1
|
Bonato P, Camilios-Neto D, Tadra-Sfeir MZ, Mota FJT, Muller-Santos M, Wassem R, de Souza EM, de Oliveira Pedrosa F, Chubatsu LS. The role of NtrC in the adaptation of Herbaspirillum seropedicae SmR1 to nitrogen limitation and to nitrate. Arch Microbiol 2024; 206:310. [PMID: 38896324 DOI: 10.1007/s00203-024-04044-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/08/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024]
Abstract
The RNA-Seq profiling of Herbaspirillum seropedicae SmR1 wild-type and ntrC mutant was performed under aerobic and three nitrogen conditions (ammonium limitation, ammonium shock, and nitrate shock) to identify the major metabolic pathways modulated by these nitrogen sources and those dependent on NtrC. Under ammonium limitation, H. seropedicae scavenges nitrogen compounds by activating transporter systems and metabolic pathways to utilize different nitrogen sources and by increasing proteolysis, along with genes involved in carbon storage, cell protection, and redox balance, while downregulating those involved in energy metabolism and protein synthesis. Growth on nitrate depends on the narKnirBDHsero_2899nasA operon responding to nitrate and NtrC. Ammonium shock resulted in a higher number of genes differently expressed when compared to nitrate. Our results showed that NtrC activates a network of transcriptional regulators to prepare the cell for nitrogen starvation, and also synchronizes nitrogen metabolism with carbon and redox balance pathways.
Collapse
Affiliation(s)
- Paloma Bonato
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Doumit Camilios-Neto
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, Londrina, PR, Brazil
| | | | - Francisco J Teles Mota
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Marcelo Muller-Santos
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Roseli Wassem
- Department of Genetics, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio de Oliveira Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Leda Satie Chubatsu
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil.
| |
Collapse
|
2
|
Mapping Genetic Variation in Arabidopsis in Response to Plant Growth-Promoting Bacterium Azoarcus olearius DQS-4T. Microorganisms 2023; 11:microorganisms11020331. [PMID: 36838296 PMCID: PMC9961961 DOI: 10.3390/microorganisms11020331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 02/03/2023] Open
Abstract
Plant growth-promoting bacteria (PGPB) can enhance plant health by facilitating nutrient uptake, nitrogen fixation, protection from pathogens, stress tolerance and/or boosting plant productivity. The genetic determinants that drive the plant-bacteria association remain understudied. To identify genetic loci highly correlated with traits responsive to PGPB, we performed a genome-wide association study (GWAS) using an Arabidopsis thaliana population treated with Azoarcus olearius DQS-4T. Phenotypically, the 305 Arabidopsis accessions tested responded differently to bacterial treatment by improving, inhibiting, or not affecting root system or shoot traits. GWA mapping analysis identified several predicted loci associated with primary root length or root fresh weight. Two statistical analyses were performed to narrow down potential gene candidates followed by haplotype block analysis, resulting in the identification of 11 loci associated with the responsiveness of Arabidopsis root fresh weight to bacterial inoculation. Our results showed considerable variation in the ability of plants to respond to inoculation by A. olearius DQS-4T while revealing considerable complexity regarding statistically associated loci with the growth traits measured. This investigation is a promising starting point for sustainable breeding strategies for future cropping practices that may employ beneficial microbes and/or modifications of the root microbiome.
Collapse
|
3
|
da Cunha ET, Pedrolo AM, Bueno JCF, Pereira TP, Soares CRFS, Arisi ACM. Inoculation of Herbaspirillum seropedicae strain SmR1 increases biomass in maize roots DKB 390 variety in the early stages of plant development. Arch Microbiol 2022; 204:373. [PMID: 35672591 DOI: 10.1007/s00203-022-02986-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 11/26/2022]
Abstract
Herbaspirillum seropedicae is a plant growth-promoting bacteria isolated from diverse plant species. In this work, the main objective was to investigate the efficiency of H. seropedicae strain SmR1 in colonizing and increasing maize growth (DKB 390 variety) in the early stages of development under greenhouse conditions. Inoculation with H. seropedicae resulted in 19.43 % (regarding High and Low N controls) and 10.51% (regarding Low N control) in mean of increase of root biomass, for 1st and 2nd greenhouse experiments, respectively, mainly in the initial stages of plant development, at 21 days after emergence (DAE). Quantification of H. seropedicae in roots and leaves was performed by quantitative PCR. H. seropedicae was detected only in maize inoculated roots by qPCR, and a slight decrease in DNA copy number g-1 of fresh root weight was observed from 7 to 21 DAE, suggesting that there was initial effective colonization on maize plants. H. seropedicae strain SmR1 efficiently increased maize root biomass exhibiting its potential to be used as inoculant in agricultures systems.
Collapse
Affiliation(s)
- Elisandra Triches da Cunha
- Food Science and Technology Department, CAL CCA UFSC, Federal University of Santa Catarina, Rod Admar Gonzaga, 1346, Florianópolis, SC, 88034-001, Brazil
| | - Ana Marina Pedrolo
- Food Science and Technology Department, CAL CCA UFSC, Federal University of Santa Catarina, Rod Admar Gonzaga, 1346, Florianópolis, SC, 88034-001, Brazil
| | - Jessica Cavalheiro Ferreira Bueno
- Food Science and Technology Department, CAL CCA UFSC, Federal University of Santa Catarina, Rod Admar Gonzaga, 1346, Florianópolis, SC, 88034-001, Brazil
| | - Tomás Pelizzaro Pereira
- Food Science and Technology Department, CAL CCA UFSC, Federal University of Santa Catarina, Rod Admar Gonzaga, 1346, Florianópolis, SC, 88034-001, Brazil
- Public Policy Coordination Department, EPAGRI, Santa Catarina Agricultural Research and Rural Extension Company, Rio do Sul, SC, Brazil
| | - Cláudio Roberto Fônseca Sousa Soares
- Microbiology, Immunology and Parasitology Department, MIP CCB UFSC, Federal University of Santa Catarina, Av Prof Henrique da Silva Fontes, 2754, Florianópolis, SC, 88040-900, Brazil
| | - Ana Carolina Maisonnave Arisi
- Food Science and Technology Department, CAL CCA UFSC, Federal University of Santa Catarina, Rod Admar Gonzaga, 1346, Florianópolis, SC, 88034-001, Brazil.
| |
Collapse
|
4
|
High Genomic Identity between Clinical and Environmental Strains of Herbaspirillum frisingense Suggests Pre-Adaptation to Different Hosts and Intrinsic Resistance to Multiple Drugs. Antibiotics (Basel) 2021; 10:antibiotics10111409. [PMID: 34827347 PMCID: PMC8614823 DOI: 10.3390/antibiotics10111409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/27/2021] [Accepted: 10/31/2021] [Indexed: 12/15/2022] Open
Abstract
The genus Herbaspirillum is widely studied for its ability to associate with grasses and to perform biological nitrogen fixation. However, the bacteria of the Herbaspirillum genus have frequently been isolated from clinical samples. Understanding the genomic characteristics that allow these bacteria to switch environments and become able to colonize human hosts is essential for monitoring emerging pathogens and predicting outbreaks. In this work, we describe the sequencing, assembly, and annotation of the genome of H. frisingense AU14559 isolated from the sputum of patients with cystic fibrosis, and its comparison with the genomes of the uropathogenic strain VT-16-41 and the environmental strains GSF30, BH-1, IAC152, and SG826. The genes responsible for biological nitrogen fixation were absent from all strains except for GSF30. On the other hand, genes encoding virulence and host interaction factors were mostly shared with environmental strains. We also identified a large set of intrinsic antibiotic resistance genes that were shared across all strains. Unlike other strains, in addition to unique genomic islands, AU14559 has a mutation that renders the biosynthesis of rhamnose and its incorporation into the exopolysaccharide unfeasible. These data suggest that H. frisingense has characteristics that provide it with the metabolic diversity needed to infect and colonize human hosts.
Collapse
|
5
|
Grillo-Puertas M, Villegas JM, Pankievicz VCS, Tadra-Sfeir MZ, Teles Mota FJ, Hebert EM, Brusamarello-Santos L, Pedraza RO, Pedrosa FO, Rapisarda VA, Souza EM. Transcriptional Responses of Herbaspirillum seropedicae to Environmental Phosphate Concentration. Front Microbiol 2021; 12:666277. [PMID: 34177845 PMCID: PMC8222739 DOI: 10.3389/fmicb.2021.666277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/29/2021] [Indexed: 12/02/2022] Open
Abstract
Herbaspirillum seropedicae is a nitrogen-fixing endophytic bacterium associated with important cereal crops, which promotes plant growth, increasing their productivity. The understanding of the physiological responses of this bacterium to different concentrations of prevailing nutrients as phosphate (Pi) is scarce. In some bacteria, culture media Pi concentration modulates the levels of intracellular polyphosphate (polyP), modifying their cellular fitness. Here, global changes of H. seropedicae SmR1 were evaluated in response to environmental Pi concentrations, based on differential intracellular polyP levels. Cells grown in high-Pi medium (50 mM) maintained high polyP levels in stationary phase, while those grown in sufficient Pi medium (5 mM) degraded it. Through a RNA-seq approach, comparison of transcriptional profiles of H. seropedicae cultures revealed that 670 genes were differentially expressed between both Pi growth conditions, with 57% repressed and 43% induced in the high Pi condition. Molecular and physiological analyses revealed that aspects related to Pi metabolism, biosynthesis of flagella and chemotaxis, energy production, and polyhydroxybutyrate metabolism were induced in the high-Pi condition, while those involved in adhesion and stress response were repressed. The present study demonstrated that variations in environmental Pi concentration affect H. seropedicae traits related to survival and other important physiological characteristics. Since environmental conditions can influence the effectiveness of the plant growth-promoting bacteria, enhancement of bacterial robustness to withstand different stressful situations is an interesting challenge. The obtained data could serve not only to understand the bacterial behavior in respect to changes in rhizospheric Pi gradients but also as a base to design strategies to improve different bacterial features focusing on biotechnological and/or agricultural purposes.
