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Balsanelli E, Tadra-Sfeir MZ, Faoro H, Pankievicz VC, de Baura VA, Pedrosa FO, de Souza EM, Dixon R, Monteiro RA. Molecular adaptations of Herbaspirillum seropedicae during colonization of the maize rhizosphere. Environ Microbiol 2015; 18:2343-56. [PMID: 25923055 DOI: 10.1111/1462-2920.12887] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 04/21/2015] [Indexed: 12/21/2022]
Abstract
Molecular mechanisms of plant recognition and colonization by diazotrophic bacteria are barely understood. Herbaspirillum seropedicae is a Betaproteobacterium capable of colonizing epiphytically and endophytically commercial grasses, to promote plant growth. In this study, we utilized RNA-seq to compare the transcriptional profiles of planktonic and maize root-attached H. seropedicae SmR1 recovered 1 and 3 days after inoculation. The results indicated that nitrogen metabolism was strongly activated in the rhizosphere and polyhydroxybutyrate storage was mobilized in order to assist the survival of H. seropedicae during the early stages of colonization. Epiphytic cells showed altered transcription levels of several genes associated with polysaccharide biosynthesis, peptidoglycan turnover and outer membrane protein biosynthesis, suggesting reorganization of cell wall envelope components. Specific methyl-accepting chemotaxis proteins and two-component systems were differentially expressed between populations over time, suggesting deployment of an extensive bacterial sensory system for adaptation to the plant environment. An insertion mutation inactivating a methyl-accepting chemosensor induced in planktonic bacteria, decreased chemotaxis towards the plant and attachment to roots. In summary, analysis of mutant strains combined with transcript profiling revealed several molecular adaptations that enable H. seropedicae to sense the plant environment, attach to the root surface and survive during the early stages of maize colonization.
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Affiliation(s)
- Eduardo Balsanelli
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Michelle Z Tadra-Sfeir
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Helisson Faoro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Vânia Cs Pankievicz
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Valter A de Baura
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio O Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Emanuel M de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Ray Dixon
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Rose A Monteiro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
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Batista MB, Wassem R, Pedrosa FDO, de Souza EM, Dixon R, Monteiro RA. Enhanced oxygen consumption in Herbaspirillum seropedicae fnr mutants leads to increased NifA mediated transcriptional activation. BMC Microbiol 2015; 15:95. [PMID: 25947294 PMCID: PMC4422417 DOI: 10.1186/s12866-015-0432-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/24/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Orthologous proteins of the Crp/Fnr family have been previously implicated in controlling expression and/or activity of the NifA transcriptional activator in some diazotrophs. This study aimed to address the role of three Fnr-like proteins from H. seropedicae SmR1 in controlling NifA activity and consequent NifA-mediated transcription activation. RESULTS The activity of NifA-dependent transcriptional fusions (nifA::lacZ and nifB::lacZ) was analysed in a series of H. seropedicae fnr deletion mutant backgrounds. We found that combined deletions in both the fnr1 and fnr3 genes lead to higher expression of both the nifA and nifB genes and also an increased level of nifH transcripts. Expression profiles of nifB under different oxygen concentrations, together with oxygen consumption measurements suggest that the triple fnr mutant has higher respiratory activity when compared to the wild type, which we believe to be responsible for greater stability of the oxygen sensitive NifA protein. This conclusion was further substantiated by measuring the levels of NifA protein and its activity in fnr deletion strains in comparison with the wild-type. CONCLUSIONS Fnr proteins are indirectly involved in controlling the activity of NifA in H. seropedicae, probably as a consequence of their influence on respiratory activity in relation to oxygen availability. Additionally we can suggest that there is some redundancy in the physiological function of the three Fnr paralogs in this organism, since altered respiration and effects on NifA activity are only observed in deletion strains lacking both fnr1 and fnr3.
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Affiliation(s)
- Marcelo Bueno Batista
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, P.O. Box 19046, Curitiba, PR, 81531-990, Brazil.
| | - Roseli Wassem
- Department of Genetics, Universidade Federal do Paraná, P.O. Box 19071, Curitiba, PR, 81531-990, Brazil.
| | - Fábio de Oliveira Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, P.O. Box 19046, Curitiba, PR, 81531-990, Brazil.
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, P.O. Box 19046, Curitiba, PR, 81531-990, Brazil.
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK.
| | - Rose Adele Monteiro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, P.O. Box 19046, Curitiba, PR, 81531-990, Brazil.
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Nishikawa CY, Araújo LM, Kadowaki MAS, Monteiro RA, Steffens MBR, Pedrosa FO, Souza EM, Chubatsu LS. Expression and characterization of an N-truncated form of the NifA protein of Azospirillum brasilense. Braz J Med Biol Res 2012; 45:113-7. [PMID: 22267004 PMCID: PMC3854256 DOI: 10.1590/s0100-879x2012007500006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 01/09/2012] [Indexed: 12/03/2022] Open
Abstract
Azospirillum brasilense is a nitrogen-fixing bacterium associated with important agricultural crops such as rice, wheat and maize. The expression of genes responsible for nitrogen fixation (nif genes) in this bacterium is dependent on the transcriptional activator NifA. This protein contains three structural domains: the N-terminal domain is responsible for the negative control by fixed nitrogen; the central domain interacts with the RNA polymerase σ54 factor and the C-terminal domain is involved in DNA binding. The central and C-terminal domains are linked by the interdomain linker (IDL). A conserved four-cysteine motif encompassing the end of the central domain and the IDL is probably involved in the oxygen-sensitivity of NifA. In the present study, we have expressed, purified and characterized an N-truncated form of A. brasilense NifA. The protein expression was carried out in Escherichia coli and the N-truncated NifA protein was purified by chromatography using an affinity metal-chelating resin followed by a heparin-bound resin. Protein homogeneity was determined by densitometric analysis. The N-truncated protein activated in vivo nifH::lacZ transcription regardless of fixed nitrogen concentration (absence or presence of 20 mM NH4Cl) but only under low oxygen levels. On the other hand, the aerobically purified N-truncated NifA protein bound to the nifB promoter, as demonstrated by an electrophoretic mobility shift assay, implying that DNA-binding activity is not strictly controlled by oxygen levels. Our data show that, while the N-truncated NifA is inactive in vivo under aerobic conditions, it still retains DNA-binding activity, suggesting that the oxidized form of NifA bound to DNA is not competent to activate transcription.
