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Liebrenz K, Gómez C, Brambilla S, Frare R, Stritzler M, Maguire V, Ruiz O, Soldini D, Pascuan C, Soto G, Ayub N. Whole-Genome Resequencing of Spontaneous Oxidative Stress-Resistant Mutants Reveals an Antioxidant System of Bradyrhizobium japonicum Involved in Soybean Colonization. MICROBIAL ECOLOGY 2022; 84:1133-1140. [PMID: 34782938 DOI: 10.1007/s00248-021-01925-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Soybean is the most inoculant-consuming crop in the world, carrying strains belonging to the extremely related species Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens. Currently, it is well known that B. japonicum has higher efficiency of soybean colonization than B. diazoefficiens, but the molecular mechanism underlying this differential symbiotic performance remains unclear. In the present study, genome resequencing of four spontaneous oxidative stress-resistant mutants derived from the commercial strain B. japonicum E109 combined with molecular and physiological studies allowed identifying an antioxidant cluster (BjAC) containing a transcriptional regulator (glxA) that controls the expression of a catalase (catA) and a phosphohydrolase (yfbR) related to the hydrolysis of hydrogen peroxide and oxidized nucleotides, respectively. Integrated synteny and phylogenetic analyses supported the fact that BjAC emergence in the B. japonicum lineage occurred after its divergence from the B. diazoefficiens lineage. The transformation of the model bacterium B. diazoefficiens USDA110 with BjAC from E109 significantly increased its ability to colonize soybean roots, experimentally recapitulating the beneficial effects of the occurrence of BjAC in B. japonicum. In addition, the glxA mutation significantly increased the nodulation competitiveness and plant growth-promoting efficiency of E109. Finally, the potential applications of these types of non-genetically modified mutant microbes in soybean production worldwide are discussed.
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Affiliation(s)
- Karen Liebrenz
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Cristina Gómez
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Silvina Brambilla
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Romina Frare
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Margarita Stritzler
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Vanina Maguire
- Instituto Tecnológico Chascomús (INTECH-CONICET), Buenos Aires, Argentina
| | - Oscar Ruiz
- Instituto Tecnológico Chascomús (INTECH-CONICET), Buenos Aires, Argentina
| | - Diego Soldini
- Estación Experimental Agropecuaria Marcos Juárez, INTA, Córdoba, Argentina
| | - Cecilia Pascuan
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Gabriela Soto
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Nicolás Ayub
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina.
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina.
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Utilization of Legume-Nodule Bacterial Symbiosis in Phytoremediation of Heavy Metal-Contaminated Soils. BIOLOGY 2022; 11:biology11050676. [PMID: 35625404 PMCID: PMC9138774 DOI: 10.3390/biology11050676] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 02/04/2023]
Abstract
Simple Summary The legume–rhizobium symbiosis is one of the most beneficial interactions with high importance in agriculture, as it delivers nitrogen to plants and soil, thereby enhancing plant growth. Currently, this symbiosis is increasingly being exploited in phytoremediation of metal contaminated soil to improve soil fertility and simultaneously metal extraction or stabilization. Rhizobia increase phytoremediation directly by nitrogen fixation, protection of plants from pathogens, and production of plant growth-promoting factors and phytohormones. Abstract With the increasing industrial activity of the growing human population, the accumulation of various contaminants in soil, including heavy metals, has increased rapidly. Heavy metals as non-biodegradable elements persist in the soil environment and may pollute crop plants, further accumulating in the human body causing serious conditions. Hence, phytoremediation of land contamination as an environmental restoration technology is desirable for both human health and broad-sense ecology. Legumes (Fabaceae), which play a special role in nitrogen cycling, are dominant plants in contaminated areas. Therefore, the use of legumes and associated nitrogen-fixing rhizobia to reduce the concentrations or toxic effects of contaminants in the soil is environmentally friendly and becomes a promising strategy for phytoremediation and phytostabilization. Rhizobia, which have such plant growth-promoting (PGP) features as phosphorus solubilization, phytohormone synthesis, siderophore release, production of beneficial compounds for plants, and most of all nitrogen fixation, may promote legume growth while diminishing metal toxicity. The aim of the present review is to provide a comprehensive description of the main effects of metal contaminants in nitrogen-fixing leguminous plants and the benefits of using the legume–rhizobium symbiosis with both wild-type and genetically modified plants and bacteria to enhance an efficient recovery of contaminated lands.
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Hawkins JP, Oresnik IJ. The Rhizobium-Legume Symbiosis: Co-opting Successful Stress Management. FRONTIERS IN PLANT SCIENCE 2022; 12:796045. [PMID: 35046982 PMCID: PMC8761673 DOI: 10.3389/fpls.2021.796045] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/02/2021] [Indexed: 05/20/2023]
Abstract
The interaction of bacteria with plants can result in either a positive, negative, or neutral association. The rhizobium-legume interaction is a well-studied model system of a process that is considered a positive interaction. This process has evolved to require a complex signal exchange between the host and the symbiont. During this process, rhizobia are subject to several stresses, including low pH, oxidative stress, osmotic stress, as well as growth inhibiting plant peptides. A great deal of work has been carried out to characterize the bacterial response to these stresses. Many of the responses to stress are also observed to have key roles in symbiotic signaling. We propose that stress tolerance responses have been co-opted by the plant and bacterial partners to play a role in the complex signal exchange that occurs between rhizobia and legumes to establish functional symbiosis. This review will cover how rhizobia tolerate stresses, and how aspects of these tolerance mechanisms play a role in signal exchange between rhizobia and legumes.