Collapse
Affiliation(s)
- Mariana Grillo-Puertas
- Instituto de Química Biológica, “Dr. Bernabé Bloj”, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán (UNT) and Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, San Miguel de Tucumán, Argentina
| | - Josefina M. Villegas
- Instituto de Química Biológica, “Dr. Bernabé Bloj”, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán (UNT) and Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, San Miguel de Tucumán, Argentina
| | - Vânia C. S. Pankievicz
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Michelle Z. Tadra-Sfeir
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Francisco J. Teles Mota
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Elvira M. Hebert
- Centro de Referencia para Lactobacilos (CERELA-CONICET), San Miguel de Tucumán, Argentina
| | | | - Raul O. Pedraza
- Facultad de Agronomía y Zootecnia, Universidad Nacional de Tucumán (UNT), San Miguel de Tucumán, Argentina
| | - Fabio O. Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Viviana A. Rapisarda
- Instituto de Química Biológica, “Dr. Bernabé Bloj”, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán (UNT) and Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, San Miguel de Tucumán, Argentina
| | - Emanuel M. Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| |
Collapse
|
6
|
Abstract
There is growing interest in the use of associative, plant growth-promoting bacteria (PGPB) as biofertilizers to serve as a sustainable alternative for agriculture application. While a variety of mechanisms have been proposed to explain bacterial plant growth promotion, the molecular details of this process remain unclear. The plant rhizosphere harbors a diverse population of microorganisms, including beneficial plant growth-promoting bacteria (PGPB), that colonize plant roots and enhance growth and productivity. In order to specifically define bacterial traits that contribute to this beneficial interaction, we used high-throughput transposon mutagenesis sequencing (TnSeq) in two model root-bacterium systems associated with Setaria viridis: Azoarcus olearius DQS4T and Herbaspirillum seropedicae SmR1. This approach identified ∼100 significant genes for each bacterium that appeared to confer a competitive advantage for root colonization. Most of the genes identified specifically in A. olearius encoded metabolism functions, whereas genes identified in H. seropedicae were motility related, suggesting that each strain requires unique functions for competitive root colonization. Genes were experimentally validated by site-directed mutagenesis, followed by inoculation of the mutated bacteria onto S. viridis roots individually, as well as in competition with the wild-type strain. The results identify key bacterial functions involved in iron uptake, polyhydroxybutyrate metabolism, and regulation of aromatic metabolism as important for root colonization. The hope is that by improving our understanding of the molecular mechanisms used by PGPB to colonize plants, we can increase the adoption of these bacteria in agriculture to improve the sustainability of modern cropping systems.
Collapse
|
7
|
Dobrzanski T, Pobre V, Moreno LF, Barbosa HCDS, Monteiro RA, de Oliveira Pedrosa F, de Souza EM, Arraiano CM, Steffens MBR. In silico prediction and expression profile analysis of small non-coding RNAs in Herbaspirillum seropedicae SmR1. BMC Genomics 2020; 21:134. [PMID: 32039705 PMCID: PMC7011215 DOI: 10.1186/s12864-019-6402-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 12/15/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Herbaspirillum seropedicae is a diazotrophic bacterium from the β-proteobacteria class that colonizes endophytically important gramineous species, promotes their growth through phytohormone-dependent stimulation and can express nif genes and fix nitrogen inside plant tissues. Due to these properties this bacterium has great potential as a commercial inoculant for agriculture. The H. seropedicae SmR1 genome is completely sequenced and annotated but despite the availability of diverse structural and functional analysis of this genome, studies involving small non-coding RNAs (sRNAs) has not yet been done. We have conducted computational prediction and RNA-seq analysis to select and confirm the expression of sRNA genes in the H. seropedicae SmR1 genome, in the presence of two nitrogen independent sources and in presence of naringenin, a flavonoid secreted by some plants. RESULTS This approach resulted in a set of 117 sRNAs distributed in riboswitch, cis-encoded and trans-encoded categories and among them 20 have Rfam homologs. The housekeeping sRNAs tmRNA, ssrS and 4.5S were found and we observed that a large number of sRNAs are more expressed in the nitrate condition rather than the control condition and in the presence of naringenin. Some sRNAs expression were confirmed in vitro and this work contributes to better understand the post transcriptional regulation in this bacterium. CONCLUSIONS H. seropedicae SmR1 express sRNAs in the presence of two nitrogen sources and/or in the presence of naringenin. The functions of most of these sRNAs remains unknown but their existence in this bacterium confirms the evidence that sRNAs are involved in many different cellular activities to adapt to nutritional and environmental changes.
Collapse
Affiliation(s)
- Tatiane Dobrzanski
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná (UFPR), Av. Coronel. Francisco H. dos Santos, 210, PoBox 19046, Curitiba, 81.531-980, Paraná, Brazil
| | - Vânia Pobre
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
| | - Leandro Ferreira Moreno
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná (UFPR), Av. Coronel. Francisco H. dos Santos, 210, PoBox 19046, Curitiba, 81.531-980, Paraná, Brazil
| | - Helba Cirino de Souza Barbosa
- Graduate Program in Bioinformatics, Universidade Federal do Paraná (UFPR), Rua Alcides Vieira Arcoverde, 1225, Curitiba, 81520-260, Brazil
| | - Rose Adele Monteiro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná (UFPR), Av. Coronel. Francisco H. dos Santos, 210, PoBox 19046, Curitiba, 81.531-980, Paraná, Brazil.,Graduate Program in Bioinformatics, Universidade Federal do Paraná (UFPR), Rua Alcides Vieira Arcoverde, 1225, Curitiba, 81520-260, Brazil
| | - Fábio de Oliveira Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná (UFPR), Av. Coronel. Francisco H. dos Santos, 210, PoBox 19046, Curitiba, 81.531-980, Paraná, Brazil
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná (UFPR), Av. Coronel. Francisco H. dos Santos, 210, PoBox 19046, Curitiba, 81.531-980, Paraná, Brazil
| | - Cecília Maria Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Maria Berenice Reynaud Steffens
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná (UFPR), Av. Coronel. Francisco H. dos Santos, 210, PoBox 19046, Curitiba, 81.531-980, Paraná, Brazil.
| |
Collapse
|
8
|
Agtuca BJ, Stopka SA, Tuleski TR, do Amaral FP, Evans S, Liu Y, Xu D, Monteiro RA, Koppenaal DW, Paša-Tolić L, Anderton CR, Vertes A, Stacey G. In-Situ Metabolomic Analysis of Setaria viridis Roots Colonized by Beneficial Endophytic Bacteria. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:272-283. [PMID: 31544655 DOI: 10.1094/mpmi-06-19-0174-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Over the past decades, crop yields have risen in parallel with increasing use of fossil fuel-derived nitrogen (N) fertilizers but with concomitant negative impacts on climate and water resources. There is a need for more sustainable agricultural practices, and biological nitrogen fixation (BNF) could be part of the solution. A variety of nitrogen-fixing, epiphytic, and endophytic plant growth-promoting bacteria (PGPB) are known to stimulate plant growth. However, compared with the rhizobium-legume symbiosis, little mechanistic information is available as to how PGPB affect plant metabolism. Therefore, we investigated the metabolic changes in roots of the model grass species Setaria viridis upon endophytic colonization by Herbaspirillum seropedicae SmR1 (fix+) or a fix- mutant strain (SmR54) compared with uninoculated roots. Endophytic colonization of the root is highly localized and, hence, analysis of whole-root segments dilutes the metabolic signature of those few cells impacted by the bacteria. Therefore, we utilized in-situ laser ablation electrospray ionization mass spectrometry to sample only those root segments at or adjacent to the sites of bacterial colonization. Metabolites involved in purine, zeatin, and riboflavin pathways were significantly more abundant in inoculated plants, while metabolites indicative of nitrogen, starch, and sucrose metabolism were reduced in roots inoculated with the fix- strain or uninoculated, presumably due to N limitation. Interestingly, compounds, involved in indole-alkaloid biosynthesis were more abundant in the roots colonized by the fix- strain, perhaps reflecting a plant defense response.
Collapse
Affiliation(s)
- Beverly J Agtuca
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
| | - Sylwia A Stopka
- Department of Chemistry, The George Washington University, Washington, DC 20052, U.S.A
| | - Thalita R Tuleski
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, CP 19046, 81.531-990 Curitiba, PR, Brazil
| | - Fernanda P do Amaral
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
| | - Sterling Evans
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
| | - Yang Liu
- Department of Electrical Engineering and Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri Columbia
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri Columbia
| | - Rose Adele Monteiro
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, CP 19046, 81.531-990 Curitiba, PR, Brazil
| | - David W Koppenaal
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, U.S.A
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, U.S.A
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, U.S.A
| | - Akos Vertes
- Department of Chemistry, The George Washington University, Washington, DC 20052, U.S.A
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
| |
Collapse
|
9
|
Batista MB, Chandra G, Monteiro RA, de Souza EM, Dixon R. Hierarchical interactions between Fnr orthologs allows fine-tuning of transcription in response to oxygen in Herbaspirillum seropedicae. Nucleic Acids Res 2019. [PMID: 29529262 PMCID: PMC5934665 DOI: 10.1093/nar/gky142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Bacteria adjust the composition of their electron transport chain (ETC) to efficiently adapt to oxygen gradients. This involves differential expression of various ETC components to optimize energy generation. In Herbaspirillum seropedicae, reprogramming of gene expression in response to oxygen availability is controlled at the transcriptional level by three Fnr orthologs. Here, we characterised Fnr regulons using a combination of RNA-Seq and ChIP-Seq analysis. We found that Fnr1 and Fnr3 directly regulate discrete groups of promoters (Groups I and II, respectively), and that a third group (Group III) is co-regulated by both transcription factors. Comparison of DNA binding motifs between the three promoter groups suggests Group III promoters are potentially co-activated by Fnr3–Fnr1 heterodimers. Specific interaction between Fnr1 and Fnr3, detected in two-hybrid assays, was dependent on conserved residues in their dimerization interfaces, indicative of heterodimer formation in vivo. The requirements for co-activation of the fnr1 promoter, belonging to Group III, suggest either sequential activation by Fnr3 and Fnr1 homodimers or the involvement of Fnr3–Fnr1 heterodimers. Analysis of Fnr proteins with swapped activation domains provides evidence that co-activation by Fnr1 and Fnr3 at Group III promoters optimises interactions with RNA polymerase to fine-tune transcription in response to prevailing oxygen concentrations.