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Affiliation(s)
- C Y Nishikawa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
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Kadowaki MAS, Müller-Santos M, Rego FGM, Souza EM, Yates MG, Monteiro RA, Pedrosa FO, Chubatsu LS, Steffens MBR. Identification and characterization of PhbF: a DNA binding protein with regulatory role in the PHB metabolism of Herbaspirillum seropedicae SmR1. BMC Microbiol 2011; 11:230. [PMID: 21999748 PMCID: PMC3206438 DOI: 10.1186/1471-2180-11-230] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 10/14/2011] [Indexed: 11/25/2022] Open
Abstract
Background Herbaspirillum seropedicae SmR1 is a nitrogen fixing endophyte associated with important agricultural crops. It produces polyhydroxybutyrate (PHB) which is stored intracellularly as granules. However, PHB metabolism and regulatory control is not yet well studied in this organism. Results In this work we describe the characterization of the PhbF protein from H. seropedicae SmR1 which was purified and characterized after expression in E. coli. The purified PhbF protein was able to bind to eleven putative promoters of genes involved in PHB metabolism in H. seropedicae SmR1. In silico analyses indicated a probable DNA-binding sequence which was shown to be protected in DNA footprinting assays using purified PhbF. Analyses using lacZ fusions showed that PhbF can act as a repressor protein controlling the expression of PHB metabolism-related genes. Conclusions Our results indicate that H. seropedicae SmR1 PhbF regulates expression of phb-related genes by acting as a transcriptional repressor. The knowledge of the PHB metabolism of this plant-associated bacterium may contribute to the understanding of the plant-colonizing process and the organism's resistance and survival in planta.
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Affiliation(s)
- Marco A S Kadowaki
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba-PR, Brazil
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Noindorf L, Bonatto AC, Monteiro RA, Souza EM, Rigo LU, Pedrosa FO, Steffens MBR, Chubatsu LS. Role of PII proteins in nitrogen fixation control of Herbaspirillum seropedicae strain SmR1. BMC Microbiol 2011; 11:8. [PMID: 21223584 PMCID: PMC3023670 DOI: 10.1186/1471-2180-11-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Accepted: 01/11/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The PII protein family comprises homotrimeric proteins which act as transducers of the cellular nitrogen and carbon status in prokaryotes and plants. In Herbaspirillum seropedicae, two PII-like proteins (GlnB and GlnK), encoded by the genes glnB and glnK, were identified. The glnB gene is monocistronic and its expression is constitutive, while glnK is located in the nlmAglnKamtB operon and is expressed under nitrogen-limiting conditions. RESULTS In order to determine the involvement of the H. seropedicae glnB and glnK gene products in nitrogen fixation, a series of mutant strains were constructed and characterized. The glnK- mutants were deficient in nitrogen fixation and they were complemented by plasmids expressing the GlnK protein or an N-truncated form of NifA. The nitrogenase post-translational control by ammonium was studied and the results showed that the glnK mutant is partially defective in nitrogenase inactivation upon addition of ammonium while the glnB mutant has a wild-type phenotype. CONCLUSIONS Our results indicate that GlnK is mainly responsible for NifA activity regulation and ammonium-dependent post-translational regulation of nitrogenase in H. seropedicae.
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Affiliation(s)
- Lilian Noindorf
- National Institute of Science and Technology for Biological Nitrogen Fixation, Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, Curitiba, PR, 81531-980, Brazil
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Souza ALF, Invitti AL, Rego FGM, Monteiro RA, Klassen G, Souza EM, Chubatsu LS, Pedrosa FO, Rigo LU. The involvement of the nif-associated ferredoxin-like genes fdxA and fdxN of Herbaspirillum seropedicae in nitrogen fixation. J Microbiol 2010; 48:77-83. [PMID: 20221733 DOI: 10.1007/s12275-009-0077-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Accepted: 07/26/2009] [Indexed: 10/19/2022]
Abstract
The pathway of electron transport to nitrogenase in the endophytic beta-Proteobacterium Herbaspirillum seropedicae has not been characterized. We have generated mutants in two nif-associated genes encoding putative ferredoxins, fdxA and fdxN. The fdxA gene is part of the operon nifHDKENXorf1orf2fdxAnifQmodABC and is transcribed from the nifH promoter, as revealed by lacZ gene fusion. The fdxN gene is probably cotranscribed with the nifB gene. Mutational analysis suggests that the FdxA protein is essential for maximum nitrogenase activity, since the nitrogenase activity of the fdxA mutant strain was reduced to about 30% of that of the wild-type strain. In addition, the fdxA mutation had no effect on the nitrogenase switch-off in response to ammonium. Nitrogenase activity of a mutant strain lacking the fdxN gene was completely abolished. This phenotype was reverted by complementation with fdxN expressed under lacZ promoter control. The results suggest that the products of both the fdxA and fdxN genes are probably involved in electron transfer during nitrogen fixation.
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Affiliation(s)
- André L F Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Brazil
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