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Affiliation(s)
| | - Ivan J. Oresnik
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
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Zhu J, Jiang X, Guan D, Kang Y, Li L, Cao F, Zhao B, Ma M, Zhao J, Li J. Effects of rehydration on physiological and transcriptional responses of a water-stressed rhizobium. J Microbiol 2022; 60:31-46. [PMID: 34826097 DOI: 10.1007/s12275-022-1325-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/23/2021] [Accepted: 09/29/2021] [Indexed: 01/02/2023]
Abstract
As a microsymbiont of soybean, Bradyrhizobium japonicum plays an important role in symbiotic nitrogen fixation and sustainable agriculture. However, the survival of B. japonicum cells under water-deplete (e.g., drought) and water-replete (e.g., flood) conditions is a major concern affecting their nitrogen-fixing ability by establishing the symbiotic relationship with the host. In this study, we isolated a water stress tolerant rhizobium from soybean root nodules and tested its survival under water-deplete conditions. The rhizobium was identified as Bradyrhizobium japonicum and named strain 5038. Interestingly, both plate counting and live/dead fluorescence staining assays indicate that a number of viable but non-culturable cells exist in the culture medium upon the rehydration process which could cause dilution stress. Bradyrhizobium japonicum 5038 cells increased production of exopolysaccharide (EPS) and trehalose when dehydrated, suggesting that protective responses were stimulated. As expected, cells reduced their production upon the subsequent rehydration. To examine differential gene expression of B. japonicum 5038 when exposed to water-deplete and subsequent water-replete conditions, whole-genome transcriptional analysis was performed under 10% relative humidity (RH), and subsequent 100% RH, respectively. A total of 462 differentially expressed genes (DEGs, > 2.0-fold) were identified under the 10% RH condition, while 3,776 genes showed differential expression during the subsequent rehydration (100% RH) process. Genes involved in signal transduction, inorganic ion transport, energy production and metabolisms of carbohydrates, amino acids, and lipids were far more up-regulated than down-regulated in the 10% RH condition. Notably, trehalose biosynthetic genes (otsAB, treS, and treYZ), genes ligD, oprB, and a sigma factor rpoH were significantly induced by 10% RH. Under the subsequent 100% RH condition, genes involved in transcription, translation, cell membrane regulation, replication and repair, and protein processing were highly up-regulated. Interestingly, most of 10%-RH inducible genes displayed rehydration-repressed, except three genes encoding heat shock (Hsp20) proteins. Therefore, this study provides molecular evidence for the switch of gene expression of B. japonicum cells when encountered the opposite water availability from water-deplete to water-replete conditions.
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Affiliation(s)
- Jie Zhu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
- School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, P. R. China
| | - Xin Jiang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China.
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, P. R. China.
| | - Dawei Guan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Yaowei Kang
- Life Sciences College of Zhaoqing University, Zhaoqing, 526061, P. R. China
| | - Li Li
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, P. R. China
| | - Fengming Cao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, P. R. China
| | - Baisuo Zhao
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, P. R. China
| | - Mingchao Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, P. R. China
| | - Ji Zhao
- School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, P. R. China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China.
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, P. R. China.
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Oxidative Stress Produced by Paraquat Reduces Nitrogen Fixation in Soybean-Bradyrhizobium diazoefficiens Symbiosis by Decreasing Nodule Functionality. NITROGEN 2021. [DOI: 10.3390/nitrogen2010003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Soybean (Glycine max.) is one of the most important legumes cultivated worldwide. Its productivity can be altered by some biotic and abiotic stresses like global warming, soil metal pollution or over-application of herbicides like paraquat (1,1’-dimethyl-4,4’-bipyridinium dichloride). In this study, the effect of oxidative stress produced by paraquat addition (0, 20, 50 and 100 µM) during plant growth on symbiotic nitrogen fixation (SNF) and functionality of Bradyrhizobium diazoefficiens-elicited soybean nodules were evaluated. Results showed that the 50 µM was the threshold that B. diazoefficiens can tolerate under free-living conditions. In symbiosis with soybean, the paraquat addition statistically reduced the shoot and root dry weight of soybean plants, and number and development of the nodules. SNF was negatively affected by paraquat, which reduced total nitrogen content and fixed nitrogen close to 50% when 100 µM was added. These effects were due to the impairment of nodule functionality and the increased oxidative status of the nodules, as revealed by the lower leghaemoglobin content and the higher lipid peroxidation in soybean nodules from paraquat-treated plants.
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Mortimer M, Li D, Wang Y, Holden PA. Physical Properties of Carbon Nanomaterials and Nanoceria Affect Pathways Important to the Nodulation Competitiveness of the Symbiotic N 2 -Fixing Bacterium Bradyrhizobium diazoefficiens. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1906055. [PMID: 31899607 DOI: 10.1002/smll.201906055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/21/2019] [Indexed: 05/07/2023]
Abstract
The pathogenicity and antimicrobial properties of engineered nanomaterials (ENMs) are relatively well studied. However, less is known regarding the interactions of ENMs and agriculturally beneficial microorganisms that affect food security. Nanoceria (CeO2 nanoparticles (NPs)), multiwall carbon nanotubes (MWCNTs), graphene nanoplatelets (GNPs), and carbon black (CB) have been previously shown to inhibit symbiotic N2 fixation in soybeans, but direct rhizobial susceptibility is uncertain. Here, Bradyrhizobium diazoefficiens associated with symbiotic N2 fixation in soybeans is assessed, evaluating the role of soybean root exudates (RE) on ENM-bacterial interactions and the effects of CeO2 NPs, MWCNTs, GNPs, and CB on bacterial growth and gene expression. Although bacterial growth is inhibited by 50 mg L-1 CeO2 NPs, MWCNTs, and CB, all ENMs at 0.1 and 10 mg L-1 cause a global transcriptomic response that is mitigated by RE. ENMs may interfere with plant-bacterial signaling, as evidenced by suppressed upregulation of genes induced by RE, and downregulation of genes encoding transport RNA, which facilitates nodulation signaling. MWCNTs and CeO2 NPs inhibit the expression of genes conferring B. diazoefficiens nodulation competitiveness. Surprisingly, the transcriptomic effects on B. diazoefficiens are similar for these two ENMs, indicating that physical, not chemical, ENM properties explain the observed effects.
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Affiliation(s)
- Monika Mortimer
- Institute of Environmental and Health Sciences, College of Quality and Safety Engineering, China Jiliang University, Hangzhou, Zhejiang, 310018, China
- Bren School of Environmental Science and Management and Earth Research Institute, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
- University of California Center for the Environmental Implications of Nanotechnology (UC CEIN), University of California, Santa Barbara, CA, 93106, USA
| | - Dong Li
- Bren School of Environmental Science and Management and Earth Research Institute, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Ying Wang
- Bren School of Environmental Science and Management and Earth Research Institute, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
- University of California Center for the Environmental Implications of Nanotechnology (UC CEIN), University of California, Santa Barbara, CA, 93106, USA
| | - Patricia A Holden
- Bren School of Environmental Science and Management and Earth Research Institute, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
- University of California Center for the Environmental Implications of Nanotechnology (UC CEIN), University of California, Santa Barbara, CA, 93106, USA
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Puri A, Bajaj A, Verma H, Kumar R, Singh Y, Lal R. Complete genome sequence of Paracoccus sp. strain AK26: Insights into multipartite genome architecture and methylotropy. Genomics 2020; 112:2572-2582. [PMID: 32057914 DOI: 10.1016/j.ygeno.2020.02.010] [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: 07/07/2019] [Revised: 01/01/2020] [Accepted: 02/10/2020] [Indexed: 11/26/2022]
Abstract
The present study reports the functional annotation of complete genome of methylotrophic bacterium Paracoccus sp. strain AK26. The 3.6 Mb genome with average GC content of 65.7% was distributed across five replicons; including chromosome (2.7 Mb) and four extrachromosomal replicons pAK1 (471Kb), pAK2 (189Kb), pAK3 (129Kb) and pAK4 (84 Kb). Interestingly, nearly 23% of the Cluster of Orthologous Group (COG) of proteins were annotated on extrachromosomal replicons and 185Kb genome content was attributed to segregated 19 genomic island regions. Among the four replicons, pAK4 was identified as essential and integral part of the genome, as supported by codon usage, GC content (66%) and synteny analysis. Comparative genome analysis for methylotrophy showed mechanistic variations in oxidation and assimilation of C1 compounds among closely related Paracoccus spp. Collectively, present study reports the functional characterization and genomic architecture of strain AK26 and provides genetic basis for quinone and isoprenoid based secondary metabolites synthesis using strain AK26.
