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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] [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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Ambrosio R, Burgos Herrera G, Do Nascimento M, Pagnussat LA, Curatti L. Competitive fitness and stability of ammonium-excreting Azotobacter vinelandii strains in the soil. Appl Microbiol Biotechnol 2024; 108:378. [PMID: 38888816 PMCID: PMC11189346 DOI: 10.1007/s00253-024-13231-1] [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: 04/03/2024] [Revised: 06/03/2024] [Accepted: 06/08/2024] [Indexed: 06/20/2024]
Abstract
Non-symbiotic N2-fixation would greatly increase the versatility of N-biofertilizers for sustainable agriculture. Genetic modification of diazotrophic bacteria has successfully enhanced NH4+ release. In this study, we compared the competitive fitness of A. vinelandii mutant strains, which allowed us to analyze the burden of NH4+ release under a broad dynamic range. Long-term competition assays under regular culture conditions confirmed a large burden for NH4+ release, exclusion by the wt strain, phenotypic instability, and loss of the ability to release NH4+. In contrast, co-inoculation in mild autoclaved soil showed a much longer co-existence with the wt strain and a stable NH4+ release phenotype. All genetically modified strains increased the N content and changed its chemical speciation in the soil. This study contributes one step forward towards bridging a knowledge gap between molecular biology laboratory research and the incorporation of N from the air into the soil in a molecular species suitable for plant nutrition, a crucial requirement for developing improved bacterial inoculants for economic and environmentally sustainable agriculture. KEY POINTS: • Genetic engineering for NH4+ excretion imposes a fitness burden on the culture medium • Large phenotypic instability for NH4+-excreting bacteria in culture medium • Lower fitness burden and phenotypic instability for NH4+-excreting bacteria in soil.
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Affiliation(s)
- Rafael Ambrosio
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC), Consejo Nacional de Investigaciones Científicas y Técnicas, Vieytes 3103, 7600, Mar del PlataBuenos Aires, Argentina
- Fundación para Investigaciones Biológicas Aplicadas, Mar del Plata, Buenos Aires, Argentina
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Santa Fe, Santa Fe, Argentina
| | - Gonzalo Burgos Herrera
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC), Consejo Nacional de Investigaciones Científicas y Técnicas, Vieytes 3103, 7600, Mar del PlataBuenos Aires, Argentina
- Fundación para Investigaciones Biológicas Aplicadas, Mar del Plata, Buenos Aires, Argentina
| | - Mauro Do Nascimento
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC), Consejo Nacional de Investigaciones Científicas y Técnicas, Vieytes 3103, 7600, Mar del PlataBuenos Aires, Argentina
- Fundación para Investigaciones Biológicas Aplicadas, Mar del Plata, Buenos Aires, Argentina
| | - Luciana Anabella Pagnussat
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC), Consejo Nacional de Investigaciones Científicas y Técnicas, Vieytes 3103, 7600, Mar del PlataBuenos Aires, Argentina
- Fundación para Investigaciones Biológicas Aplicadas, Mar del Plata, Buenos Aires, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Buenos Aires, Argentina
| | - Leonardo Curatti
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC), Consejo Nacional de Investigaciones Científicas y Técnicas, Vieytes 3103, 7600, Mar del PlataBuenos Aires, Argentina.
- Fundación para Investigaciones Biológicas Aplicadas, Mar del Plata, Buenos Aires, Argentina.
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3
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Chakraborty S, Venkataraman M, Infante V, Pfleger BF, Ané JM. Scripting a new dialogue between diazotrophs and crops. Trends Microbiol 2024; 32:577-589. [PMID: 37770375 PMCID: PMC10950843 DOI: 10.1016/j.tim.2023.08.007] [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: 05/27/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 09/30/2023]
Abstract
Diazotrophs are bacteria and archaea that can reduce atmospheric dinitrogen (N2) into ammonium. Plant-diazotroph interactions have been explored for over a century as a nitrogen (N) source for crops to improve agricultural productivity and sustainability. This scientific quest has generated much information about the molecular mechanisms underlying the function, assembly, and regulation of nitrogenase, ammonium assimilation, and plant-diazotroph interactions. This review presents various approaches to manipulating N fixation activity, ammonium release by diazotrophs, and plant-diazotroph interactions. We discuss the research avenues explored in this area, propose potential future routes, emphasizing engineering at the metabolic level via biorthogonal signaling, and conclude by highlighting the importance of biocontrol measures and public acceptance.