Collapse
Affiliation(s)
- Marcelo Bueno Batista
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - Govind Chandra
- 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 Parana, P.O. Box 19046, Curitiba, PR 81531-990, Brazil
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Parana, P.O. Box 19046, Curitiba, PR 81531-990, Brazil
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| |
Collapse
|
10
|
Modulation of defence and iron homeostasis genes in rice roots by the diazotrophic endophyte Herbaspirillum seropedicae. Sci Rep 2019; 9:10573. [PMID: 31332206 PMCID: PMC6646362 DOI: 10.1038/s41598-019-45866-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 06/06/2019] [Indexed: 11/30/2022] Open
Abstract
Rice is staple food of nearly half the world’s population. Rice yields must therefore increase to feed ever larger populations. By colonising rice and other plants, Herbaspirillum spp. stimulate plant growth and productivity. However the molecular factors involved are largely unknown. To further explore this interaction, the transcription profiles of Nipponbare rice roots inoculated with Herbaspirillum seropedicae were determined by RNA-seq. Mapping the 104 million reads against the Oryza sativa cv. Nipponbare genome produced 65 million unique mapped reads that represented 13,840 transcripts each with at least two-times coverage. About 7.4% (1,014) genes were differentially regulated and of these 255 changed expression levels more than two times. Several of the repressed genes encoded proteins related to plant defence (e.g. a putative probenazole inducible protein), plant disease resistance as well as enzymes involved in flavonoid and isoprenoid synthesis. Genes related to the synthesis and efflux of phytosiderophores (PS) and transport of PS-iron complexes were induced by the bacteria. These data suggest that the bacterium represses the rice defence system while concomitantly activating iron uptake. Transcripts of H. seropedicae were also detected amongst which transcripts of genes involved in nitrogen fixation, cell motility and cell wall synthesis were the most expressed.
Collapse
|
11
|
Tuleski TR, Baura VAD, Donatti L, Pedrosa FDO, Souza EMD, Monteiro RA. Cellulose production increases sorghum colonization and the pathogenic potential of Herbaspirillum rubrisubalbicans M1. Sci Rep 2019; 9:4041. [PMID: 30858484 PMCID: PMC6412066 DOI: 10.1038/s41598-019-40600-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 02/19/2019] [Indexed: 11/13/2022] Open
Abstract
Three species of the β-Proteobacterial genus Herbaspirillum are able to fix nitrogen in endophytic associations with such important agricultural crops as maize, rice, sorghum, sugar-cane and wheat. In addition, Herbaspirillum rubrisubalbicans causes the mottled-stripe disease in susceptible sugar-cane cultivars as well as the red-stripe disease in some sorghum cultivars. The xylem of these cultivars exhibited a massive colonisation of mucus-producing bacteria leading to blocking the vessels. A cluster of eight genes (bcs) are involved in cellulose synthesis in Herbaspirillum rubrisubalbicans. Mutation of bcsZ, that encodes a 1,4-endoglucanase, impaired the exopolysaccharide production, the ability to form early biofilm and colonize sorghum when compared to the wild-type strain M1. This mutation also impaired the ability of Herbaspirillum rubrisubalbicans M1 to cause the red-stripe disease in Sorghum bicolor. We show cellulose synthesis is involved in the biofilm formation and as a consequence significantly modulates bacterial-plant interactions, indicating the importance of cellulose biosynthesis in this process.
Collapse
Affiliation(s)
- Thalita Regina Tuleski
- Department of Biochemistry and Molecular Biology, Federal University of Parana, Curitiba, Paraná, Brazil
| | - Valter Antônio de Baura
- Department of Biochemistry and Molecular Biology, Federal University of Parana, Curitiba, Paraná, Brazil
| | - Lucélia Donatti
- Department of Cellular and Molecular Biology, Federal University of Parana, Curitiba, Paraná, Brazil
| | - Fabio de Oliveira Pedrosa
- Department of Biochemistry and Molecular Biology, Federal University of Parana, Curitiba, Paraná, Brazil
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Federal University of Parana, Curitiba, Paraná, Brazil
| | - Rose Adele Monteiro
- Department of Biochemistry and Molecular Biology, Federal University of Parana, Curitiba, Paraná, Brazil.
| |
Collapse
|
12
|
To Fix or Not To Fix: Controls on Free-Living Nitrogen Fixation in the Rhizosphere. Appl Environ Microbiol 2019; 85:AEM.02546-18. [PMID: 30658971 DOI: 10.1128/aem.02546-18] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Free-living nitrogen fixation (FLNF) in the rhizosphere, or N fixation by heterotrophic bacteria living on/near root surfaces, is ubiquitous and a significant source of N in some terrestrial systems. FLNF is also of interest in crop production as an alternative to chemical fertilizer, potentially reducing production costs and ameliorating negative environmental impacts of fertilizer N additions. Despite this interest, a mechanistic understanding of controls (e.g., carbon, oxygen, nitrogen, and nutrient availability) on FLNF in the rhizosphere is lacking but necessary. FLNF is distinct from and occurs under more diverse and dynamic conditions than symbiotic N fixation; therefore, predicting FLNF rates and understanding controls on FLNF has proven difficult. This has led to large gaps in our understanding of FLNF, and studies aimed at identifying controls on FLNF are needed. Here, we provide a mechanistic overview of FLNF, including how various controls may influence FLNF in the rhizosphere in comparison with symbiotic N fixation occurring in plant nodules where environmental conditions are moderated by the plant. We apply this knowledge to a real-world example, the bioenergy crop switchgrass (Panicum virgatum), to provide context of how FLNF may function in a managed system. We also highlight future challenges to assessing FLNF and understanding how FLNF functions in the environment and significantly contributes to plant N availability and productivity.
Collapse
|
13
|
Dall’Asta P, Velho AC, Pereira TP, Stadnik MJ, Arisi ACM. Herbaspirillum seropedicae promotes maize growth but fails to control the maize leaf anthracnose. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:167-176. [PMID: 30804639 PMCID: PMC6352535 DOI: 10.1007/s12298-018-0616-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/28/2018] [Accepted: 10/09/2018] [Indexed: 05/21/2023]
Abstract
Herbaspirillum seropedicae is an endophytic diazotrophic bacterium and a plant growth promoting bacteria. Colletotrichum graminicola causes the anthracnose, one of the most destructive maize diseases worldwide. The main objective of this work was to evaluate the effects of H. seropedicae SmR1 strain on the plant growth and leaf anthracnose of maize plants grown in substrate amended or not amended with humic substances. In the first assay, plants were pre-treated with H. seropedicae and inoculated with C. graminicola at 7, 14 and 21 days after treatment (DAT). In the second assay, plants were treated with H. seropedicae, grown in substrate amended with humic substances and inoculated at 3 and 7 DAT. The anthracnose severity was assessed by measurement of necrotic and chlorotic leaf area, and bacteria were quantified in leaves by quantitative PCR. H. seropedicae did not affect the disease severity in maize leaves, although it efficiently colonized the leaf tissues and it promoted maize leaf growth. Humic substances improved H. seropedicae colonization in maize.
Collapse
Affiliation(s)
- Pâmela Dall’Asta
- Laboratory of Molecular Biology, Department of Food Science and Technology, Federal University of Santa Catarina, Rod. Admar Gonzaga 1346, 88034-001 Florianópolis, SC Brazil
| | - Aline Cristina Velho
- Laboratory of Plant Pathology, Department of Phytotechny, Federal University of Santa Catarina, Rod. Admar Gonzaga 1346, 88034-001 Florianópolis, SC Brazil
| | - Tomás Pellizzaro Pereira
- Laboratory of Molecular Biology, Department of Food Science and Technology, Federal University of Santa Catarina, Rod. Admar Gonzaga 1346, 88034-001 Florianópolis, SC Brazil
| | - Marciel João Stadnik
- Laboratory of Plant Pathology, Department of Phytotechny, Federal University of Santa Catarina, Rod. Admar Gonzaga 1346, 88034-001 Florianópolis, SC Brazil
| | - Ana Carolina Maisonnave Arisi
- Laboratory of Molecular Biology, Department of Food Science and Technology, Federal University of Santa Catarina, Rod. Admar Gonzaga 1346, 88034-001 Florianópolis, SC Brazil
| |
Collapse
|
14
|
Trovero MF, Scavone P, Platero R, de Souza EM, Fabiano E, Rosconi F. Herbaspirillum seropedicae Differentially Expressed Genes in Response to Iron Availability. Front Microbiol 2018; 9:1430. [PMID: 30018605 PMCID: PMC6037834 DOI: 10.3389/fmicb.2018.01430] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 06/11/2018] [Indexed: 01/20/2023] Open
Abstract
Herbaspirillum seropedicae Z67 is a nitrogen-fixing endophyte that colonizes many important crops. Like in almost all organisms, vital cellular processes of this endophyte are iron dependent. In order to efficiently acquire iron to fulfill its requirements, this bacterium produces the siderophores serobactins. However, the presence in its genome of many others iron acquisition genes suggests that serobactins are not the only strategy used by H. seropedicae to overcome metal deficiency. The aim of this work was to identify genes and proteins differentially expressed by cells growing in low iron conditions in order to describe H. seropedicae response to iron limitation stress. For this purpose, and by using a transcriptomic approach, we searched and identified a set of genes up-regulated when iron was scarce. One of them, Hsero_2337, codes for a TonB-dependent transporter/transducer present in the serobactins biosynthesis genomic locus, with an unknown function. Another TonB-dependent receptor, the one encoded by Hsero_1277, and an inner membrane ferrous iron permease, coded by Hsero_2720, were also detected. By using a proteomic approach focused in membrane proteins, we identified the specific receptor for iron-serobactin internalization SbtR and two non-characterized TonB-dependent receptors (coded by genes Hsero_1277 and Hsero_3255). We constructed mutants on some of the identified genes and characterized them by in vitro growth, biofilm formation, and interaction with rice plants. Characterization of mutants in gene Hsero_2337 showed that the TonB-dependent receptor coded by this gene has a regulatory role in the biosynthesis of serobactins, probably by interacting with the alternative sigma factor PfrI, coded by gene Hsero_2338. Plant colonization of the mutant strains was not affected, since the mutant strain normally colonize the root and aerial part of rice plants. These results suggest that the strategies used by H. seropedicae to acquire iron inside plants are far more diverse than the ones characterized in this work. In vivo expression studies or colonization competition experiments between the different mutant strains could help us in future works to determine the relative importance of the different iron acquisition systems in the interaction of H. seropedicae with rice plants.
Collapse
Affiliation(s)
- María F Trovero
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Paola Scavone
- Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Raúl Platero
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Emanuel M de Souza
- Departamento de Bioquimica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Brazil
| | - Elena Fabiano
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Federico Rosconi
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| |
Collapse
|
15
|
Batista MB, Teixeira CS, Sfeir MZT, Alves LPS, Valdameri G, Pedrosa FDO, Sassaki GL, Steffens MBR, de Souza EM, Dixon R, Müller-Santos M. PHB Biosynthesis Counteracts Redox Stress in Herbaspirillum seropedicae. Front Microbiol 2018; 9:472. [PMID: 29599762 PMCID: PMC5862806 DOI: 10.3389/fmicb.2018.00472] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 02/28/2018] [Indexed: 11/25/2022] Open
Abstract
The ability of bacteria to produce polyhydroxyalkanoates such as poly(3-hydroxybutyrate) (PHB) enables provision of a carbon storage molecule that can be mobilized under demanding physiological conditions. However, the precise function of PHB in cellular metabolism has not been clearly defined. In order to determine the impact of PHB production on global physiology, we have characterized the properties of a ΔphaC1 mutant strain of the diazotrophic bacterium Herbaspirillum seropedicae. The absence of PHB in the mutant strain not only perturbs redox balance and increases oxidative stress, but also influences the activity of the redox-sensing Fnr transcription regulators, resulting in significant changes in expression of the cytochrome c-branch of the electron transport chain. The synthesis of PHB is itself dependent on the Fnr1 and Fnr3 proteins resulting in a cyclic dependency that couples synthesis of PHB with redox regulation. Transcriptional profiling of the ΔphaC1 mutant reveals that the loss of PHB synthesis affects the expression of many genes, including approximately 30% of the Fnr regulon.