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Affiliation(s)
- Akshita Puri
- Department of Zoology, University of Delhi, Delhi, India
| | - Abhay Bajaj
- Department of Zoology, University of Delhi, Delhi, India; National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Helianthous Verma
- Department of Zoology, University of Delhi, Delhi, India; Ramjas college, University of Delhi, India
| | - Roshan Kumar
- Department of Zoology, University of Delhi, Delhi, India; P.G. Department of Zoology, Magadh University, Bodh-Gaya, 824234, Bihar, India
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, India.
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, India; NASI Senior Scientist Platinum Jubilee Fellow, The Energy and Resources Institute Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi 110003, India.
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Najmuldeen H, Alghamdi R, Alghofaili F, Yesilkaya H. Functional assessment of microbial superoxide dismutase isozymes suggests a differential role for each isozyme. Free Radic Biol Med 2019; 134:215-228. [PMID: 30658083 DOI: 10.1016/j.freeradbiomed.2019.01.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/06/2018] [Accepted: 01/14/2019] [Indexed: 12/21/2022]
Abstract
Microbes can have multiple enzymes that are able to catalyse the same enzymatic reactions but may differ in structure. These are known as isozymes. It is assumed that isozymes have the same functional role for cells. Contrary to this assumption, we hypothesised that isozymes can confer different functions for microbial cells despite catalysing the same reactions. To test this hypothesis, we studied the role of superoxide dismutases (SOD) in Klebsiella pneumoniae, the causative agent of several nosocomial and community-acquired infections, in infection relevant assays. SODs are responsible for detoxification of toxic superoxide radicals. K. pneumoniae genome contains three superoxide dismutase genes, sodA, sodB, and sodC coding for Mn-, Fe- and CuZn- co-factored SODs, respectively. By creating and testing single, double, and triple SOD mutants, we investigated the regulatory interactions among SOD and determined the role of each isozyme in oxidative stress resistance, biofilm formation, cell morphology, metabolism, and in vivo colonization and persistence. Our results demonstrate that SOD isozymes in K. pneumoniae have unique roles beyond oxidative stress resistance, and there is a regulatory interplay among SODs.
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Affiliation(s)
- Hastyar Najmuldeen
- Department of Infection, Immunity and Inflammation, University of Leicester, University Road, Leicester LE1 9HN, UK; Department of Biology, College of Science, University of Sulaimani, Sulaymaniyah, Kurdistan Region, Iraq
| | - Rashed Alghamdi
- Department of Infection, Immunity and Inflammation, University of Leicester, University Road, Leicester LE1 9HN, UK
| | - Fayez Alghofaili
- Department of Infection, Immunity and Inflammation, University of Leicester, University Road, Leicester LE1 9HN, UK; Department of Biology, College of Science, Majmaah University, Majmaah 11952, Saudi Arabia
| | - Hasan Yesilkaya
- Department of Infection, Immunity and Inflammation, University of Leicester, University Road, Leicester LE1 9HN, UK.
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diCenzo GC, Zamani M, Checcucci A, Fondi M, Griffitts JS, Finan TM, Mengoni A. Multidisciplinary approaches for studying rhizobium–legume symbioses. Can J Microbiol 2019; 65:1-33. [DOI: 10.1139/cjm-2018-0377] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The rhizobium–legume symbiosis is a major source of fixed nitrogen (ammonia) in the biosphere. The potential for this process to increase agricultural yield while reducing the reliance on nitrogen-based fertilizers has generated interest in understanding and manipulating this process. For decades, rhizobium research has benefited from the use of leading techniques from a very broad set of fields, including population genetics, molecular genetics, genomics, and systems biology. In this review, we summarize many of the research strategies that have been employed in the study of rhizobia and the unique knowledge gained from these diverse tools, with a focus on genome- and systems-level approaches. We then describe ongoing synthetic biology approaches aimed at improving existing symbioses or engineering completely new symbiotic interactions. The review concludes with our perspective of the future directions and challenges of the field, with an emphasis on how the application of a multidisciplinary approach and the development of new methods will be necessary to ensure successful biotechnological manipulation of the symbiosis.
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Affiliation(s)
- George C. diCenzo
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Maryam Zamani
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alice Checcucci
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Marco Fondi
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Joel S. Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Turlough M. Finan
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
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Atieno M, Lesueur D. Opportunities for improved legume inoculants: enhanced stress tolerance of rhizobia and benefits to agroecosystems. Symbiosis 2018. [DOI: 10.1007/s13199-018-0585-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Cogo C, Pérez-Giménez J, Rajeswari CB, Luna MF, Lodeiro AR. Induction by Bradyrhizobium diazoefficiens of Different Pathways for Growth in D-mannitol or L-arabinose Leading to Pronounced Differences in CO 2 Fixation, O 2 Consumption, and Lateral-Flagellum Production. Front Microbiol 2018; 9:1189. [PMID: 29922265 PMCID: PMC5996035 DOI: 10.3389/fmicb.2018.01189] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/16/2018] [Indexed: 11/20/2022] Open
Abstract
Bradyrhizobium diazoefficiens, a soybean N2-fixing symbiont, constitutes the basic input in one of the most prominent inoculant industries worldwide. This bacterium may be cultured with D-mannitol or L-arabinose as carbon-plus-energy source (C-source) with similar specific growth rates, but with higher biomass production with D-mannitol. To better understand the bacterium’s carbon metabolism, we analyzed, by liquid chromatography and tandem mass spectrometry (MS), the whole set of proteins obtained from cells grown on each C-source. Among 3,334 proteins identified, 266 were overproduced in D-mannitol and 237 in L-arabinose, but among these, only 22% from D-mannitol cultures and 35% from L-arabinose cultures were annotated with well defined functions. In the D-mannitol-differential pool we found 19 enzymes of the pentose-phosphate and Calvin–Benson–Bassham pathways and accordingly observed increased extracellular-polysaccharide production by D-mannitol grown bacteria in a CO2-enriched atmosphere. Moreover, poly-3-hydroxybutyrate biosynthesis was increased, suggesting a surplus of reducing power. In contrast, the L-arabinose-differential pool contained 11 enzymes of the L-2-keto-3-deoxyarabonate pathway, 4 enzymes for the synthesis of nicotinamide-adenine dinucleotide from aspartate, with those cultures having a threefold higher O2-consumption rate than the D-mannitol cultures. The stoichiometric balances deduced from the modeled pathways, however, resulted in similar O2 consumptions and ATP productions per C-mole of substrate. These results suggested higher maintenance-energy demands in L-arabinose, which energy may be used partly for flagella-driven motility. Since B. diazoefficiens produces the lateral-flagella system in only L-arabinose, we calculated the O2-consumption rates of a lafR::Km mutant devoid of lateral flagella cultured in L-arabinose or D-mannitol. Contrary to that of the wild-type, the O2-consumption rate of this mutant was similar on both C-sources, and accordingly outcompeted the wild-type in coculture, suggesting that the lateral flagella behaved as parasitic structures under these conditions. Proteomic data are available via ProteomeXchange with identifier PXD008263.
