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Author Donoso, R.; Leiva-Novoa, P.; Zuniga, A.; Timmermann, T.; Recabarren-Gajardo, G.; Gonzalez, B. pdf  doi
openurl 
  Title Biochemical and Genetic Bases of Indole-3-Acetic Acid (Auxin Phytohormone) Degradation by the Plant-Growth-Promoting Rhizobacterium Paraburkholderia phytofirmans PsJN Type
  Year 2017 Publication Applied And Environmental Microbiology Abbreviated Journal Appl. Environ. Microbiol.  
  Volume 83 Issue 1 Pages 20 pp  
  Keywords indole-3-acetic acid catabolism; iac genes; Paraburkholderia phytofirmans; plant-growth-promoting rhizobacteria  
  Abstract Several bacteria use the plant hormone indole-3-acetic acid (IAA) as a sole carbon and energy source. A cluster of genes (named iac) encoding IAA degradation has been reported in Pseudomonas putida 1290, but the functions of these genes are not completely understood. The plant-growth-promoting rhizobacterium Paraburkholderia phytofirmans PsJN harbors iac gene homologues in its genome, but with a different gene organization and context than those of P. putida 1290. The iac gene functions enable P. phytofirmans to use IAA as a sole carbon and energy source. Employing a heterologous expression system approach, P. phytofirmans iac genes with previously undescribed functions were associated with specific biochemical steps. In addition, two uncharacterized genes, previously unreported in P. putida and found to be related to major facilitator and tautomerase superfamilies, are involved in removal of an IAA metabolite called dioxindole-3-acetate. Similar to the case in strain 1290, IAA degradation proceeds through catechol as intermediate, which is subsequently degraded by ortho-ring cleavage. A putative two-component regulatory system and a LysR-type regulator, which apparently respond to IAA and dioxindole-3-acetate, respectively, are involved in iac gene regulation in P. phytofirmans. These results provide new insights about unknown gene functions and complex regulatory mechanisms in IAA bacterial catabolism. IMPORTANCE This study describes indole-3-acetic acid (auxin phytohormone) degradation in the well-known betaproteobacterium P. phytofirmans PsJN and comprises a complete description of genes, some of them with previously unreported functions, and the general basis of their gene regulation. This work contributes to the understanding of how beneficial bacteria interact with plants, helping them to grow and/or to resist environmental stresses, through a complex set of molecular signals, in this case through degradation of a highly relevant plant hormone.  
  Address [Donoso, Raul; Leiva-Novoa, Pablo; Zuniga, Ana; Timmermann, Tania; Gonzalez, Bernardo] Univ Adolfo Ibanez, Fac Ingn & Ciencias, Santiago, Chile, Email: bernardo.gonzalez@uai.cl  
  Corporate Author Thesis  
  Publisher Amer Soc Microbiology Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0099-2240 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000393205400001 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 699  
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Author Ledger, T.; Zuniga, A.; Kraiser, T.; Dasencich, P.; Donoso, R.; Perez-Pantoja, D.; Gonzalez, B. pdf  doi
openurl 
  Title Aromatic compounds degradation plays a role in colonization of Arabidopsis thaliana and Acacia caven by Cupriavidus pinatubonensis JMP134 Type
  Year 2012 Publication Antonie Van Leeuwenhoek International Journal Of General And Molecular Microbiology Abbreviated Journal Antonie Van Leeuwenhoek  
  Volume 101 Issue 4 Pages 713-723  
  Keywords Acacia caven; Arabidopsis thaliana; Aromatic compounds; Cupriavidus pinatubonensis JMP134; Plant growth; Rhizosphere  
  Abstract Plant rhizosphere and internal tissues may constitute a relevant habitat for soil bacteria displaying high catabolic versatility towards xenobiotic aromatic compounds. Root exudates contain various molecules that are structurally related to aromatic xenobiotics and have been shown to stimulate bacterial degradation of aromatic pollutants in the rhizosphere. The ability to degrade specific aromatic components of root exudates could thus provide versatile catabolic bacteria with an advantage for rhizosphere colonization and growth. In this work, Cupriavidus pinatubonensis JMP134, a well-known aromatic compound degrader (including the herbicide 2,4-dichlorophenoxyacetate, 2,4-D), was shown to stably colonize Arabidopsis thaliana and Acacia caven plants both at the rhizoplane and endorhizosphere levels and to use root exudates as a sole carbon and energy source. No deleterious effects were detected on these colonized plants. When a toxic concentration of 2,4-D was applied to colonized A. caven, a marked resistance was induced in the plant, showing that strain JMP134 was both metabolically active and potentially beneficial to its host. The role for the beta-ketoadipate aromatic degradation pathway during plant root colonization by C. pinatubonensis JMP134 was investigated by gene inactivation. A C. pinatubonensis mutant derivative strain displayed a reduced ability to catabolise root exudates isolated from either plant host. In this mutant strain, a lower competence in the rhizosphere of A. caven was also shown, both in gnotobiotic in vitro cultures and in plant/soil microcosms.  
