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Ghitti E, Rolli E, Vergani L, Borin S. Flavonoids influence key rhizocompetence traits for early root colonization and PCB degradation potential of Paraburkholderia xenovorans LB400. FRONTIERS IN PLANT SCIENCE 2024; 15:1325048. [PMID: 38371405 PMCID: PMC10869545 DOI: 10.3389/fpls.2024.1325048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/15/2024] [Indexed: 02/20/2024]
Abstract
Introduction Flavonoids are among the main plant root exudation components, and, in addition to their role in symbiosis, they can broadly affect the functionality of plant-associated microbes: in polluted environments, for instance, flavonoids can induce the expression of the enzymatic degradative machinery to clean-up soils from xenobiotics like polychlorinated biphenyls (PCBs). However, their involvement in root community recruitment and assembly involving non-symbiotic beneficial interactions remains understudied and may be crucial to sustain the holobiont fitness under PCB stress. Methods By using a set of model pure flavonoid molecules and a natural blend of root exudates (REs) with altered flavonoid composition produced by Arabidopsis mutant lines affected in flavonoid biosynthesis and abundance (null mutant tt4, flavonoid aglycones hyperproducer tt8, and flavonoid conjugates hyperaccumulator ttg), we investigated flavonoid contribution in stimulating rhizocompetence traits and the catabolic potential of the model bacterial strain for PCB degradation Paraburkholderia xenovorans LB400. Results Flavonoids influenced the traits involved in bacterial recruitment in the rhizoplane by improving chemotaxis and motility responses, by increasing biofilm formation and by promoting the growth and activation of the PCB-degradative pathway of strain LB400, being thus potentially exploited as carbon sources, stimulating factors and chemoattractant molecules. Indeed, early rhizoplane colonization was favored in plantlets of the tt8 Arabidopsis mutant and reduced in the ttg line. Bacterial growth was promoted by the REs of mutant lines tt4 and tt8 under control conditions and reduced upon PCB-18 stress, showing no significant differences compared with the WT and ttg, indicating that unidentified plant metabolites could be involved. PCB stress presumably altered the Arabidopsis root exudation profile, although a sudden "cry-for-help" response to recruit strain LB400 was excluded and flavonoids appeared not to be the main determinants. In the in vitro plant-microbe interaction assays, plant growth promotion and PCB resistance promoted by strain LB400 seemed to act through flavonoid-independent mechanisms without altering bacterial colonization efficiency and root adhesion pattern. Discussions This study further contributes to elucidate the vast array of functions provided by flavonoids in orchestrating the early events of PCB-degrading strain LB400 recruitment in the rhizosphere and to support the holobiont fitness by stimulating the catabolic machinery involved in xenobiotics decomposition and removal.
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Affiliation(s)
| | - Eleonora Rolli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
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Herbaspirillum seropedicae strain HRC54 expression profile in response to sugarcane apoplastic fluid. 3 Biotech 2021; 11:292. [PMID: 34136329 DOI: 10.1007/s13205-021-02848-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/17/2021] [Indexed: 10/21/2022] Open
Abstract
Bacterial transcriptome profiling in the presence of plant fluids or extracts during microbial growth may provide relevant information on plant-bacteria interactions. Here, RNA sequencing (RNA-Seq) was used to determine the transcriptomic profile of Herbaspirillum seropedicae strain HRC54 at the early stages of response to sugarcane apoplastic fluid. Differentially expressed gene (DEG) analysis was performed using the DESeq2 and edgeR packages, followed by functional annotation using Blast2GO and gene ontology enrichment analysis using the COG and KEGG databases. After 2 h of sugarcane apoplastic fluid addition to the H. seropedicae HRC54 culture, respectively, 44 and 45 genes were upregulated and downregulated. These genes were enriched in bacterial metabolism (e.g., oxidoreductase and transferase), ABC transporters, motility, secretion systems, and signal transduction. RNA-Seq expression profiles of 12 genes identified in data analyses were verified by RT-qPCR. The results suggested that H. seropedicae HRC54 recognized sugarcane apoplastic fluid as the host signal, and some DEGs were closely involved at the early stages of the establishment of plant-bacteria interactions. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02848-y.