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Affiliation(s)
- Carolina Cogo
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas-UNLP y CCT La Plata-CONICET, La Plata, Argentina.,Departamento de Ciencias Básicas, Facultad de Ingeniería-UNLP, La Plata, Argentina
| | - Julieta Pérez-Giménez
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas-UNLP y CCT La Plata-CONICET, La Plata, Argentina
| | - Chandrasekar B Rajeswari
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas-UNLP y CCT La Plata-CONICET, La Plata, Argentina
| | - María F Luna
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, Facultad de Ciencias Exactas-UNLP y CCT La Plata-CONICET, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires, La Plata, Argentina
| | - Aníbal R Lodeiro
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas-UNLP y CCT La Plata-CONICET, La Plata, Argentina
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Hawkins JP, Geddes BA, Oresnik IJ. Succinoglycan Production Contributes to Acidic pH Tolerance in Sinorhizobium meliloti Rm1021. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:1009-1019. [PMID: 28871850 DOI: 10.1094/mpmi-07-17-0176-r] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this work, the hypothesis that exopolysaccharide plays a role in the survival of Sinorhizobium meliloti at low pH levels is addressed. When S. meliloti was grown at pH 5.75, synthesis of succinoglycan increased, whereas synthesis of galactoglucan decreased. Succinoglycan that was isolated from cultures grown at low pH had a lower degree of polymerization relative to that which was isolated from cultures grown at neutral pH, suggesting that low-molecular weight (LMW) succinoglycan might play a role in adaptation to low pH. Mutants unable to produce succinoglycan or only able to produce high-molecular weight polysaccharide were found to be sensitive to low pH. However, strains unable to produce LMW polysaccharide were 10-fold more sensitive. In response to low pH, transcription of genes encoding proteins for succinoglycan, glycogen, and cyclic β(1-2) glucans biosynthesis increased, while those encoding proteins necessary for the biosynthesis of galactoglucan decreased. While changes in pH did not affect the production of glycogen or cyclic β(1-2) glucan, it was found that the inability to produce cyclic β(1-2) glucan did contribute to pH tolerance in the absence of succinoglycan. Finally, in addition to being sensitive to low pH, a strain carrying mutations in exoK and exsH, which encode the glycanases responsible for the cleavage of succinoglycan to LMW succinoglycan, exhibited a delay in nodulation and was uncompetitive for nodule occupancy. Taken together, the data suggest that the role for LMW succinoglycan in nodule development may be to enhance survival in the colonized curled root hair.
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Affiliation(s)
- Justin P Hawkins
- Dept. of Microbiology, University of Manitoba, Winnipeg, R3T 2N2, Canada
| | - Barney A Geddes
- Dept. of Microbiology, University of Manitoba, Winnipeg, R3T 2N2, Canada
| | - Ivan J Oresnik
- Dept. of Microbiology, University of Manitoba, Winnipeg, R3T 2N2, Canada
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Mongiardini EJ, Quelas JI, Dardis C, Althabegoiti MJ, Lodeiro AR. Transcriptional Control of the Lateral-Flagellar Genes of Bradyrhizobium diazoefficiens. J Bacteriol 2017; 199:e00253-17. [PMID: 28533217 PMCID: PMC5512216 DOI: 10.1128/jb.00253-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 05/16/2017] [Indexed: 11/20/2022] Open
Abstract
Bradyrhizobium diazoefficiens, a soybean N2-fixing symbiont, possesses a dual flagellar system comprising a constitutive subpolar flagellum and inducible lateral flagella. Here, we analyzed the genomic organization and biosynthetic regulation of the lateral-flagellar genes. We found that these genes are located in a single genomic cluster, organized in two monocistronic transcriptional units and three operons, one possibly containing an internal transcription start site. Among the monocistronic units is blr6846, homologous to the class IB master regulators of flagellum synthesis in Brucella melitensis and Ensifer meliloti and required for the expression of all the lateral-flagellar genes except lafA2, whose locus encodes a single lateral flagellin. We therefore named blr6846 lafR (lateral-flagellar regulator). Despite its similarity to two-component response regulators and its possession of a phosphorylatable Asp residue, lafR behaved as an orphan response regulator by not requiring phosphorylation at this site. Among the genes induced by lafR is flbTL , a class III regulator. We observed different requirements for FlbTL in the synthesis of each flagellin subunit. Although the accumulation of lafA1, but not lafA2, transcripts required FlbTL, the production of both flagellin polypeptides required FlbTL Moreover, the regulation cascade of this lateral-flagellar regulon appeared to be not as strictly ordered as those found in other bacterial species.IMPORTANCE Bacterial motility seems essential for the free-living style in the environment, and therefore these microorganisms allocate a great deal of their energetic resources to the biosynthesis and functioning of flagella. Despite energetic costs, some bacterial species possess dual flagellar systems, one of which is a primary system normally polar or subpolar, and the other is a secondary, lateral system that is produced only under special circumstances. Bradyrhizobium diazoefficiens, an N2-fixing symbiont of soybean plants, possesses dual flagellar systems, including the lateral system that contributes to swimming in wet soil and competition for nodulation and is expressed under high energy availability, as well as under requirement for high torque by the flagella. The structural organization and transcriptional regulation of the 41 genes that comprise this secondary flagellar system seem adapted to adjust bacterial energy expenditures for motility to the soil's environmental dynamics.