  Address [Ledger, Thomas; Zuniga, Ana; Dasencich, Paola; Donoso, Raul; Gonzalez, Bernardo] Univ Adolfo Ibanez, Fac Ingn & Ciencias, Santiago 7941169, Chile, Email: bernardo.gonzalez@uai.cl  
  Corporate Author Thesis  
  Publisher Springer Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0003-6072 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000303402400003 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 214  
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Author Poupin, M.J.; Timmermann, T.; Vega, A.; Zuniga, A.; Gonzalez, B. pdf  doi
openurl 
  Title Effects of the Plant Growth-Promoting Bacterium Burkholderia phytofirmans PsJN throughout the Life Cycle of Arabidopsis thaliana Type
  Year 2013 Publication Plos One Abbreviated Journal PLoS One  
  Volume 8 Issue 7 Pages 15 pp  
  Keywords  
  Abstract Plant growth-promoting rhizobacteria (PGPR) induce positive effects in plants, such as increased growth or reduced stress susceptibility. The mechanisms behind PGPR/plant interaction are poorly understood, as most studies have described short-term responses on plants and only a few studies have analyzed plant molecular responses under PGPR colonization. Here, we studied the effects of the PGPR bacterial model Burkholderia phytofirmans PsJN on the whole life cycle of Arabidopsis thaliana plants. We reported that at different plant developmental points, strain PsJN can be found in the rhizosphere and also colonizing their internal tissues. In early ontogeny, strain PsJN increased several growth parameters and accelerated growth rate of the plants. Also, an Arabidopsis transcriptome analysis revealed that 408 genes showed differential expression in PsJN-inoculated plants; some of these genes are involved in stress response and hormone pathways. Specifically, genes implicated in auxin and gibberellin pathways were induced. Quantitative transcriptional analyses of selected genes in different developmental stages revealed that the beginning of these changes could be evidenced early in development, especially among the down-regulated genes. The inoculation with heat-killed bacteria provoked a more severe transcriptional response in plants, but was not able to induce plant growth-promotion. Later in ontogeny, the growth rates of inoculated plants decreased with respect to the non-inoculated group and, interestingly, the inoculation accelerated the flowering time and the appearance of senescence signs in plants; these modifications correlate with the early up-regulation of flowering control genes. Then, we show that a single inoculation with a PGPR could affect the whole life cycle of a plant, accelerating its growth rate and shortening its vegetative period, both effects relevant for most crops. Thus, these findings provide novel and interesting aspects of these relevant biological interactions.  
  Address [Josefina Poupin, Maria; Timmermann, Tania; Zuniga, Ana; Gonzalez, Bernardo] Univ Adolfo Ibanez, Fac Ingn & Ciencias, Lab Bioingn, Santiago, Chile, Email: mpoupin@uai.cl  
  Corporate Author Thesis  
  Publisher Public Library Science Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1932-6203 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000323110600043 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 306  
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Author Ruz, G.A.; Zuniga, A.; Goles, E. doi  openurl
  Title A Boolean network model of bacterial quorum-sensing systems Type
  Year 2018 Publication International Journal Of Data Mining And Bioinformatics Abbreviated Journal Int. J. Data Min. Bioinform.  
  Volume 21 Issue 2 Pages 123-144  
  Keywords gene regulatory networks; quorum-sensing systems; Boolean networks; neural networks; network inference  
  Abstract There are several mathematical models to represent gene regulatory networks, one of the simplest is the Boolean network paradigm. In this paper, we reconstruct a regulatory network of bacterial quorum-sensing systems, in particular, we consider Paraburkholderia phytofirmans PsJN which is a plant growth promoting bacteria that produces positive effects in horticultural crops like tomato, potato and grape. To learn the regulatory network from temporal expression pattern of quorum-sensing genes at root plants, we present a methodology that considers the training of perceptrons for each gene and then the integration into one Boolean regulatory network. Using the proposed approach, we were able to infer a regulatory network model whose topology and dynamic exhibited was helpful to gain insight on the quorum-sensing systems regulation mechanism. We compared our results with REVEAL and Best-Fit extension algorithm, showing that the proposed neural network approach obtained a more biologically meaningful network and dynamics, demonstrating the effectiveness of the proposed method.  
  Address [Ruz, Gonzalo A.; Zuniga, Ana; Goles, Eric] Univ Adolfo Ibanez, Fac Ingn & Ciencias, Av Diagonal Torres 2640, Santiago, Chile, Email: gonzalo.ruz@uai.cl;  
  Corporate Author Thesis  
  Publisher Inderscience Enterprises Ltd Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1748-5673 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000451832900003 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 933  
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Author Zuniga, A.; de la Fuente, F.; Federici, F.; Lionne, C.; Bonnet, J.; de Lorenzo, V.; Gonzalez, B. pdf  doi
openurl 
  Title An Engineered Device for Indoleacetic Acid Production under Quorum Sensing Signals Enables Cupriavidus pinatubonensis JMP134 To Stimulate Plant Growth Type
  Year 2018 Publication Acs Synthetic Biology Abbreviated Journal ACS Synth. Biol.  