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Affiliation(s)
- Sanhita Chakraborty
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA
| | - Maya Venkataraman
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Valentina Infante
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA; Department of Agronomy, University of Wisconsin - Madison, Madison, WI, USA.
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4
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Ragland CJ, Shih KY, Dinneny JR. Choreographing root architecture and rhizosphere interactions through synthetic biology. Nat Commun 2024; 15:1370. [PMID: 38355570 PMCID: PMC10866969 DOI: 10.1038/s41467-024-45272-5] [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: 07/17/2023] [Accepted: 01/18/2024] [Indexed: 02/16/2024] Open
Abstract
Climate change is driving extreme changes to the environment, posing substantial threats to global food security and bioenergy. Given the direct role of plant roots in mediating plant-environment interactions, engineering the form and function of root systems and their associated microbiota may mitigate these effects. Synthetic genetic circuits have enabled sophisticated control of gene expression in microbial systems for years and a surge of advances has heralded the extension of this approach to multicellular plant species. Targeting these tools to affect root structure, exudation, and microbe activity on root surfaces provide multiple strategies for the advancement of climate-ready crops.
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Affiliation(s)
- Carin J Ragland
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Kevin Y Shih
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
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5
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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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6
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Carlson ED, Rajniak J, Sattely ES. Multiplicity of the Agrobacterium Infection of Nicotiana benthamiana for Transient DNA Delivery. ACS Synth Biol 2023; 12:2329-2338. [PMID: 37558215 PMCID: PMC10443027 DOI: 10.1021/acssynbio.3c00148] [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: 03/09/2023] [Indexed: 08/11/2023]
Abstract
Biological DNA transfer into plant cells mediated by Agrobacterium represents one of the most powerful tools for the engineering and study of plant systems. Transient expression of transfer DNA (T-DNA) in particular enables rapid testing of gene products and has been harnessed for facile combinatorial expression of multiple genes. In analogous mammalian cell-based gene expression systems, a clear sense of the multiplicity of infection (MOI) allows users to predict and control viral transfection frequencies for applications requiring single versus multiple transfection events per cell. Despite the value of Agrobacterium-mediated transient transformation of plants, MOI has not been quantified. Here, we analyze the Poisson probability distribution of the T-DNA transfer in leaf pavement cells to determine the MOI for the widely used model system Agrobacterium GV3101/Nicotiana benthamiana. These data delineate the relationship between an individual Agrobacterium strain infiltration OD600, plant cell perimeter, and leaf age, as well as plant cell coinfection rates. Our analysis establishes experimental regimes where the probability of near-simultaneous delivery of >20 unique T-DNAs to a given plant cell remains high throughout the leaf at infiltration OD600 above ∼0.2 for individual strains. In contrast, single-strain T-DNA delivery can be achieved at low strain infiltration OD600: at OD600 0.02, we observe that ∼40% of plant cells are infected, with 80% of those infected cells containing T-DNA product from just a single strain. We anticipate that these data will enable users to develop new approaches to in-leaf library development using Agrobacterium transient expression and reliable combinatorial assaying of multiple heterologous proteins in a single plant cell.