Collapse
Affiliation(s)
- Marcelo B Batista
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil.,Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Cícero S Teixeira
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Michelle Z T Sfeir
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Luis P S Alves
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Glaucio Valdameri
- Department of Clinical Analysis, Universidade Federal do Paraná, Curitiba, Brazil
| | | | - Guilherme L Sassaki
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Maria B R Steffens
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Emanuel M de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Marcelo Müller-Santos
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| |
Collapse
|
16
|
Valdameri G, Alberton D, Moure VR, Kokot TB, Kukolj C, Brusamarello-Santos LCC, Monteiro RA, Pedrosa FDO, de Souza EM. Herbaspirillum rubrisubalbicans, a mild pathogen impairs growth of rice by augmenting ethylene levels. PLANT MOLECULAR BIOLOGY 2017; 94:625-640. [PMID: 28674938 DOI: 10.1007/s11103-017-0629-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 06/23/2017] [Indexed: 06/07/2023]
Abstract
Herbaspirillum rubrisubalbicans decreases growth of rice. Inoculation of rice with H. rubrisubalbicans increased the ACCO mRNA levels and ethylene production. The H. rubrisubalbicans rice interactions were further characterized by proteomic approach. Herbaspirillum rubrisubalbicans is a well-known growth-promoting rhizobacteria that can also act as a mild phyto-pathogen. During colonisation of rice, RT-qPCR analyses showed that H. rubrisubalbicans up-regulates the methionine recycling pathway as well as phyto-siderophore synthesis genes. mRNA levels of ACC oxidase and ethylene levels also increased in rice roots but inoculation with H. rubrisubalbicans impaired growth of the rice plant. A proteomic approach was used to identify proteins specifically modulated by H. rubrisubalbicans in rice and amongst the differentially expressed proteins a V-ATPase and a 14-3-3 protein were down-regulated. Several proteins of H. rubrisubalbicans were identified, including the type VI secretion system effector Hcp1, suggesting that protein secretion play a role colonisation in rice. Finally, the alkyl hydroperoxide reductase, a primary scavenger of endogenous hydrogen peroxide was also identified. Monitoring the levels of reactive oxygen species in the epiphytic bacteria by flow cytometry revealed that H. rubrisubalbicans is subjected to oxidative stress, suggesting that the alkyl hydroperoxide reductase is an important regulator of redox homeostasis in plant-bacteria interactions.
Collapse
Affiliation(s)
- Glaucio Valdameri
- Department of Biochemistry and Molecular Biology, Centro Politécnico, Setor de Ciências Biológicas, Jardim das Américas, Federal University of Parana, Curitiba, 19046, PR, Brazil
- Department of Clinical Analysis, Federal University of Parana, Curitiba, PR, Brazil
| | - Dayane Alberton
- Department of Biochemistry and Molecular Biology, Centro Politécnico, Setor de Ciências Biológicas, Jardim das Américas, Federal University of Parana, Curitiba, 19046, PR, Brazil
- Department of Clinical Analysis, Federal University of Parana, Curitiba, PR, Brazil
| | - Vivian Rotuno Moure
- Department of Biochemistry and Molecular Biology, Centro Politécnico, Setor de Ciências Biológicas, Jardim das Américas, Federal University of Parana, Curitiba, 19046, PR, Brazil
| | - Thiago Borba Kokot
- Department of Biochemistry and Molecular Biology, Centro Politécnico, Setor de Ciências Biológicas, Jardim das Américas, Federal University of Parana, Curitiba, 19046, PR, Brazil
| | - Caroline Kukolj
- Department of Biochemistry and Molecular Biology, Centro Politécnico, Setor de Ciências Biológicas, Jardim das Américas, Federal University of Parana, Curitiba, 19046, PR, Brazil
| | - Liziane Cristina Campos Brusamarello-Santos
- Department of Biochemistry and Molecular Biology, Centro Politécnico, Setor de Ciências Biológicas, Jardim das Américas, Federal University of Parana, Curitiba, 19046, PR, Brazil
| | - Rose Adele Monteiro
- Department of Biochemistry and Molecular Biology, Centro Politécnico, Setor de Ciências Biológicas, Jardim das Américas, Federal University of Parana, Curitiba, 19046, PR, Brazil
| | - Fabio de Oliveira Pedrosa
- Department of Biochemistry and Molecular Biology, Centro Politécnico, Setor de Ciências Biológicas, Jardim das Américas, Federal University of Parana, Curitiba, 19046, PR, Brazil
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Centro Politécnico, Setor de Ciências Biológicas, Jardim das Américas, Federal University of Parana, Curitiba, 19046, PR, Brazil.
| |
Collapse
|
17
|
Brusamarello-Santos LC, Gilard F, Brulé L, Quilleré I, Gourion B, Ratet P, Maltempi de Souza E, Lea PJ, Hirel B. Metabolic profiling of two maize (Zea mays L.) inbred lines inoculated with the nitrogen fixing plant-interacting bacteria Herbaspirillum seropedicae and Azospirillum brasilense. PLoS One 2017; 12:e0174576. [PMID: 28362815 PMCID: PMC5375134 DOI: 10.1371/journal.pone.0174576] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 03/10/2017] [Indexed: 11/19/2022] Open
Abstract
Maize roots can be colonized by free-living atmospheric nitrogen (N2)-fixing bacteria (diazotrophs). However, the agronomic potential of non-symbiotic N2-fixation in such an economically important species as maize, has still not been fully exploited. A preliminary approach to improve our understanding of the mechanisms controlling the establishment of such N2-fixing associations has been developed, using two maize inbred lines exhibiting different physiological characteristics. The bacterial-plant interaction has been characterized by means of a metabolomic approach. Two established model strains of Nif+ diazotrophic bacteria, Herbaspirillum seropedicae and Azospirillum brasilense and their Nif- couterparts defficient in nitrogenase activity, were used to evaluate the impact of the bacterial inoculation and of N2 fixation on the root and leaf metabolic profiles. The two N2-fixing bacteria have been used to inoculate two genetically distant maize lines (FV252 and FV2), already characterized for their contrasting physiological properties. Using a well-controlled gnotobiotic experimental system that allows inoculation of maize plants with the two diazotrophs in a N-free medium, we demonstrated that both maize lines were efficiently colonized by the two bacterial species. We also showed that in the early stages of plant development, both bacterial strains were able to reduce acetylene, suggesting that they contain functional nitrogenase activity and are able to efficiently fix atmospheric N2 (Fix+). The metabolomic approach allowed the identification of metabolites in the two maize lines that were representative of the N2 fixing plant-bacterial interaction, these included mannitol and to a lesser extend trehalose and isocitrate. Whilst other metabolites such as asparagine, although only exhibiting a small increase in maize roots following bacterial infection, were specific for the two Fix+ bacterial strains, in comparison to their Fix- counterparts. Moreover, a number of metabolites exhibited a maize-genotype specific pattern of accumulation, suggesting that the highly diverse maize genetic resources could be further exploited in terms of beneficial plant-bacterial interactions for optimizing maize growth, with reduced N fertilization inputs.
Collapse
Affiliation(s)
- Liziane Cristina Brusamarello-Santos
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Centro Politécnico, Curutiba, Paraná, Brazil
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 INRA-Agro-ParisTech, Equipe de Recherche Labellisée 3559, Centre National de la Recherche Scientifique, Versailles, France
| | - Françoise Gilard
- Plateforme Métabolisme-Métabolome, Institute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Sud, Université Evry, Université Paris-Diderot, Université Paris-Saclay, Orsay, France
| | - Lenaïg Brulé
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 INRA-Agro-ParisTech, Equipe de Recherche Labellisée 3559, Centre National de la Recherche Scientifique, Versailles, France
| | - Isabelle Quilleré
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 INRA-Agro-ParisTech, Equipe de Recherche Labellisée 3559, Centre National de la Recherche Scientifique, Versailles, France
| | - Benjamin Gourion
- Institute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Sud, Université Evry, Université Paris-Diderot, Université Paris-Saclay, Orsay, France
| | - Pascal Ratet
- Institute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Sud, Université Evry, Université Paris-Diderot, Université Paris-Saclay, Orsay, France
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Centro Politécnico, Curutiba, Paraná, Brazil
| | - Peter J. Lea
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | - Bertrand Hirel
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 INRA-Agro-ParisTech, Equipe de Recherche Labellisée 3559, Centre National de la Recherche Scientifique, Versailles, France
| |
Collapse
|
18
|
Wassem R, Marin AM, Daddaoua A, Monteiro RA, Chubatsu LS, Ramos J, Deakin WJ, Broughton WJ, Pedrosa FO, Souza EM. A NodD-like protein activates transcription of genes involved with naringenin degradation in a flavonoid-dependent manner inHerbaspirillum seropedicae. Environ Microbiol 2017; 19:1030-1040. [DOI: 10.1111/1462-2920.13604] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/16/2016] [Indexed: 11/29/2022]
Affiliation(s)
- R. Wassem
- Departamento de Genética; Universidade Federal do Paraná; Curitiba PR Brazil
| | - A. M. Marin
- Departamento de Bioquímica; Universidade Federal do Paraná; Curitiba PR Brazil
| | - A. Daddaoua
- Department of Environmental Protection; Estación Experimental del Zaídin CSIC; Granada Spain
| | - R. A. Monteiro
- Departamento de Bioquímica; Universidade Federal do Paraná; Curitiba PR Brazil
| | - L. S. Chubatsu
- Departamento de Bioquímica; Universidade Federal do Paraná; Curitiba PR Brazil
| | - J.L. Ramos
- Department of Environmental Protection; Estación Experimental del Zaídin CSIC; Granada Spain
| | - W. J. Deakin
- Laboratoire de Biologie Moléculaire des Plantes Supérieures (LBMPS), Département de Biologie végétale; Sciences III, 30 Quai Ernest-Ansermet, Université de Genève; Genève 4 CH-1211 Switzerland
| | - W. J. Broughton
- Laboratoire de Biologie Moléculaire des Plantes Supérieures (LBMPS), Département de Biologie végétale; Sciences III, 30 Quai Ernest-Ansermet, Université de Genève; Genève 4 CH-1211 Switzerland
| | - F. O. Pedrosa
- Departamento de Bioquímica; Universidade Federal do Paraná; Curitiba PR Brazil
| | - E. M. Souza
- Departamento de Bioquímica; Universidade Federal do Paraná; Curitiba PR Brazil
| |
Collapse
|
19
|
Essential Genes for In Vitro Growth of the Endophyte Herbaspirillum seropedicae SmR1 as Revealed by Transposon Insertion Site Sequencing. Appl Environ Microbiol 2016; 82:6664-6671. [PMID: 27590816 PMCID: PMC5086560 DOI: 10.1128/aem.02281-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 08/31/2016] [Indexed: 01/04/2023] Open
Abstract
The interior of plants contains microorganisms (referred to as endophytes) that are distinct from those present at the root surface or in the surrounding soil. Herbaspirillum seropedicae strain SmR1, belonging to the betaproteobacteria, is an endophyte that colonizes crops, including rice, maize, sugarcane, and sorghum. Different approaches have revealed genes and pathways regulated during the interactions of H. seropedicae with its plant hosts. However, functional genomic analysis of transposon (Tn) mutants has been hampered by the lack of genetic tools. Here we successfully employed a combination of in vivo high-density mariner Tn mutagenesis and targeted Tn insertion site sequencing (Tn-seq) in H. seropedicae SmR1. The analysis of multiple gene-saturating Tn libraries revealed that 395 genes are essential for the growth of H. seropedicae SmR1 in tryptone-yeast extract medium. A comparative analysis with the Database of Essential Genes (DEG) showed that 25 genes are uniquely essential in H. seropedicae SmR1. The Tn mutagenesis protocol developed and the gene-saturating Tn libraries generated will facilitate elucidation of the genetic mechanisms of the H. seropedicae endophytic lifestyle. IMPORTANCE A focal point in the study of endophytes is the development of effective biofertilizers that could help to reduce the input of agrochemicals in croplands. Besides the ability to promote plant growth, a good biofertilizer should be successful in colonizing its host and competing against the native microbiota. By using a systematic Tn-based gene-inactivation strategy and massively parallel sequencing of Tn insertion sites (Tn-seq), it is possible to study the fitness of thousands of Tn mutants in a single experiment. We have applied the combination of these techniques to the plant-growth-promoting endophyte Herbaspirillum seropedicae SmR1. The Tn mutant libraries generated will enable studies into the genetic mechanisms of H. seropedicae-plant interactions. The approach that we have taken is applicable to other plant-interacting bacteria.