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Insights into the early stages of plant-endophytic bacteria interaction. World J Microbiol Biotechnol 2021; 37:13. [PMID: 33392741 DOI: 10.1007/s11274-020-02966-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/21/2020] [Indexed: 12/11/2022]
Abstract
The plant holobiont is a complex entity composed of the plant and the organisms that live in and on it including its microbiota. The plant microbiota includes, among other microorganisms, bacterial endophytes, which are bacteria that can invade living plant tissues without causing symptoms of disease. The interaction between the endophytic bacterial microbiota and their plant host has profound influences on their fitness and depends on biotic and abiotic factors. For these interactions to be established, the bacteria have to be present at the right time, in the right place either colonizing the soil or the seed. In this review we summarize the current knowledge regarding the sources of the bacterial endophytic microbiome and the processes involved in the assemblage of the resulting community during the initial stages of plant development. The adaptations that allow the spatial approximation of soil- and seed-borne bacteria towards infection and colonization of the internal tissues of plants will be addressed in this review.
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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.
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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.
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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.
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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: 10] [Impact Index Per Article: 2.0] [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.
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Defining the Genetic Basis of Plant⁻Endophytic Bacteria Interactions. Int J Mol Sci 2019; 20:ijms20081947. [PMID: 31010043 PMCID: PMC6515357 DOI: 10.3390/ijms20081947] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 01/17/2023] Open
Abstract
Endophytic bacteria, which interact closely with their host, are an essential part of the plant microbiome. These interactions enhance plant tolerance to environmental changes as well as promote plant growth, thus they have become attractive targets for increasing crop production. Numerous studies have aimed to characterise how endophytic bacteria infect and colonise their hosts as well as conferring important traits to the plant. In this review, we summarise the current knowledge regarding endophytic colonisation and focus on the insights that have been obtained from the mutants of bacteria and plants as well as ‘omic analyses. These show how endophytic bacteria produce various molecules and have a range of activities related to chemotaxis, motility, adhesion, bacterial cell wall properties, secretion, regulating transcription and utilising a substrate in order to establish a successful interaction. Colonisation is mediated by plant receptors and is regulated by the signalling that is connected with phytohormones such as auxin and jasmonic (JA) and salicylic acids (SA). We also highlight changes in the expression of small RNAs and modifications of the cell wall properties. Moreover, in order to exploit the beneficial plant-endophytic bacteria interactions in agriculture successfully, we show that the key aspects that govern successful interactions remain to be defined.
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Arraiano CM. Stories of the future: manipulating RNA and Intra/Interkingdom communication. Microb Biotechnol 2019; 12:48-50. [PMID: 30485669 PMCID: PMC6302701 DOI: 10.1111/1751-7915.13344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 11/09/2018] [Indexed: 11/30/2022] Open
Affiliation(s)
- Cecilia Maria Arraiano
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da República2780‐157OeirasPortugal
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9
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da Silva PRA, Vidal MS, Soares CDP, Polese V, Tadra-Sfeir MZ, de Souza EM, Simões-Araújo JL, Baldani JI. Sugarcane apoplast fluid modulates the global transcriptional profile of the diazotrophic bacteria Paraburkholderia tropica strain Ppe8. PLoS One 2018; 13:e0207863. [PMID: 30550601 PMCID: PMC6294378 DOI: 10.1371/journal.pone.0207863] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 11/07/2018] [Indexed: 11/18/2022] Open
Abstract
The stalk apoplast fluid of sugarcane contains different sugars, organic acids and amino acids that may supply the demand for carbohydrates by endophytic bacteria including diazotrophs P. tropica (syn. B. tropica) strain Ppe8, isolated from sugarcane, is part of the bacterial consortium recommended as inoculant to sugarcane. However, little information has been accumulated regarding this plant-bacterium interaction considering that it colonizes internal sugarcane tissues. Here, we made use of the RNA-Seq transcriptomic analysis to study the influence of sugarcane stalk apoplast fluid on Ppe8 gene expression. The bacterium was grown in JMV liquid medium (100 ml), divided equally and then supplemented with 50 ml of fresh JMV medium or 50 ml of apoplast fluid extracted from sugarcane variety RB867515. Total RNA was extracted 2 hours later, the rRNAs were depleted and mRNAs used to construct libraries to sequence the fragments using Ion Torrent technology. The mapping and statistical analysis were carried out with CLC Genomics Workbench software. The RNA-seq data was validated by RT-qPCR using the reference genes fliP1, paaF, and groL. The data analysis showed that 544 genes were repressed and 153 genes were induced in the presence of apoplast fluid. Genes that induce plant defense responses, genes related to chemotaxis and movements were repressed in the presence of apoplast fluid, indicating that strain Ppe8 recognizes the apoplast fluid as a plant component. The expression of genes involved in bacterial metabolism was regulated (up and down), suggesting that the metabolism of strain Ppe8 is modulated by the apoplast fluid. These results suggest that Ppe8 alters its gene expression pattern in the presence of apoplast fluid mainly in order to use compounds present in the fluid as well as to avoid the induction of plant defense mechanisms. This is a pioneer study showing the role played by the sugarcane apoplast fluid on the global modulation of genes in P. tropica strain Ppe8.