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Affiliation(s)
- Erik D. Carlson
- Department
of Chemical Engineering, Department of Bioengineering, and Howard Hughes
Medical Institute, Stanford University, Stanford, California 94305, United States
| | - Jakub Rajniak
- Department
of Chemical Engineering, Department of Bioengineering, and Howard Hughes
Medical Institute, Stanford University, Stanford, California 94305, United States
| | - Elizabeth S. Sattely
- Department
of Chemical Engineering, Department of Bioengineering, and Howard Hughes
Medical Institute, Stanford University, Stanford, California 94305, United States
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7
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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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8
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Haskett TL, Geddes BA, Paramasivan P, Green P, Chitnavis S, Mendes MD, Jorrín B, Knights HE, Bastholm TR, Ramsay JP, Oldroyd GED, Poole PS. Rhizopine biosensors for plant-dependent control of bacterial gene expression. Environ Microbiol 2023; 25:383-396. [PMID: 36428208 PMCID: PMC10107442 DOI: 10.1111/1462-2920.16288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022]
Abstract
Engineering signalling between plants and microbes could be exploited to establish host-specificity between plant-growth-promoting bacteria and target crops in the environment. We previously engineered rhizopine-signalling circuitry facilitating exclusive signalling between rhizopine-producing (RhiP) plants and model bacterial strains. Here, we conduct an in-depth analysis of rhizopine-inducible expression in bacteria. We characterize two rhizopine-inducible promoters and explore the bacterial host-range of rhizopine biosensor plasmids. By tuning the expression of rhizopine uptake genes, we also construct a new biosensor plasmid pSIR05 that has minimal impact on host cell growth in vitro and exhibits markedly improved stability of expression in situ on RhiP barley roots compared to the previously described biosensor plasmid pSIR02. We demonstrate that a sub-population of Azorhizobium caulinodans cells carrying pSIR05 can sense rhizopine and activate gene expression when colonizing RhiP barley roots. However, these bacteria were mildly defective for colonization of RhiP barley roots compared to the wild-type parent strain. This work provides advancement towards establishing more robust plant-dependent control of bacterial gene expression and highlights the key challenges remaining to achieve this goal.
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Affiliation(s)
| | - Barney A Geddes
- Department of Plant Sciences, University of Oxford, Oxford, UK
- Department of Microbiological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | | | - Patrick Green
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Samir Chitnavis
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Marta D Mendes
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Beatriz Jorrín
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | | - Tahlia R Bastholm
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, Western Australia, Australia
| | - Joshua P Ramsay
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, Western Australia, Australia
| | - Giles E D Oldroyd
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Crop Science Centre, University of Cambridge, Cambridge, UK
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, UK
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9
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Molecular Mechanism and Agricultural Application of the NifA-NifL System for Nitrogen Fixation. Int J Mol Sci 2023; 24:ijms24020907. [PMID: 36674420 PMCID: PMC9866876 DOI: 10.3390/ijms24020907] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
Nitrogen-fixing bacteria execute biological nitrogen fixation through nitrogenase, converting inert dinitrogen (N2) in the atmosphere into bioavailable nitrogen. Elaborating the molecular mechanisms of orderly and efficient biological nitrogen fixation and applying them to agricultural production can alleviate the "nitrogen problem". Azotobacter vinelandii is a well-established model bacterium for studying nitrogen fixation, utilizing nitrogenase encoded by the nif gene cluster to fix nitrogen. In Azotobacter vinelandii, the NifA-NifL system fine-tunes the nif gene cluster transcription by sensing the redox signals and energy status, then modulating nitrogen fixation. In this manuscript, we investigate the transcriptional regulation mechanism of the nif gene in autogenous nitrogen-fixing bacteria. We discuss how autogenous nitrogen fixation can better be integrated into agriculture, providing preliminary comprehensive data for the study of autogenous nitrogen-fixing regulation.
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10
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Dundas CM, Dinneny JR. Genetic Circuit Design in Rhizobacteria. BIODESIGN RESEARCH 2022; 2022:9858049. [PMID: 37850138 PMCID: PMC10521742 DOI: 10.34133/2022/9858049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/31/2022] [Indexed: 10/19/2023] Open
Abstract
Genetically engineered plants hold enormous promise for tackling global food security and agricultural sustainability challenges. However, construction of plant-based genetic circuitry is constrained by a lack of well-characterized genetic parts and circuit design rules. In contrast, advances in bacterial synthetic biology have yielded a wealth of sensors, actuators, and other tools that can be used to build bacterial circuitry. As root-colonizing bacteria (rhizobacteria) exert substantial influence over plant health and growth, genetic circuit design in these microorganisms can be used to indirectly engineer plants and accelerate the design-build-test-learn cycle. Here, we outline genetic parts and best practices for designing rhizobacterial circuits, with an emphasis on sensors, actuators, and chassis species that can be used to monitor/control rhizosphere and plant processes.
