial interactions between roots and root-associated microorganisms for growth promotion, disease suppression, and nutrient availability. This includes the ability of free-living diazotrophic bacteria to supply nitrogen, an ecological role that has been long underappreciated in modern agriculture for efficient crop production systems. Long-term ecological studies in legume-rhizobia interactions have shown that elevated nitrogen inputs can lead to the evolution of less cooperative nitrogen-fixing mutualists. Here we describe how reprogramming the genetic regulation of nitrogen fixation and assimilation in a novel root-associated diazotroph can restore ammonium production in the presence of exogenous nitrogen inputs. We isolated a strain of the plant-associated proteobacterium Kosakonia sacchari from corn roots, characterized its nitrogen regulatory network, and targeted key nodes for gene editing to optimize nitrogen fixation in corn. While the wild-type strain exhibits repression of nitrogen fixation in conditions replete with bioavailable nitrogen, such as fertilized greenhouse and field experiments, remodeled strains show elevated levels in the rhizosphere of corn in the greenhouse and field even in the presence of exogenous nitrogen. Such strains could be used in commercial applications to supply fixed nitrogen to cereal crops.
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