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Affiliation(s)
- Elías J Mongiardini
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata y CCT-La Plata, CONICET, La Plata, Argentina
| | - J Ignacio Quelas
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata y CCT-La Plata, CONICET, La Plata, Argentina
| | - Carolina Dardis
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata y CCT-La Plata, CONICET, La Plata, Argentina
| | - M Julia Althabegoiti
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata y CCT-La Plata, CONICET, La Plata, Argentina
| | - Aníbal R Lodeiro
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata y CCT-La Plata, CONICET, La Plata, Argentina
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Regulation of Polyhydroxybutyrate Synthesis in the Soil Bacterium Bradyrhizobium diazoefficiens. Appl Environ Microbiol 2016; 82:4299-4308. [PMID: 27208130 DOI: 10.1128/aem.00757-16] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/02/2016] [Indexed: 02/06/2023] Open
Abstract
Polyhydroxybutyrate (PHB) is a carbon and energy reserve polymer in various prokaryotic species. We determined that, when grown with mannitol as the sole carbon source, Bradyrhizobium diazoefficiens produces a homopolymer composed only of 3-hydroxybutyrate units (PHB). Conditions of oxygen limitation (such as microoxia, oxic stationary phase, and bacteroids inside legume nodules) were permissive for the synthesis of PHB, which was observed as cytoplasmic granules. To study the regulation of PHB synthesis, we generated mutations in the regulator gene phaR and the phasin genes phaP1 and phaP4 Under permissive conditions, mutation of phaR impaired PHB accumulation, and a phaP1 phaP4 double mutant produced more PHB than the wild type, which was accumulated in a single, large cytoplasmic granule. Moreover, PhaR negatively regulated the expression of phaP1 and phaP4 as well as the expression of phaA1 and phaA2 (encoding a 3-ketoacyl coenzyme A [CoA] thiolases), phaC1 and phaC2 (encoding PHB synthases), and fixK2 (encoding a cyclic AMP receptor protein [CRP]/fumarate and nitrate reductase regulator [FNR]-type transcription factor of genes for microoxic lifestyle). In addition to the depressed PHB cycling, phaR mutants accumulated more extracellular polysaccharides and promoted higher plant shoot dry weight and competitiveness for nodulation than the wild type, in contrast to the phaC1 mutant strain, which is defective in PHB synthesis. These results suggest that phaR not only regulates PHB granule formation by controlling the expression of phasins and biosynthetic enzymes but also acts as a global regulator of excess carbon allocation and symbiosis by controlling fixK2 IMPORTANCE: In this work, we investigated the regulation of polyhydroxybutyrate synthesis in the soybean-nodulating bacterium Bradyrhizobium diazoefficiens and its influence in bacterial free-living and symbiotic lifestyles. We uncovered a new interplay between the synthesis of this carbon reserve polymer and the network responsible for microoxic metabolism through the interaction between the gene regulators phaR and fixK2 These results contribute to the understanding of the physiological conditions required for polyhydroxybutyrate biosynthesis. The interaction between these two main metabolic pathways is also reflected in the symbiotic phenotypes of soybeans inoculated with phaR mutants, which were more competitive for nodulation and enhanced dry matter production by the plants. Therefore, this knowledge may be applied to the development of superior strains to be used as improved inoculants for soybean crops.
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Thaweethawakorn A, Parks D, So JS, Chang WS. Role of the extracytoplasmic function sigma factor CarQ in oxidative response of Bradyrhizobium japonicum. J Microbiol 2015; 53:526-34. [PMID: 26224455 DOI: 10.1007/s12275-015-5308-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 07/17/2015] [Accepted: 07/21/2015] [Indexed: 12/11/2022]
Abstract
As a nitrogen-fixing bacterium, Bradyrhizobium japonicum can establish a symbiotic relationship with the soybean plant (Glycine max). To be a successful symbiont, B. japonicum must deal with plant defense responses, such as an oxidative burst. Our previous functional genomics study showed that carQ (bll1028) encoding extracytoplasmic function (ECF) sigma factor was highly expressed (107.8-fold induction) under oxidative stress. Little is known about the underlying mechanisms of how CarQ responds to oxidative stress. In this study, a carQ knock-out mutant was constructed using site-specific mutagenesis to identify the role of carQ in the oxidative response of B. japonicum. The carQ mutant showed a longer generation time than the wild type and exhibited significantly decreased survival at 10 mM H(2)O(2) for 10 min of exposure. Surprisingly, there was no significant difference in expression of oxidative stress-responsive genes such as katG and sod between the wild type and carQ mutant. The mutant also showed a significant increase in susceptibility to H(2)O(2) compared to the wild type in the zone inhibition assay. Nodulation phenotypes of the carQ mutant were distinguishable compared to those of the wild type, including lower numbers of nodules, decreased nodule dry weight, decreased plant dry weight, and a lower nitrogen fixation capability. Moreover, desiccation of mutant cells also resulted in significantly lower percent of survival in both early (after 4 h) and late (after 24 h) desiccation periods. Taken together, this information will provide an insight into the role of the ECF sigma factor in B. japonicum to deal with a plant-derived oxidative burst.
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Noh JG, Jeon HE, So JS, Chang WS. Effects of the Bradyrhizobium japonicum waaL (rfaL) Gene on Hydrophobicity, Motility, Stress Tolerance, and Symbiotic Relationship with Soybeans. Int J Mol Sci 2015; 16:16778-91. [PMID: 26213919 PMCID: PMC4581169 DOI: 10.3390/ijms160816778] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 07/16/2015] [Accepted: 07/22/2015] [Indexed: 11/16/2022] Open
Abstract
We cloned and sequenced the waaL (rfaL) gene from Bradyrhizobium japonicum, which infects soybean and forms nitrogen-fixing nodules on soybean roots. waaL has been extensively studied in the lipopolysaccharide (LPS) biosynthesis of enteric bacteria, but little is known about its function in (brady)rhizobial LPS architecture. To characterize its role as O-antigen ligase in the LPS biosynthesis pathway, we constructed a waaL knock-out mutant and its complemented strain named JS015 and CS015, respectively. LPS analysis showed that an LPS structure of JS015 is deficient in O-antigen as compared to that of the wild type and complemented strain CS015, suggesting that WaaL ligates the O-antigen to lipid A-core oligosaccharide to form a complete LPS. JS015 also revealed increased cell surface hydrophobicity, but it showed decreased motility in soft agar plates. In addition to the alteration in cell surface properties, disruption of the waaL gene caused increased sensitivity of JS015 to hydrogen peroxide, osmotic pressure, and novobiocin. Specifically, plant tests revealed that JS015 failed to nodulate the host plant soybean, indicating that the rhizobial waaL gene is responsible for the establishment of a symbiotic relationship between soybean and B. japonicum.