Collapse
|
20
|
Bonato P, Alves LR, Osaki JH, Rigo LU, Pedrosa FO, Souza EM, Zhang N, Schumacher J, Buck M, Wassem R, Chubatsu LS. The NtrY-NtrX two-component system is involved in controlling nitrate assimilation in Herbaspirillum seropedicae strain SmR1. FEBS J 2016; 283:3919-3930. [PMID: 27634462 DOI: 10.1111/febs.13897] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 08/15/2016] [Accepted: 09/13/2016] [Indexed: 10/21/2022]
Abstract
Herbaspirillum seropedicae is a diazotrophic β-Proteobacterium found endophytically associated with gramineae (Poaceae or graminaceous plants) such as rice, sorghum and sugar cane. In this work we show that nitrate-dependent growth in this organism is regulated by the master nitrogen regulatory two-component system NtrB-NtrC, and by NtrY-NtrX, which functions to specifically regulate nitrate metabolism. NtrY is a histidine kinase sensor protein predicted to be associated with the membrane and NtrX is the response regulator partner. The ntrYntrX genes are widely distributed in Proteobacteria. In α-Proteobacteria they are frequently located downstream from ntrBC, whereas in β-Proteobacteria these genes are located downstream from genes encoding an RNA methyltransferase and a proline-rich protein with unknown function. The NtrX protein of α-Proteobacteria has an AAA+ domain, absent in those from β-Proteobacteria. An ntrY mutant of H. seropedicae showed the wild-type nitrogen fixation phenotype, but the nitrate-dependent growth was abolished. Gene fusion assays indicated that NtrY is involved in the expression of genes coding for the assimilatory nitrate reductase as well as the nitrate-responsive two-component system NarX-NarL (narK and narX promoters, respectively). The purified NtrX protein was capable of binding the narK and narX promoters, and the binding site at the narX promoter for the NtrX protein was determined by DNA footprinting. In silico analyses revealed similar sequences in other promoter regions of H. seropedicae that are related to nitrate assimilation, supporting the role of the NtrY-NtrX system in regulating nitrate metabolism in H. seropedicae.
Collapse
Affiliation(s)
- Paloma Bonato
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Lysangela R Alves
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Juliana H Osaki
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Liu U Rigo
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Fabio O Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Emanuel M Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Nan Zhang
- Department of Life Sciences, Imperial College London, UK
| | | | - Martin Buck
- Department of Life Sciences, Imperial College London, UK
| | - Roseli Wassem
- Department of Genetics, Universidade Federal do Paraná, Curitiba, Brazil
| | - Leda S Chubatsu
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| |
Collapse
|
21
|
Bonato P, Batista MB, Camilios-Neto D, Pankievicz VCS, Tadra-Sfeir MZ, Monteiro RA, Pedrosa FO, Souza EM, Chubatsu LS, Wassem R, Rigo LU. RNA-seq analyses reveal insights into the function of respiratory nitrate reductase of the diazotroph Herbaspirillum seropedicae. Environ Microbiol 2016; 18:2677-88. [DOI: 10.1111/1462-2920.13422] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 06/07/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Paloma Bonato
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba PR Brazil
| | - Marcelo B. Batista
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba PR Brazil
| | - Doumit Camilios-Neto
- Department of Biochemistry and Biotechnology; Universidade Estadual de Londrina; Londrina PR Brazil
| | - Vânia C. S. Pankievicz
- 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
| | - Rose Adele Monteiro
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba PR Brazil
| | - Fabio O. Pedrosa
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba PR Brazil
| | - Emanuel M. Souza
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba PR Brazil
| | - Leda S. Chubatsu
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba PR Brazil
| | - Roseli Wassem
- Department of Genetics; Universidade Federal do Paraná; Curitiba PR Brazil
| | - Liu Un Rigo
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba PR Brazil
| |
Collapse
|
22
|
Maria Marin A, de la Torre J, Ricardo Marques Oliveira A, Barison A, Satie Chubatsu L, Adele Monteiro R, de Oliveira Pedrosa F, Maltempi de Souza E, Wassem R, Duque E, Ramos JL. Genetic and functional characterization of a novel meta-pathway for degradation of naringenin inHerbaspirillum seropedicaeSmR1. Environ Microbiol 2016; 18:4653-4661. [DOI: 10.1111/1462-2920.13313] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 03/20/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Anelis Maria Marin
- Department of Biochemistry and Molecular Biology; Nitrogen Fixation Group, UFPR; Brazil
| | - Jésus de la Torre
- Department of Environmental Protection; Estación Experimental del Zaídin CSIC; Spain
| | | | | | - Leda Satie Chubatsu
- Department of Biochemistry and Molecular Biology; Nitrogen Fixation Group, UFPR; Brazil
| | - Rose Adele Monteiro
- Department of Biochemistry and Molecular Biology; Nitrogen Fixation Group, UFPR; Brazil
| | | | | | | | - Estrella Duque
- Department of Environmental Protection; Estación Experimental del Zaídin CSIC; Spain
| | - Juan-Luis Ramos
- Department of Environmental Protection; Estación Experimental del Zaídin CSIC; Spain
- Department of Biotechnology, Abengoa Research; Spain
| |
Collapse
|
23
|
do Amaral FP, Pankievicz VCS, Arisi ACM, de Souza EM, Pedrosa F, Stacey G. Differential growth responses of Brachypodium distachyon genotypes to inoculation with plant growth promoting rhizobacteria. PLANT MOLECULAR BIOLOGY 2016; 90:689-697. [PMID: 26873699 DOI: 10.1007/s11103-016-0449-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 02/05/2016] [Indexed: 06/05/2023]
Abstract
Plant growth promoting rhizobacteria (PGPR) can associate and enhance the growth of important crop grasses. However, in most cases, the molecular mechanisms responsible for growth promotion are not known. Such research could benefit by the adoption of a grass model species that showed a positive response to bacterial inoculation and was amenable to genetic and molecular research methods. In this work we inoculated different genotypes of the model grass Brachypodium distachyon with two, well-characterized PGPR bacteria, Azospirillum brasilense and Herbaspirillum seropedicae, and evaluated the growth response. Plants were grown in soil under no nitrogen or with low nitrogen (i.e., 0.5 mM KNO3). A variety of growth parameters (e.g., shoot height, root length, number of lateral roots, fresh and dry weight) were measured 35 days after inoculation. The data indicate that plant genotype plays a very important role in determining the plant response to PGPR inoculation. A positive growth response was observed with only four genotypes grown under no nitrogen and three genotypes tested under low nitrogen. However, in contrast, relatively good root colonization was seen with most genotypes, as measured by drop plate counting and direct, microscopic examination of roots. In particular, the endophytic bacteria H. seropedicae showed strong epiphytic and endophytic colonization of roots.
Collapse
Affiliation(s)
- Fernanda P do Amaral
- Divisions of Plant Science and Biochemistry, C. S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA
| | - Vânia C S Pankievicz
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, 81531-980, Brazil
| | - Ana Carolina M Arisi
- Department of Food Science and Technology, Federal University of Santa Catarina, Florianópolis, 88034-001, Brazil
| | - Emanuel M de Souza
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, 81531-980, Brazil
| | - Fabio Pedrosa
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, 81531-980, Brazil
| | - Gary Stacey
- Divisions of Plant Science and Biochemistry, C. S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA.
| |
Collapse
|
24
|
Pankievicz VCS, Camilios-Neto D, Bonato P, Balsanelli E, Tadra-Sfeir MZ, Faoro H, Chubatsu LS, Donatti L, Wajnberg G, Passetti F, Monteiro RA, Pedrosa FO, Souza EM. RNA-seq transcriptional profiling of Herbaspirillum seropedicae colonizing wheat (Triticum aestivum) roots. PLANT MOLECULAR BIOLOGY 2016; 90:589-603. [PMID: 26801330 DOI: 10.1007/s11103-016-0430-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 01/04/2016] [Indexed: 05/23/2023]
Abstract
Herbaspirillum seropedicae is a diazotrophic and endophytic bacterium that associates with economically important grasses promoting plant growth and increasing productivity. To identify genes related to bacterial ability to colonize plants, wheat seedlings growing hydroponically in Hoagland's medium were inoculated with H. seropedicae and incubated for 3 days. Total mRNA from the bacteria present in the root surface and in the plant medium were purified, depleted from rRNA and used for RNA-seq profiling. RT-qPCR analyses were conducted to confirm regulation of selected genes. Comparison of RNA profile of root attached and planktonic bacteria revealed extensive metabolic adaptations to the epiphytic life style. These adaptations include expression of specific adhesins and cell wall re-modeling to attach to the root. Additionally, the metabolism was adapted to the microxic environment and nitrogen-fixation genes were expressed. Polyhydroxybutyrate (PHB) synthesis was activated, and PHB granules were stored as observed by microscopy. Genes related to plant growth promotion, such as auxin production were expressed. Many ABC transporter genes were regulated in the bacteria attached to the roots. The results provide new insights into the adaptation of H. seropedicae to the interaction with the plant.