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Affiliation(s)
| | - José R. Dinneny
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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11
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Control of nitrogen fixation and ammonia excretion in Azorhizobium caulinodans. PLoS Genet 2022; 18:e1010276. [PMID: 35727841 PMCID: PMC9249168 DOI: 10.1371/journal.pgen.1010276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/01/2022] [Accepted: 05/26/2022] [Indexed: 11/19/2022] Open
Abstract
Due to the costly energy demands of nitrogen (N) fixation, diazotrophic bacteria have evolved complex regulatory networks that permit expression of the catalyst nitrogenase only under conditions of N starvation, whereas the same condition stimulates upregulation of high-affinity ammonia (NH3) assimilation by glutamine synthetase (GS), preventing excess release of excess NH3 for plants. Diazotrophic bacteria can be engineered to excrete NH3 by interference with GS, however control is required to minimise growth penalties and prevent unintended provision of NH3 to non-target plants. Here, we tested two strategies to control GS regulation and NH3 excretion in our model cereal symbiont Azorhizobium caulinodans AcLP, a derivative of ORS571. We first attempted to recapitulate previous work where mutation of both PII homologues glnB and glnK stimulated GS shutdown but found that one of these genes was essential for growth. Secondly, we expressed unidirectional adenylyl transferases (uATs) in a ΔglnE mutant of AcLP which permitted strong GS shutdown and excretion of NH3 derived from N2 fixation and completely alleviated negative feedback regulation on nitrogenase expression. We placed a uAT allele under control of the NifA-dependent promoter PnifH, permitting GS shutdown and NH3 excretion specifically under microaerobic conditions, the same cue that initiates N2 fixation, then deleted nifA and transferred a rhizopine nifAL94Q/D95Q-rpoN controller plasmid into this strain, permitting coupled rhizopine-dependent activation of N2 fixation and NH3 excretion. This highly sophisticated and multi-layered control circuitry brings us a step closer to the development of a "synthetic symbioses” where N2 fixation and NH3 excretion could be specifically activated in diazotrophic bacteria colonising transgenic rhizopine producing cereals, targeting delivery of fixed N to the crop while preventing interaction with non-target plants. Inoculation of cereal crops with associative diazotrophic bacteria that convert atmospheric nitrogen (N2) into ammonia (NH3) could be used to sustainably improve delivery of nitrogen to crops. However, due to the costly energy demands of N2 fixation, bacteria restrict excess production of NH3 and release to the plants. Diazotrophs can be engineered for excess NH3 production and release, however genetic control is required to minimise growth penalties and prevent unintended provision of NH3 to non-target weed species. Here, we engineer coupled control of N2 fixation and NH3 release in response to the signalling molecule rhizopine supplemented in vitro. This control circuitry represents a prototype for the future development of a “synthetic symbiosis” where bacterial N2 fixation and NH3 excretion could be specifically activated following colonisation of transgenic rhizopine producing cereals in the field, minimising bacterial energy requirements and preventing provision of NH3 to non-target plants.