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Affiliation(s)
- Jun-Gu Noh
- Department of Biological Engineering, Inha University, Incheon 402-751, Korea.
| | - Han-Eul Jeon
- Department of Biological Engineering, Inha University, Incheon 402-751, Korea.
| | - Jae-Seong So
- Department of Biological Engineering, Inha University, Incheon 402-751, Korea.
| | - Woo-Suk Chang
- Department of Biology, University of Texas, Arlington, TX 76019, USA.
- Division of Biotechnology, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan 570-752, Korea.
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Jeon JM, Lee HI, Sadowsky MJ, Sugawara M, Chang WS. Characterization of a Functional Role of the Bradyrhizobium japonicum Isocitrate Lyase in Desiccation Tolerance. Int J Mol Sci 2015. [PMID: 26204840 PMCID: PMC4519974 DOI: 10.3390/ijms160716695] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Bradyrhizobium japonicum is a nitrogen-fixing symbiont of soybean. In previous studies, transcriptomic profiling of B. japonicum USDA110, grown under various environmental conditions, revealed the highly induced gene aceA, encoding isocitrate lyase (ICL). The ICL catalyzes the conversion of isocitrate to succinate and glyoxylate in the glyoxylate bypass of the TCA cycle. Here, we evaluated the functional role of B. japonicum ICL under desiccation-induced stress conditions. We purified AceA (molecular mass = 65 kDa) from B. japonicum USDA110, using a His-tag and Ni-NTA column approach, and confirmed its ICL enzyme activity. The aceA mutant showed higher sensitivity to desiccation stress (27% relative humidity (RH)), compared to the wild type. ICL activity of the wild type strain increased approximately 2.5-fold upon exposure to 27% RH for 24 h. The aceA mutant also showed an increased susceptibility to salt stress. Gene expression analysis of aceA using qRT-PCR revealed a 148-fold induction by desiccation, while other genes involved in the glyoxylate pathway were not differentially expressed in this condition. Transcriptome analyses revealed that stress-related genes, such as chaperones, were upregulated in the wild-type under desiccating conditions, even though fold induction was not dramatic (ca. 1.5-2.5-fold).
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Affiliation(s)
- Jeong-Min Jeon
- Department of Biology, University of Texas, Arlington, TX 76019, USA.
| | - Hae-In Lee
- Department of Biology, University of Texas, Arlington, TX 76019, USA.
| | - Michael J Sadowsky
- Department of Soil, Water & Climate, and The BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA.
| | - Masayuki Sugawara
- Department of Soil, Water & Climate, and The BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA.
| | - Woo-Suk Chang
- Department of Biology, University of Texas, Arlington, TX 76019, USA.
- Division of Biotechnology, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan 570-752, Korea.
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Proteomic responses to a methyl viologen-induced oxidative stress in the wild type and FerB mutant strains of Paracoccus denitrificans. J Proteomics 2015; 125:68-75. [DOI: 10.1016/j.jprot.2015.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 04/24/2015] [Accepted: 05/01/2015] [Indexed: 01/17/2023]
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DNA Microarray-Based Identification of Genes Regulated by NtrC in Bradyrhizobium japonicum. Appl Environ Microbiol 2015; 81:5299-308. [PMID: 26025905 DOI: 10.1128/aem.00609-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/18/2015] [Indexed: 11/20/2022] Open
Abstract
The Bradyrhizobium japonicum NtrBC two-component system is a critical regulator of cellular nitrogen metabolism, including the acquisition and catabolism of nitrogenous compounds. To better define the roles of this system, genome-wide transcriptional profiling was performed to identify the NtrC regulon during the response to nitrogen limitation. Upon cells perceiving low intracellular nitrogen, they stimulate the phosphorylation of NtrC, which induces genes responsible for alteration of the core glutamine synthetase/glutamate synthase nitrogen assimilation pathway, including the genes for the glutamine synthetases and PII proteins. In addition, genes responsible for the import and utilization of multiple nitrogen sources, specifically nitrate and nitrite, were upregulated by NtrC activation. Mutational analysis of a candidate nitrite reductase revealed a role for NtrC in regulating the assimilation of nitrite, since mutations in both ntrC and the gene encoding the candidate nitrite reductase abolished the ability to grow on nitrite as a sole nitrogen source.
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Ramírez M, Guillén G, Fuentes SI, Iñiguez LP, Aparicio-Fabre R, Zamorano-Sánchez D, Encarnación-Guevara S, Panzeri D, Castiglioni B, Cremonesi P, Strozzi F, Stella A, Girard L, Sparvoli F, Hernández G. Transcript profiling of common bean nodules subjected to oxidative stress. PHYSIOLOGIA PLANTARUM 2013; 149:389-407. [PMID: 23432573 DOI: 10.1111/ppl.12040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 01/25/2013] [Accepted: 01/28/2013] [Indexed: 06/01/2023]
Abstract
Several environmental stresses generate high amounts of reactive oxygen species (ROS) in plant cells, resulting in oxidative stress. Symbiotic nitrogen fixation (SNF) in the legume-rhizobia symbiosis is sensitive to damage from oxidative stress. Active nodules of the common bean (Phaseolus vulgaris) exposed to the herbicide paraquat (1,1'-dimethyl-4,4'-bipyridinium dichloride hydrate), which stimulates ROS accumulation, exhibited reduced nitrogenase activity and ureide content. We analyzed the global gene response of nodules subjected to oxidative stress using the Bean Custom Array 90K, which includes probes from 30,000 expressed sequence tags (ESTs). A total of 4280 ESTs were differentially expressed in stressed bean nodules; of these, 2218 were repressed. Based on Gene Ontology analysis, these genes were grouped into 42 different biological process categories. Analysis with the PathExpress bioinformatic tool, adapted for bean, identified five significantly repressed metabolic pathways related to carbon/nitrogen metabolism, which is crucial for nodule function. Quantitative reverse transcription (qRT)-PCR analysis of transcription factor (TF) gene expression showed that 67 TF genes were differentially expressed in nodules exposed to oxidative stress. Putative cis-elements recognized by highly responsive TF were detected in promoter regions of oxidative stress regulated genes. The expression of oxidative stress responsive genes and of genes important for SNF in bacteroids analyzed in stressed nodules revealed that these conditions elicited a transcriptional response.