Collapse
Affiliation(s)
- V C S Pankievicz
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - D Camilios-Neto
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, Londrina, PR, Brazil
| | - P Bonato
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - E Balsanelli
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - M Z Tadra-Sfeir
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - H Faoro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - L S Chubatsu
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - L Donatti
- Department of Cellular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - G Wajnberg
- Bioinformatics Unit, Clinical Research Coordination, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - F Passetti
- Bioinformatics Unit, Clinical Research Coordination, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - R A Monteiro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - F O Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - E M Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil.
| |
Collapse
|
25
|
Rosconi F, Trovero MF, de Souza EM, Fabiano E. Serobactins-mediated iron acquisition systems optimize competitive fitness of Herbaspirillum seropedicae inside rice plants. Environ Microbiol 2015; 18:2523-33. [PMID: 26715074 DOI: 10.1111/1462-2920.13202] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 12/27/2015] [Indexed: 02/02/2023]
Abstract
Herbaspirillum seropedicae Z67 is a diazotrophic endophyte able to colonize the interior of many economically relevant crops such as rice, wheat, corn and sorghum. Under iron-deficient conditions, this organism secretes serobactins, a suite of lipopetide siderophores. The role of siderophores in the interaction between endophytes and their plant hosts are not well understood. In this work, we aimed to determine the importance of serobactins-mediated iron acquisition systems in the interaction of H. seropedicae with rice plants. First we provide evidence, by using a combination of genome analysis, proteomic and genetic studies, that the Hsero_2345 gene encodes a TonB-dependent receptor involved in iron-serobactin complex internalization when iron bioavailability is low. Our results show that survival of the Hsero_2345 mutant inside rice plants was not significantly different from that of the wild-type strain. However, when plants were co-inoculated at equal ratios with the wild-type strain and with a double mutant defective in serobactins synthesis and internalization, recovery of mutant was significantly impaired after 8 days post-inoculation. These results demonstrate that serobactins-mediated iron acquisition contributes to competitive fitness of H. seropedicae inside host plants.
Collapse
Affiliation(s)
- Federico Rosconi
- Departamento de Bioquímica y Genómica Microbianas, IIBCE, Montevideo, Uruguay
| | - María F Trovero
- Departamento de Bioquímica y Genómica Microbianas, IIBCE, Montevideo, Uruguay
| | | | - Elena Fabiano
- Departamento de Bioquímica y Genómica Microbianas, IIBCE, Montevideo, Uruguay
| |
Collapse
|
26
|
Microscopic and proteomic analysis of Zea mays roots (P30F53 variety) inoculated with Azospirillum brasilense strain FP2. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s12892-014-0061-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
27
|
Aquino B, Stefanello AA, Oliveira MAS, Pedrosa FO, Souza EM, Monteiro RA, Chubatsu LS. Effect of point mutations on Herbaspirillum seropedicae NifA activity. ACTA ACUST UNITED AC 2015; 48:683-90. [PMID: 26176311 PMCID: PMC4541686 DOI: 10.1590/1414-431x20154522] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 03/26/2015] [Indexed: 11/21/2022]
Abstract
NifA is the transcriptional activator of the nif genes in
Proteobacteria. It is usually regulated by nitrogen and oxygen, allowing biological
nitrogen fixation to occur under appropriate conditions. NifA proteins have a typical
three-domain structure, including a regulatory N-terminal GAF domain, which is
involved in control by fixed nitrogen and not strictly required for activity, a
catalytic AAA+ central domain, which catalyzes open complex formation, and a
C-terminal domain involved in DNA-binding. In Herbaspirillum
seropedicae, a β-proteobacterium capable of colonizing Graminae of
agricultural importance, NifA regulation by ammonium involves its N-terminal GAF
domain and the signal transduction protein GlnK. When the GAF domain is removed, the
protein can still activate nif genes transcription; however,
ammonium regulation is lost. In this work, we generated eight constructs resulting in
point mutations in H. seropedicae NifA and analyzed their effect on
nifH transcription in Escherichia coli and
H. seropedicae. Mutations K22V, T160E, M161V, L172R, and A215D
resulted in inactive proteins. Mutations Q216I and S220I produced partially active
proteins with activity control similar to wild-type NifA. However, mutation G25E,
located in the GAF domain, resulted in an active protein that did not require GlnK
for activity and was partially sensitive to ammonium. This suggested that G25E may
affect the negative interaction between the N-terminal GAF domain and the catalytic
central domain under high ammonium concentrations, thus rendering the protein
constitutively active, or that G25E could lead to a conformational change comparable
with that when GlnK interacts with the GAF domain.
Collapse
Affiliation(s)
- B Aquino
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - A A Stefanello
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - M A S Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - F O Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - E M Souza
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - R A Monteiro
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - L S Chubatsu
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| |
Collapse
|
28
|
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] [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.
Collapse
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
| |
Collapse
|
29
|
Tadra-Sfeir MZ, Faoro H, Camilios-Neto D, Brusamarello-Santos L, Balsanelli E, Weiss V, Baura VA, Wassem R, Cruz LM, De Oliveira Pedrosa F, Souza EM, Monteiro RA. Genome wide transcriptional profiling of Herbaspirillum seropedicae SmR1 grown in the presence of naringenin. Front Microbiol 2015; 6:491. [PMID: 26052319 PMCID: PMC4440368 DOI: 10.3389/fmicb.2015.00491] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 05/04/2015] [Indexed: 11/13/2022] Open
Abstract
Herbaspirillum seropedicae is a diazotrophic bacterium which associates endophytically with economically important gramineae. Flavonoids such as naringenin have been shown to have an effect on the interaction between H. seropedicae and its host plants. We used a high-throughput sequencing based method (RNA-Seq) to access the influence of naringenin on the whole transcriptome profile of H. seropedicae. Three hundred and four genes were downregulated and seventy seven were upregulated by naringenin. Data analysis revealed that genes related to bacterial flagella biosynthesis, chemotaxis and biosynthesis of peptidoglycan were repressed by naringenin. Moreover, genes involved in aromatic metabolism and multidrug transport efllux were actived.
Collapse
Affiliation(s)
- Michelle Z Tadra-Sfeir
- Nitrogen Fixation group, Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná Curitiba, Brazil
| | - Helisson Faoro
- Nitrogen Fixation group, Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná Curitiba, Brazil ; Instituto Carlos Chagas, Fundação Oswaldo Cruz, Fiocruz-PR Curitiba, Brazil
| | - Doumit Camilios-Neto
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina Londrina, Brazil
| | - Liziane Brusamarello-Santos
- Nitrogen Fixation group, Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná Curitiba, Brazil
| | - Eduardo Balsanelli
- Nitrogen Fixation group, Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná Curitiba, Brazil
| | - Vinicius Weiss
- Nitrogen Fixation group, Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná Curitiba, Brazil
| | - Valter A Baura
- Nitrogen Fixation group, Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná Curitiba, Brazil
| | - Roseli Wassem
- Department of Genetics, Universidade Federal do Paraná Curitiba, Brazil
| | - Leonardo M Cruz
- Nitrogen Fixation group, Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná Curitiba, Brazil
| | - Fábio De Oliveira Pedrosa
- Nitrogen Fixation group, Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná Curitiba, Brazil
| | - Emanuel M Souza
- Nitrogen Fixation group, Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná Curitiba, Brazil
| | - Rose A Monteiro
- Nitrogen Fixation group, Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná Curitiba, Brazil
| |
Collapse
|
30
|
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] [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.
Collapse
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.
| |
Collapse
|
31
|
Zhang LH, Chen SF. Influence of different factors on the nitrogenase activity of the engineered Escherichia coli 78-7. World J Microbiol Biotechnol 2015; 31:921-7. [PMID: 25850532 DOI: 10.1007/s11274-015-1846-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/19/2015] [Indexed: 10/23/2022]
Abstract
The engineered Escherichia coli 78-7 is a derivative of E. coli JM109 carrying a nitrogen fixation (nif) gene cluster composed of nine genes (nifB, nifH, nifD, nifK, nifE, nifN, nifX, hesA and nifV) and its own σ(70)-dependent nif promoter from a gram-positive bacterium Paenibacillus sp. WLY78. The physiological and biochemical characteristics of the engineered E. coli 78-7 were analyzed by using Biolog GEN III MicroPlate, with E. coli JM109 and JM109/pHY300PLK (E. coli JM109 carrying empty vector) as controls. Analysis of 94 phenotypic tests: 71 carbon source utilization assays and 23 chemical sensitivity tests showed that the engineered E. coli 78-7, E. coli JM109 and JM109/pHY300PLK gave similar patterns of utilization of various substrates as carbon and energy sources. Furthermore, the effect of carbon source, nitrogen source, culture temperature on the nitrogenase activity of the engineered E. coli 78-7 was investigated. Our study demonstrates that the nif capacity of E. coli 78-7 was affected significantly by the different culture condition. The significant nitrogenase activity of E. coli 78-7 were obtained when cells were cultivated in the medium containing 4 g/l glucose (carbon source) and 2 mM glutamate (nitrogen source) and at 30 °C.