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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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Singh RK, Singh P, Guo DJ, Sharma A, Li DP, Li X, Verma KK, Malviya MK, Song XP, Lakshmanan P, Yang LT, Li YR. Root-Derived Endophytic Diazotrophic Bacteria Pantoea cypripedii AF1 and Kosakonia arachidis EF1 Promote Nitrogen Assimilation and Growth in Sugarcane. Front Microbiol 2021; 12:774707. [PMID: 34975800 PMCID: PMC8714890 DOI: 10.3389/fmicb.2021.774707] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/12/2021] [Indexed: 11/15/2022] Open
Abstract
Excessive, long-term application of chemical fertilizers in sugarcane crops disrupts soil microbial flora and causes environmental pollution and yield decline. The role of endophytic bacteria in improving crop production is now well-documented. In this study, we have isolated and identified several endophytic bacterial strains from the root tissues of five sugarcane species. Among them, eleven Gram-negative isolates were selected and screened for plant growth-promoting characteristics, i.e., production of siderophores, indole-3-acetic acid (IAA), ammonia, hydrogen cyanide (HCN), and hydrolytic enzymes, phosphorus solubilization, antifungal activity against plant pathogens, nitrogen-fixation, 1-aminocyclopropane-1-carboxylic acid deaminase activity, and improving tolerance to different abiotic stresses. These isolates had nifH (11 isolates), acdS (8 isolates), and HCN (11 isolates) genes involved in N-fixation, stress tolerance, and pathogen biocontrol, respectively. Two isolates Pantoea cypripedii AF1and Kosakonia arachidis EF1 were the most potent strains and they colonized and grew in sugarcane plants. Both strains readily colonized the leading Chinese sugarcane variety GT42 and significantly increased the activity of nitrogen assimilation enzymes (glutamine synthetase, NADH glutamate dehydrogenase, and nitrate reductase), chitinase, and endo-glucanase and the content of phytohormones gibberellic acid, indole-3-acetic acid, and abscisic acid. The gene expression analysis of GT42 inoculated with isolates of P. cypripedii AF1 or K. arachidis EF1 showed increased activity of nifH and nitrogen assimilation genes. Also, the inoculated diazotrophs significantly increased plant nitrogen content, which was corroborated by the 15N isotope dilution analysis. Collectively, these findings suggest that P. cypripedii and K. arachidis are beneficial endophytes that could be used as a biofertilizer to improve plant nitrogen nutrition and growth of sugarcane. To the best of our knowledge, this is the first report of sugarcane growth enhancement and nitrogen fixation by Gram-negative sugarcane root-associated endophytic bacteria P. cypripedii and K. arachidis. These strains have the potential to be utilized as sugarcane biofertilizers, thus reducing nitrogen fertilizer use and improving disease management.
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Affiliation(s)
- Rajesh Kumar Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Pratiksha Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, China
| | - Dao-Jun Guo
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bio Resources, College of Agriculture, Guangxi University, Nanning, China
| | - Anjney Sharma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Dong-Ping Li
- Microbiology Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xiang Li
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Krishan K. Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Mukesh Kumar Malviya
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Xiu-Peng Song
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Prakash Lakshmanan
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- Interdisciplinary Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing, China
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Li-Tao Yang
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bio Resources, College of Agriculture, Guangxi University, Nanning, China
| | - Yang-Rui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bio Resources, College of Agriculture, Guangxi University, Nanning, China
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Schnabel T, Sattely E. Improved Stability of Engineered Ammonia Production in the Plant-Symbiont Azospirillum brasilense. ACS Synth Biol 2021; 10:2982-2996. [PMID: 34591447 PMCID: PMC8604774 DOI: 10.1021/acssynbio.1c00287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bioavailable nitrogen is the limiting nutrient for most agricultural food production. Associative diazotrophs can colonize crop roots and fix their own bioavailable nitrogen from the atmosphere. Wild-type (WT) associative diazotrophs, however, do not release fixed nitrogen in culture and are not known to directly transfer fixed nitrogen resources to plants. Efforts to engineer diazotrophs for plant nitrogen provision as an alternative to chemical fertilization have yielded several strains that transiently release ammonia. However, these strains suffer from selection pressure for nonproducers, which rapidly deplete ammonia accumulating in culture, likely limiting their potential for plant growth promotion (PGP). Here we report engineered Azospirillum brasilense strains with significantly extend ammonia production lifetimes of up to 32 days in culture. Our approach relies on multicopy genetic redundancy of a unidirectional adenylyltransferase (uAT) as a posttranslational mechanism to induce ammonia release via glutamine synthetase deactivation. Testing our multicopy stable strains with the model monocot Setaria viridis in hydroponic monoassociation reveals improvement in plant growth promotion compared to single copy strains. In contrast, inoculation of Zea mays in nitrogen-poor, nonsterile soil does not lead to increased PGP relative to WT, suggesting strain health, resource competition, or colonization capacity in soil may also be limiting factors. In this context, we show that while engineered strains fix more nitrogen per cell compared to WT strains, the expression strength of multiple uAT copies needs to be carefully balanced to maximize ammonia production rates and avoid excessive fitness defects caused by excessive glutamine synthetase shutdown.
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Affiliation(s)
- Tim Schnabel
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Elizabeth Sattely
- Department of Chemical Engineering, Stanford University and HHMI, Stanford, California 94305, United States
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