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Affiliation(s)
- Mario Ramírez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 1001, Cuernavaca, Mor. 62209, Mexico
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Alteration of the exopolysaccharide production and the transcriptional profile of free-living Frankia strain CcI3 under nitrogen-fixing conditions. Appl Microbiol Biotechnol 2013; 97:10499-509. [PMID: 24097014 DOI: 10.1007/s00253-013-5277-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 10/26/2022]
Abstract
We investigated the effect of different nitrogen (N) sources on exopolysaccharide (EPS) production and composition by Frankia strain CcI3, a N2-fixing actinomycete that forms root nodules with Casuarina species. Frankia cells grown in the absence of NH4Cl (i.e., under N2-fixing conditions) produced 1.7-fold more EPS, with lower galactose (45.1 vs. 54.7 mol%) and higher mannose (17.3 vs. 9.7 mol%) contents than those grown in the presence of NH4Cl as a combined N-source. In the absence of the combined N-source, terminally linked and branched residue contents were nearly twice as high with 32.8 vs. 15.1 mol% and 15.1 vs. 8.7 mol%, respectively, than in its presence, while the content of linearly linked residues was lower with 52.1 mol% compared to 76.2 mol%. To find out clues for the altered EPS production at the transcriptional level, we performed whole-gene expression profiling using quantitative reverse transcription PCR and microarray technology. The transcription profiles of Frankia strain CcI3 grown in the absence of NH4Cl revealed up to 2 orders of magnitude higher transcription of nitrogen fixation-related genes compared to those of CcI3 cells grown in the presence of NH4Cl. Unexpectedly, microarray data did not provide evidence for transcriptional regulation as a mechanism for differences in EPS production. These findings indicate effects of nitrogen fixation on the production and composition of EPS in Frankia strain CcI3 and suggest posttranscriptional regulation of enhanced EPS production in the absence of the combined N-source.
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Donati AJ, Lee HI, Leveau JHJ, Chang WS. Effects of indole-3-acetic acid on the transcriptional activities and stress tolerance of Bradyrhizobium japonicum. PLoS One 2013; 8:e76559. [PMID: 24098533 PMCID: PMC3788728 DOI: 10.1371/journal.pone.0076559] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/28/2013] [Indexed: 11/18/2022] Open
Abstract
A genome-wide transcriptional profile of Bradyrhizobium japonicum, the nitrogen-fixing endosymbiont of the soybean plant, revealed differential expression of approximately 15% of the genome after a 1 mM treatment with the phytohormone indole-3-acetic acid (IAA). A total of 1,323 genes were differentially expressed (619 up-regulated and 704 down-regulated) at a two-fold cut off with q value ≤ 0.05. General stress response genes were induced, such as those involved in response to heat, cold, oxidative, osmotic, and desiccation stresses and in exopolysaccharide (EPS) biosynthesis. This suggests that IAA is effective in activating a generalized stress response in B. japonicum. The transcriptional data were corroborated by the finding that stress tolerance of B. japonicum in cell viability assays was enhanced when pre-treated with 1 mM IAA compared to controls. The IAA treatment also stimulated biofilm formation and EPS production by B. japonicum, especially acidic sugar components in the total EPS. The IAA pre-treatment did not influence the nodulation ability of B. japonicum. The data provide a comprehensive overview of the potential transcriptional responses of the symbiotic bacterium when exposed to the ubiquitous hormone of its plant host.
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Affiliation(s)
- Andrew J. Donati
- Department of Biology, University of Texas, Arlington, Texas, United States of America
| | - Hae-In Lee
- Department of Biology, University of Texas, Arlington, Texas, United States of America
| | - Johan H. J. Leveau
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
| | - Woo-Suk Chang
- Department of Biology, University of Texas, Arlington, Texas, United States of America
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Coba de la Peña T, Redondo FJ, Fillat MF, Lucas MM, Pueyo JJ. Flavodoxin overexpression confers tolerance to oxidative stress in beneficial soil bacteria and improves survival in the presence of the herbicides paraquat and atrazine. J Appl Microbiol 2013; 115:236-46. [PMID: 23594228 DOI: 10.1111/jam.12224] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 04/09/2013] [Accepted: 04/14/2013] [Indexed: 12/01/2022]
Abstract
AIM To determine whether expression of a cyanobacterial flavodoxin in soil bacteria of agronomic interest confers protection against the widely used herbicides paraquat and atrazine. METHODS AND RESULTS The model bacterium Escherichia coli, the symbiotic nitrogen-fixing bacterium Ensifer meliloti and the plant growth-promoting rhizobacterium Pseudomonas fluorescens Aur6 were transformed with expression vectors containing the flavodoxin gene of Anabaena variabilis. Expression of the cyanobacterial protein was confirmed by Western blot. Bacterial tolerance to oxidative stress was tested in solid medium supplemented with hydrogen peroxide, paraquat or atrazine. In all three bacterial strains, flavodoxin expression enhanced tolerance to the oxidative stress provoked by hydrogen peroxide and by the reactive oxygen species-inducing herbicides, witnessed by the enhanced survival of the transformed bacteria in the presence of these oxidizing agents. CONCLUSIONS Flavodoxin overexpression in beneficial soil bacteria confers tolerance to oxidative stress and improves their survival in the presence of the herbicides paraquat and atrazine. Flavodoxin could be considered as a general antioxidant resource to face oxidative challenges in different micro-organisms. SIGNIFICANCE AND IMPACT OF THE STUDY The use of plant growth-promoting rhizobacteria or nitrogen-fixing bacteria with enhanced tolerance to oxidative stress in contaminated soils is of significant agronomic interest. The enhanced tolerance of flavodoxin-expressing bacteria to atrazine and paraquat points to potential applications in herbicide-treated soils.
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Affiliation(s)
- T Coba de la Peña
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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Herbst FA, Taubert M, Jehmlich N, Behr T, Schmidt F, von Bergen M, Seifert J. Sulfur-34S stable isotope labeling of amino acids for quantification (SULAQ34) of proteomic changes in Pseudomonas fluorescens during naphthalene degradation. Mol Cell Proteomics 2013; 12:2060-9. [PMID: 23603340 DOI: 10.1074/mcp.m112.025627] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The relative quantification of proteins is one of the major techniques used to elucidate physiological reactions. Because it allows one to avoid artifacts due to chemical labeling, the metabolic introduction of heavy isotopes into proteins and peptides is the preferred method for relative quantification. For eukaryotic cells, stable isotope labeling by amino acids in cell culture (SILAC) has become the gold standard and can be readily applied in a vast number of scenarios. In the microbial realm, with its highly versatile metabolic capabilities, SILAC is often not feasible, and the use of other (13)C or (15)N labeled substrates might not be practical. Here, the incorporation of heavy sulfur isotopes is shown to be a useful alternative. We introduce (34)S stable isotope labeling of amino acids for quantification and the corresponding tools required for spectra extraction and disintegration of the isotopic overlaps caused by the small mass shift. As proof of principle, we investigated the proteomic changes related to naphthalene degradation in P. fluorescens ATCC 17483 and uncovered a specific oxidative-stress-like response.