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Affiliation(s)
| | | | | | - Valéria Polese
- Department of Crop Science—UFRRJ, BR 465, Seropédica–RJ–CEP, Brazil
| | - Michelle Zibetti Tadra-Sfeir
- Departament of Biochemistry and Molecular Biology, Centro Politecnico—UFPR, Rua XV de Novembro, Curitiba–PR–CEP, Brazil
| | - Emanuel Maltempi de Souza
- Departament of Biochemistry and Molecular Biology, Centro Politecnico—UFPR, Rua XV de Novembro, Curitiba–PR–CEP, Brazil
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10
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Polese V, de Paula Soares C, da Silva PRA, Simões-Araújo JL, Baldani JI, Vidal MS. Selection and validation of reference genes for RT-qPCR indicates that juice of sugarcane varieties modulate the expression of C metabolism genes in the endophytic diazotrophic Herbaspirillum rubrisubalbicans strain HCC103. Antonie Van Leeuwenhoek 2017; 110:1555-1568. [DOI: 10.1007/s10482-017-0906-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 06/28/2017] [Indexed: 12/24/2022]
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11
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Miao Y, Shen Y, Xu Y. Effects of Inhibitors on the Transcriptional Profiling of Gluconobater oxydans NL71 Genes after Biooxidation of Xylose into Xylonate. Front Microbiol 2017; 8:716. [PMID: 28487685 PMCID: PMC5403930 DOI: 10.3389/fmicb.2017.00716] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 04/06/2017] [Indexed: 11/13/2022] Open
Abstract
D-Xylonic acid belongs to the top 30 biomass-based platform chemicals and represents a promising application of xylose. Until today, Gluconobacter oxydans NL71 is the most efficient microbe capable of fermenting xylose into xylonate. However, its growth is seriously inhibited when concentrated lignocellulosic hydrolysates are used as substrates due to the presence of various degraded compounds formed during biomass pretreatment. Three critical lignocellulosic inhibitors were thereby identified, i.e., formic acid, furfural, and 4-hydroxybenzaldehyde. As microbe fermentation is mostly regulated at the genome level, four groups of cell transcriptomes were obtained for a comparative investigation by RNA sequencing of a control sample with samples treated separately with the above-mentioned inhibitors. The digital gene expression profiles screened 572, 714 genes, and 408 DEGs was obtained by the comparisons among four transcriptomes. A number of genes related to the different functional groups showed characteristic expression patterns induced by three inhibitors, in which 19 genes were further tested and confirmed by qRT-PCR. We extrapolated many differentially expressed genes that could explain the cellular responses to the inhibitory effects. We provide results that enable the scientific community to better define the molecular processes involved in the microbes' responses to lignocellulosic inhibitors during the cellular biooxidation of xylose into xylonic acid.
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Affiliation(s)
- Yuanyuan Miao
- Department of Bioengineering, College of Chemical Engineering, Nanjing Forestry UniversityNanjing, China.,Jiangsu Province Key Laboratory of Green Biomass-based Fuels and Chemicals, Nanjing Forestry UniversityNanjing, China.,Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry UniversityNanjing, China
| | - Yi Shen
- Department of Bioengineering, College of Chemical Engineering, Nanjing Forestry UniversityNanjing, China.,Jiangsu Province Key Laboratory of Green Biomass-based Fuels and Chemicals, Nanjing Forestry UniversityNanjing, China.,Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry UniversityNanjing, China
| | - Yong Xu
- Department of Bioengineering, College of Chemical Engineering, Nanjing Forestry UniversityNanjing, China.,Jiangsu Province Key Laboratory of Green Biomass-based Fuels and Chemicals, Nanjing Forestry UniversityNanjing, China.,Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry UniversityNanjing, China
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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
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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
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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
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15
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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: 30] [Impact Index Per Article: 3.8] [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.
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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.
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