Collapse
Affiliation(s)
- Li-hong Zhang
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Yuanmingyuan Road, Haidian District, Beijing, 100193, China,
| | | |
Collapse
|
32
|
Pankievicz VCS, do Amaral FP, Santos KFDN, Agtuca B, Xu Y, Schueller MJ, Arisi ACM, Steffens MBR, de Souza EM, Pedrosa FO, Stacey G, Ferrieri RA. Robust biological nitrogen fixation in a model grass-bacterial association. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:907-19. [PMID: 25645593 DOI: 10.1111/tpj.12777] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 01/15/2015] [Accepted: 01/20/2015] [Indexed: 05/18/2023]
Abstract
Nitrogen-fixing rhizobacteria can promote plant growth; however, it is controversial whether biological nitrogen fixation (BNF) from associative interaction contributes to growth promotion. The roots of Setaria viridis, a model C4 grass, were effectively colonized by bacterial inoculants resulting in a significant enhancement of growth. Nitrogen-13 tracer studies provided direct evidence for tracer uptake by the host plant and incorporation into protein. Indeed, plants showed robust growth under nitrogen-limiting conditions when inoculated with an ammonium-excreting strain of Azospirillum brasilense. (11)C-labeling experiments showed that patterns in central carbon metabolism and resource allocation exhibited by nitrogen-starved plants were largely reversed by bacterial inoculation, such that they resembled plants grown under nitrogen-sufficient conditions. Adoption of S. viridis as a model should promote research into the mechanisms of associative nitrogen fixation with the ultimate goal of greater adoption of BNF for sustainable crop production.
Collapse
Affiliation(s)
- Vânia C S Pankievicz
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, 81531-980, Curitiba, Brazil
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Real-time PCR quantification of the plant growth promoting bacteria Herbaspirillum seropedicae strain SmR1 in maize roots. Mol Biotechnol 2015; 56:660-70. [PMID: 24563376 DOI: 10.1007/s12033-014-9742-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The plant growth promoting bacteria Herbaspirillum seropedicae SmR1 is an endophytic diazotroph found in several economically important crops. Considering that methods to monitor the plant-bacteria interaction are required, our objective was to develop a real-time PCR method for quantification of PGPB H. seropedicae in the rhizosphere of maize seedlings. Primer pairs were designed, and their specificity was verified using DNA from 12 different bacterial species. Ten standard curves of qPCR assay using HERBAS1 primers and tenfold serial dilutions of H. seropedicae SmR1 DNA were performed, and PCR efficiency of 91 % and correlation coefficient of 0.99 were obtained. H. seropedicae SmR1 limit of detection was 10(1) copies (corresponding to 60.3 fg of bacterial DNA). qPCR assay using HERBAS1 was used to detect and quantify H. seropedicae strain SmR1 in inoculated maize roots, cultivated in vitro and in pots, harvested 1, 4, 7, and 10 days after inoculation. The estimated bacterial DNA copy number per gram of root was in the range 10(7)-10(9) for plants grown in vitro and it was around 10(6) for plants grown in pots. Primer pair HERBAS1 was able to quantify H. seropedicae SmR1, and this assay can be useful for monitoring plant-bacteria interaction.
Collapse
|
34
|
Valdameri G, Kokot T, Pedrosa FDO, de Souza E. Rapid quantification of rice root-associated bacteria by flow cytometry. Lett Appl Microbiol 2014; 60:237-41. [DOI: 10.1111/lam.12351] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/21/2014] [Accepted: 10/24/2014] [Indexed: 11/29/2022]
Affiliation(s)
- G. Valdameri
- Department of Biochemistry and Molecular Biology; Federal University of Paraná; Curitiba Paraná Brazil
| | - T.B. Kokot
- Department of Biochemistry and Molecular Biology; Federal University of Paraná; Curitiba Paraná Brazil
| | - F. de O. Pedrosa
- Department of Biochemistry and Molecular Biology; Federal University of Paraná; Curitiba Paraná Brazil
| | - E.M. de Souza
- Department of Biochemistry and Molecular Biology; Federal University of Paraná; Curitiba Paraná Brazil
| |
Collapse
|
35
|
Biochemical characteristics, adhesion, and cytotoxicity of environmental and clinical isolates of Herbaspirillum spp. J Clin Microbiol 2014; 53:302-8. [PMID: 25355763 DOI: 10.1128/jcm.02192-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Herbaspirillum bacteria are best known as plant growth-promoting rhizobacteria but have also been recovered from clinical samples. Here, biochemical tests, matrix-assisted laser deionization-time of flight (MALDI-TOF) mass spectrometry, adherence, and cytotoxicity to eukaryotic cells were used to compare clinical and environmental isolates of Herbaspirillum spp. Discrete biochemical differences were observed between human and environmental strains. All strains adhered to HeLa cells at low densities, and cytotoxic effects were discrete, supporting the view that Herbaspirillum bacteria are opportunists with low virulence potential.
Collapse
|
36
|
Balsanelli E, de Baura VA, Pedrosa FDO, de Souza EM, Monteiro RA. Exopolysaccharide biosynthesis enables mature biofilm formation on abiotic surfaces by Herbaspirillum seropedicae. PLoS One 2014; 9:e110392. [PMID: 25310013 PMCID: PMC4195743 DOI: 10.1371/journal.pone.0110392] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 09/13/2014] [Indexed: 11/26/2022] Open
Abstract
H. seropedicae associates endophytically and epiphytically with important poaceous crops and is capable of promoting their growth. The molecular mechanisms involved in plant colonization by this microrganism are not fully understood. Exopolysaccharides (EPS) are usually necessary for bacterial attachment to solid surfaces, to other bacteria, and to form biofilms. The role of H. seropedicae SmR1 exopolysaccharide in biofilm formation on both inert and plant substrates was assessed by characterization of a mutant in the espB gene which codes for a glucosyltransferase. The mutant strain was severely affected in EPS production and biofilm formation on glass wool. In contrast, the plant colonization capacity of the mutant strain was not altered when compared to the parental strain. The requirement of EPS for biofilm formation on inert surface was reinforced by the induction of eps genes in biofilms grown on glass and polypropylene. On the other hand, a strong repression of eps genes was observed in H. seropedicae cells adhered to maize roots. Our data suggest that H. seropedicae EPS is a structural component of mature biofilms, but this development stage of biofilm is not achieved during plant colonization.
Collapse
Affiliation(s)
- Eduardo Balsanelli
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Válter Antonio de Baura
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Fábio de Oliveira Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Rose Adele Monteiro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| |
Collapse
|
37
|
Expressed Proteins of Herbaspirillum seropedicae in Maize (DKB240) Roots-Bacteria Interaction Revealed Using Proteomics. Appl Biochem Biotechnol 2014; 174:2267-77. [DOI: 10.1007/s12010-014-1197-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 08/22/2014] [Indexed: 12/22/2022]
|
38
|
The Herbaspirillum seropedicae SmR1 Fnr orthologs controls the cytochrome composition of the electron transport chain. Sci Rep 2014; 3:2544. [PMID: 23996052 PMCID: PMC3759049 DOI: 10.1038/srep02544] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 08/12/2013] [Indexed: 11/08/2022] Open
Abstract
The transcriptional regulatory protein Fnr, acts as an intracellular redox sensor regulating a wide range of genes in response to changes in oxygen levels. Genome sequencing of Herbaspirillum seropedicae SmR1 revealed the presence of three fnr-like genes. In this study we have constructed single, double and triple fnr deletion mutant strains of H. seropedicae. Transcriptional profiling in combination with expression data from reporter fusions, together with spectroscopic analysis, demonstrates that the Fnr1 and Fnr3 proteins not only regulate expression of the cbb3-type respiratory oxidase, but also control the cytochrome content and other component complexes required for the cytochrome c-based electron transport pathway. Accordingly, in the absence of the three Fnr paralogs, growth is restricted at low oxygen tensions and nitrogenase activity is impaired. Our results suggest that the H. seropedicae Fnr proteins are major players in regulating the composition of the electron transport chain in response to prevailing oxygen concentrations.
Collapse
|
39
|
do Amaral FP, Bueno JCF, Hermes VS, Arisi ACM. Gene expression analysis of maize seedlings (DKB240 variety) inoculated with plant growth promoting bacterium Herbaspirillum seropedicae. Symbiosis 2014. [DOI: 10.1007/s13199-014-0270-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
40
|
Real time PCR detection targeting nifA gene of plant growth promoting bacteria Azospirillum brasilense strain FP2 in maize roots. Symbiosis 2013. [DOI: 10.1007/s13199-013-0262-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
41
|
Balsanelli E, Tuleski TR, de Baura VA, Yates MG, Chubatsu LS, de Oliveira Pedrosa F, de Souza EM, Monteiro RA. Maize root lectins mediate the interaction with Herbaspirillum seropedicae via N-acetyl glucosamine residues of lipopolysaccharides. PLoS One 2013; 8:e77001. [PMID: 24130823 PMCID: PMC3793968 DOI: 10.1371/journal.pone.0077001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 09/05/2013] [Indexed: 11/26/2022] Open
Abstract
Herbaspirillum seropedicae is a plant growth-promoting diazotrophic betaproteobacterium which associates with important crops, such as maize, wheat, rice and sugar-cane. We have previously reported that intact lipopolysaccharide (LPS) is required for H. seropedicae attachment and endophytic colonization of maize roots. In this study, we present evidence that the LPS biosynthesis gene waaL (codes for the O-antigen ligase) is induced during rhizosphere colonization by H. seropedicae. Furthermore a waaL mutant strain lacking the O-antigen portion of the LPS is severely impaired in colonization. Since N-acetyl glucosamine inhibits H. seropedicae attachment to maize roots, lectin-like proteins from maize roots (MRLs) were isolated and mass spectrometry (MS) analysis showed that MRL-1 and MRL-2 correspond to maize proteins with a jacalin-like lectin domain, while MRL-3 contains a B-chain lectin domain. These proteins showed agglutination activity against wild type H. seropedicae, but failed to agglutinate the waaL mutant strain. The agglutination reaction was severely diminished in the presence of N-acetyl glucosamine. Moreover addition of the MRL proteins as competitors in H. seropedicae attachment assays decreased 80-fold the adhesion of the wild type to maize roots. The results suggest that N-acetyl glucosamine residues of the LPS O-antigen bind to maize root lectins, an essential step for efficient bacterial attachment and colonization.