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Affiliation(s)
- Florian-Alexander Herbst
- Helmholtz Centre for Environmental Research, Department of Proteomics, Permoserstrasse 15, 04318 Leipzig, Germany
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Tiensuu T, Andersson C, Rydén P, Johansson J. Cycles of light and dark co-ordinate reversible colony differentiation in Listeria monocytogenes. Mol Microbiol 2013; 87:909-24. [PMID: 23331346 PMCID: PMC3610012 DOI: 10.1111/mmi.12140] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2012] [Indexed: 02/03/2023]
Abstract
Recently, several light receptors have been identified in non-phototrophic bacteria, but their physiological roles still remain rather elusive. Here we show that colonies of the saprophytic bacterium Listeria monocytogenes undergo synchronized multicellular behaviour on agar plates, in response to oscillating light/dark conditions, giving rise to alternating ring formation (opaque and translucent rings). On agar plates, bacteria from opaque rings survive increased levels of reactive oxygen species (ROS), as well as repeated cycles of light and dark, better than bacteria from translucent rings. The ring formation is strictly dependent on a blue-light receptor, Lmo0799, acting through the stress-sigma factor, σB. A transposon screening identified 48 mutants unable to form rings at alternating light conditions, with several of them showing a decreased σB activity/level. However, some of the tested mutants displayed a varied σB activity depending on which of the two stress conditions tested (light or H2O2 exposure). Intriguingly, the transcriptional regulator PrfA and the virulence factor ActA were shown to be required for ring formation by a mechanism involving activation of σB. All in all, this suggests a distinct pathway for Lmo0799 that converge into a common signalling pathway for σB activation. Our results show that night and day cycles co-ordinate a reversible differentiation of a L. monocytogenes colony at room temperature, by a process synchronized by a blue-light receptor and σB.
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Affiliation(s)
- Teresa Tiensuu
- Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden
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Masloboeva N, Reutimann L, Stiefel P, Follador R, Leimer N, Hennecke H, Mesa S, Fischer HM. Reactive oxygen species-inducible ECF σ factors of Bradyrhizobium japonicum. PLoS One 2012; 7:e43421. [PMID: 22916258 PMCID: PMC3420878 DOI: 10.1371/journal.pone.0043421] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 07/19/2012] [Indexed: 12/19/2022] Open
Abstract
Extracytoplasmic function (ECF) σ factors control the transcription of genes involved in different cellular functions, such as stress responses, metal homeostasis, virulence-related traits, and cell envelope structure. The genome of Bradyrhizobium japonicum, the nitrogen-fixing soybean endosymbiont, encodes 17 putative ECF σ factors belonging to nine different ECF σ factor families. The genes for two of them, ecfQ (bll1028) and ecfF (blr3038), are highly induced in response to the reactive oxygen species hydrogen peroxide (H2O2) and singlet oxygen (1O2). The ecfF gene is followed by the predicted anti-σ factor gene osrA (blr3039). Mutants lacking EcfQ, EcfF plus OsrA, OsrA alone, or both σ factors plus OsrA were phenotypically characterized. While the symbiotic properties of all mutants were indistinguishable from the wild type, they showed increased sensitivity to singlet oxygen under free-living conditions. Possible target genes of EcfQ and EcfF were determined by microarray analyses, and candidate genes were compared with the H2O2-responsive regulon. These experiments disclosed that the two σ factors control rather small and, for the most part, distinct sets of genes, with about half of the genes representing 13% of the members of H2O2-responsive regulon. To get more insight into transcriptional regulation of both σ factors, the 5′ ends of ecfQ and ecfF mRNA were determined. The presence of conserved sequence motifs in the promoter region of ecfQ and genes encoding EcfQ-like σ factors in related α-proteobacteria suggests regulation via a yet unknown transcription factor. By contrast, we have evidence that ecfF is autoregulated by transcription from an EcfF-dependent consensus promoter, and its product is negatively regulated via protein-protein interaction with OsrA. Conserved cysteine residues 129 and 179 of OsrA are required for normal function of OsrA. Cysteine 179 is essential for release of EcfF from an EcfF-OsrA complex upon H2O2 stress while cysteine 129 is possibly needed for EcfF-OsrA interaction.
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Affiliation(s)
| | | | | | | | - Nadja Leimer
- ETH, Institute of Microbiology, Zurich, Switzerland
| | | | - Socorro Mesa
- ETH, Institute of Microbiology, Zurich, Switzerland
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Jeon JM, Lee HI, Donati AJ, So JS, Emerich DW, Chang WS. Whole-genome expression profiling of Bradyrhizobium japonicum in response to hydrogen peroxide. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:1472-81. [PMID: 21864047 DOI: 10.1094/mpmi-03-11-0072] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Bradyrhizobium japonicum, a nitrogen-fixing bacterium in soil, establishes a symbiotic relationship with the leguminous soybean plant. Despite a mutualistic association between the two partners, the host plant produces an oxidative burst to protect itself from the invasion of rhizobial cells. We investigated the effects of H(2)O(2)-mediated oxidative stress on B. japonicum gene expression in both prolonged exposure (PE) and fulminant shock (FS) conditions. In total, 439 and 650 genes were differentially expressed for the PE and FS conditions, respectively, at a twofold cut-off with q < 0.05. A number of genes within the transport and binding proteins category were upregulated during PE and a majority of those genes are involved in ABC transporter systems. Many genes encoding ? factors, global stress response proteins, the FixK(2) transcription factor, and its regulatory targets were found to be upregulated in the FS condition. Surprisingly, catalase and peroxidase genes which are typically expressed in other bacteria under oxidative stress were not differentially expressed in either condition. The isocitrate lyase gene (aceA) was induced by fulminant H(2)O(2) shock, as was evident at both the transcriptional and translational levels. Interestingly, there was no significant effect of H(2)O(2) on exopolysaccharide production at the given experimental conditions.
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Affiliation(s)
- Jeong-Min Jeon
- Department of Biology, University of Texas, Arlington, TX, USA
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