Collapse
Affiliation(s)
- Eduardo Balsanelli
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Thalita Regina Tuleski
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Valter Antonio de Baura
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Marshall Geoffrey Yates
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Leda Satie Chubatsu
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Fabio de Oliveira Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Rose Adele Monteiro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| |
Collapse
|
42
|
Alberton D, Müller-Santos M, Brusamarello-Santos LCC, Valdameri G, Cordeiro FA, Yates MG, de Oliveira Pedrosa F, de Souza EM. Comparative Proteomics Analysis of the Rice Roots Colonized by Herbaspirillum seropedicae Strain SmR1 Reveals Induction of the Methionine Recycling in the Plant Host. J Proteome Res 2013; 12:4757-68. [DOI: 10.1021/pr400425f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Dayane Alberton
- Department of Biochemistry
and Molecular Biology, Federal University of Paraná, Rua
Francisco H. dos Santos s/n Centro Politécnico, Curitiba, Paraná 81531-990, Brazil
| | - Marcelo Müller-Santos
- Department of Biochemistry
and Molecular Biology, Federal University of Paraná, Rua
Francisco H. dos Santos s/n Centro Politécnico, Curitiba, Paraná 81531-990, Brazil
| | | | - Glaucio Valdameri
- Department of Biochemistry
and Molecular Biology, Federal University of Paraná, Rua
Francisco H. dos Santos s/n Centro Politécnico, Curitiba, Paraná 81531-990, Brazil
| | - Fabio Aparecido Cordeiro
- Department of Biochemistry
and Molecular Biology, Federal University of Paraná, Rua
Francisco H. dos Santos s/n Centro Politécnico, Curitiba, Paraná 81531-990, Brazil
| | - Marshall Geoffrey Yates
- Department of Biochemistry
and Molecular Biology, Federal University of Paraná, Rua
Francisco H. dos Santos s/n Centro Politécnico, Curitiba, Paraná 81531-990, Brazil
| | - Fabio de Oliveira Pedrosa
- Department of Biochemistry
and Molecular Biology, Federal University of Paraná, Rua
Francisco H. dos Santos s/n Centro Politécnico, Curitiba, Paraná 81531-990, Brazil
| | - Emanuel Maltempi de Souza
- Department of Biochemistry
and Molecular Biology, Federal University of Paraná, Rua
Francisco H. dos Santos s/n Centro Politécnico, Curitiba, Paraná 81531-990, Brazil
| |
Collapse
|
43
|
Rosconi F, Davyt D, Martínez V, Martínez M, Abin-Carriquiry JA, Zane H, Butler A, de Souza EM, Fabiano E. Identification and structural characterization of serobactins, a suite of lipopeptide siderophores produced by the grass endophyteHerbaspirillum seropedicae. Environ Microbiol 2013; 15:916-27. [DOI: 10.1111/1462-2920.12075] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 11/28/2012] [Accepted: 12/10/2012] [Indexed: 12/11/2022]
Affiliation(s)
| | - Danilo Davyt
- Cátedra de Química Farmacéutica; Facultad de Química; Montevideo; Uruguay
| | - Verónica Martínez
- Cátedra de Química Farmacéutica; Facultad de Química; Montevideo; Uruguay
| | | | | | - Hannah Zane
- Department of Chemistry and Biochemistry; UCSB; Santa Barbara; USA
| | - Alison Butler
- Department of Chemistry and Biochemistry; UCSB; Santa Barbara; USA
| | | | | |
Collapse
|
44
|
Serrato RV, Balsanelli E, Sassaki GL, Carlson RW, Muszynski A, Monteiro RA, Pedrosa FO, Souza EM, Iacomini M. Structural analysis of Herbaspirillum seropedicae lipid-A and of two mutants defective to colonize maize roots. Int J Biol Macromol 2012; 51:384-91. [DOI: 10.1016/j.ijbiomac.2012.05.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Revised: 05/16/2012] [Accepted: 05/29/2012] [Indexed: 10/28/2022]
|
45
|
Marin AM, Souza EM, Pedrosa FO, Souza LM, Sassaki GL, Baura VA, Yates MG, Wassem R, Monteiro RA. Naringenin degradation by the endophytic diazotroph Herbaspirillum seropedicae SmR1. MICROBIOLOGY-SGM 2012; 159:167-175. [PMID: 23125118 DOI: 10.1099/mic.0.061135-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Several bacteria are able to degrade flavonoids either to use them as carbon sources or as a detoxification mechanism. Degradation pathways have been proposed for several bacteria, but the genes responsible are not known. We identified in the genome of the endophyte Herbaspirillum seropedicae SmR1 an operon potentially associated with the degradation of aromatic compounds. We show that this operon is involved in naringenin degradation and that its expression is induced by naringenin and chrysin, two closely related flavonoids. Mutation of fdeA, the first gene of the operon, and fdeR, its transcriptional activator, abolished the ability of H. seropedicae to degrade naringenin.
Collapse
Affiliation(s)
- A M Marin
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| | - E M Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| | - F O Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| | - L M Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| | - G L Sassaki
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| | - V A Baura
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| | - M G Yates
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| | - R Wassem
- Department of Genetics, Universidade Federal do Paraná, CP 19071, 81531-980, Curitiba, PR, Brazil
| | - R A Monteiro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| |
Collapse
|
46
|
Zhang LH, Chen SF. Pseudacidovorax intermedius NH-1, a novel marine nitrogen-fixing bacterium isolated from the South China Sea. World J Microbiol Biotechnol 2012; 28:2839-47. [PMID: 22806723 DOI: 10.1007/s11274-012-1093-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 05/25/2012] [Indexed: 11/29/2022]
Abstract
We have taxonomically and phylogenetically characterized a novel nitrogen-fixing bacterial strain, NH-1, which was recently isolated from surface sediments of the South China Sea. The presence of the nifH gene was determined by PCR amplification. The strain NH-1 was found to belong to the genus Pseudacidovorax based on phenotypic characterization, 16S rDNA sequencing, G+C content and DNA-DNA hybridization. Isolate NH-1 was identified as Pseudacidovorax intermedius. In addition, we investigated the links between environmental factors and the nitrogenase activity of NH-1. We found that the nitrogen fixation capacity of NH-1 varied strongly when cells were grown with different ammonium ion and oxygen concentrations, amino acids and carbohydrates. This is the first report of the isolation of Pseudacidovorax from the ocean and the first study to explore the effects of different culture conditions on the nitrogenase activities of the isolate. This study provides evidence that marine nitrogen-fixing microorganisms are far more diverse than currently recognized.
Collapse
Affiliation(s)
- Li-hong Zhang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China.
| | | |
Collapse
|
47
|
Monteiro RA, Balsanelli E, Tuleski T, Faoro H, Cruz LM, Wassem R, Baura VA, Tadra-Sfeir MZ, Weiss V, DaRocha WD, Muller-Santos M, Chubatsu LS, Huergo LF, Pedrosa FO, Souza EM. Genomic comparison of the endophyte Herbaspirillum seropedicaeSmR1 and the phytopathogen Herbaspirillum rubrisubalbicansM1 by suppressive subtractive hybridization and partial genome sequencing. FEMS Microbiol Ecol 2012; 80:441-51. [PMID: 22268687 DOI: 10.1111/j.1574-6941.2012.01309.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 12/23/2011] [Accepted: 01/11/2012] [Indexed: 12/28/2022] Open
Affiliation(s)
- Rose A. Monteiro
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Eduardo Balsanelli
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Thalita Tuleski
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Helison Faoro
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Leonardo M. Cruz
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Roseli Wassem
- Department of Genetics; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Valter A. Baura
- 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
| | - Vinícius Weiss
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Wanderson D. DaRocha
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Marcelo Muller-Santos
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Leda S. Chubatsu
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Luciano F. Huergo
- 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. Souza
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| |
Collapse
|
48
|
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] [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.
Collapse
Affiliation(s)
- Marco A S Kadowaki
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba-PR, Brazil
| | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Pedrosa FO, Monteiro RA, Wassem R, Cruz LM, Ayub RA, Colauto NB, Fernandez MA, Fungaro MHP, Grisard EC, Hungria M, Madeira HMF, Nodari RO, Osaku CA, Petzl-Erler ML, Terenzi H, Vieira LGE, Steffens MBR, Weiss VA, Pereira LFP, Almeida MIM, Alves LR, Marin A, Araujo LM, Balsanelli E, Baura VA, Chubatsu LS, Faoro H, Favetti A, Friedermann G, Glienke C, Karp S, Kava-Cordeiro V, Raittz RT, Ramos HJO, Ribeiro EMSF, Rigo LU, Rocha SN, Schwab S, Silva AG, Souza EM, Tadra-Sfeir MZ, Torres RA, Dabul ANG, Soares MAM, Gasques LS, Gimenes CCT, Valle JS, Ciferri RR, Correa LC, Murace NK, Pamphile JA, Patussi EV, Prioli AJ, Prioli SMA, Rocha CLMSC, Arantes OMN, Furlaneto MC, Godoy LP, Oliveira CEC, Satori D, Vilas-Boas LA, Watanabe MAE, Dambros BP, Guerra MP, Mathioni SM, Santos KL, Steindel M, Vernal J, Barcellos FG, Campo RJ, Chueire LMO, Nicolás MF, Pereira-Ferrari L, Silva JLDC, Gioppo NMR, Margarido VP, Menck-Soares MA, Pinto FGS, Simão RDCG, Takahashi EK, Yates MG, Souza EM. Genome of Herbaspirillum seropedicae strain SmR1, a specialized diazotrophic endophyte of tropical grasses. PLoS Genet 2011; 7:e1002064. [PMID: 21589895 PMCID: PMC3093359 DOI: 10.1371/journal.pgen.1002064] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 03/18/2011] [Indexed: 01/28/2023] Open
Abstract
The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazotrophic endophytes and plants are scarcely known. Herbaspirillum seropedicae is an endophytic bacterium capable of colonizing intercellular spaces of grasses such as rice and sugar cane. The genome of H. seropedicae strain SmR1 was sequenced and annotated by The Paraná State Genome Programme--GENOPAR. The genome is composed of a circular chromosome of 5,513,887 bp and contains a total of 4,804 genes. The genome sequence revealed that H. seropedicae is a highly versatile microorganism with capacity to metabolize a wide range of carbon and nitrogen sources and with possession of four distinct terminal oxidases. The genome contains a multitude of protein secretion systems, including type I, type II, type III, type V, and type VI secretion systems, and type IV pili, suggesting a high potential to interact with host plants. H. seropedicae is able to synthesize indole acetic acid as reflected by the four IAA biosynthetic pathways present. A gene coding for ACC deaminase, which may be involved in modulating the associated plant ethylene-signaling pathway, is also present. Genes for hemagglutinins/hemolysins/adhesins were found and may play a role in plant cell surface adhesion. These features may endow H. seropedicae with the ability to establish an endophytic life-style in a large number of plant species.
Collapse
|
50
|
Schmidt M, Souza E, Baura V, Wassem R, Yates M, Pedrosa F, Monteiro R. Evidence for the endophytic colonization of Phaseolus vulgaris(common bean) roots by the diazotroph Herbaspirillum seropedicae. Braz J Med Biol Res 2011; 44:182-5. [DOI: 10.1590/s0100-879x2011007500004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Accepted: 12/15/2010] [Indexed: 11/22/2022] Open
Affiliation(s)
| | | | | | - R. Wassem
- Universidade Federal do Paraná, Brasil
| | | | | | | |
Collapse
|