  Volume 7 Issue 6 Pages 1519-1527  
  Keywords Arabidopsis thaliana; Cupriavidus pinatubonensis; quorum sensing; synthetic beneficial interaction  
  Abstract The environmental effects of chemical fertilizers and pesticides have encouraged the quest for new strategies to increase crop productivity with minimal impacts on the natural medium. Plant growth promoting rhizobacteria (PGPR) can contribute to this endeavor by improving fitness through better nutrition acquisition and stress tolerance. Using the neutral (non PGPR) rhizobacterium Cupriavidus pinatubonensis JMP134 as the host, we engineered a regulatory forward loop that triggered the synthesis of the phytohormone indole-3-acetic acid (IAA) in a manner dependent on quorum sensing (QS) signals. Implementation of the device in JMP134 yielded synthesis of IAA in an autoregulated manner, improving the growth of the roots of inoculated Arabidopsis thaliana. These results not only demonstrated the value of the designed genetic module, but also validated C. pinatubonensis JMP134 as a suitable vehicle for agricultural applications, as it is amenable to genetic manipulations.  
  Address [Zuniga, Ana; de la Fuente, Francisco; Gonzalez, Bernardo] Univ Adolfo Ibanez, Fac Ingn & Ciencias, Ctr Appl Ecol & Sustainabil, Santiago 2640, Chile, Email: ana.zuniga@cbs.cnrs.fr  
  Corporate Author Thesis  
  Publisher Amer Chemical Soc Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 2161-5063 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000435746400005 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 877  
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Author Zuniga, A.; Donoso, R.A.; Ruiz, D.; Ruz, G.A.; Gonzalez, B. pdf  doi
openurl 
  Title Quorum-Sensing Systems in the Plant Growth-Promoting Bacterium Paraburkholderia phytofirmans PsJN Exhibit Cross-Regulation and Are Involved in Biofilm Formation Type
  Year 2017 Publication Molecular Plant-Microbe Interactions Abbreviated Journal Mol. Plant-Microbe Interact.  
  Volume 30 Issue 7 Pages 557-565  
  Keywords  
  Abstract Quorum-sensing systems play important roles in host colonization and host establishment of Burkholderiales species. Beneficial Paraburkholderia species share a conserved quorum-sensing (QS) system, designated BraI/R, that controls different phenotypes. In this context, the plant growth-promoting bacterium Paraburkholderia phytofirmans PsJN possesses two different homoserine lactone QS systems BpI. 1/R.1 and BpI. 2/R.2 (BraI/R-like QS system). The BpI. 1/R.1 QS system was previously reported to be important to colonize and produce beneficial effects in Arabidopsis thaliana plants. Here, we analyzed the temporal variations of the QS gene transcript levels in the wild-type strain colonizing plant roots. The gene expression patterns showed relevant differences in both QS systems compared with the wild-type strain in the unplanted control treatment. The gene expression data were used to reconstruct a regulatory network model of QS systems in P.phytofirmans PsJN, using a Boolean network model. Also, we examined the phenotypic traits and transcript levels of genes involved in QS systems, using P. phytofirmans mutants in homoserine lactone synthases genes. We observed that the BpI. 1/R.1 QS system regulates biofilm formation production in strain PsJN and this phenotype was associated with the lower expression of a specific extracytoplasmic function sigma factor ecf26.1 gene (implicated in biofilm formation) in the bpI.1 mutant strain.  
  Address [Gonzalez, Bernardo] Univ Adolfo Ibanez, Fac Ingn & Ciencias, Millennium Nucleus Ctr Plant Syst & Synthet Biol, Santiago, Chile, Email: bernardo.gonzalez@uai.cl  
  Corporate Author Thesis  
  Publisher Amer Phytopathological Soc Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0894-0282 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000404048400004 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 739  
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Author Zuniga, A.; Poupin, M.J.; Donoso, R.; Ledger, T.; Guiliani, N.; Gutierrez, R.A.; Gonzalez, B. pdf  doi
openurl 
  Title Quorum Sensing and Indole-3-Acetic Acid Degradation Play a Role in Colonization and Plant Growth Promotion of Arabidopsis thaliana by Burkholderia phytofirmans PsJN Type
  Year 2013 Publication Molecular Plant-Microbe Interactions Abbreviated Journal Mol. Plant-Microbe Interact.  
  Volume 26 Issue 5 Pages 546-553  
  Keywords  
  Abstract Although not fully understood, molecular communication in the rhizosphere plays an important role regulating traits involved in plant-bacteria association. Burkholderia phytofirmans PsJN is a well-known plant-growth-promoting bacterium, which establishes rhizospheric and endophytic colonization in different plants. A competent colonization is essential for plant-growth-promoting effects produced by bacteria. Using appropriate mutant strains of B. phytofirmans, we obtained evidence for the importance of N-acyl homoserine lactone-mediated (quorum sensing) cell-to-cell communication in efficient colonization of Arabidopsis thaliana plants and the establishment of a beneficial interaction. We also observed that bacterial degradation of the auxin indole-3-acetic acid (IAA) plays a key role in plant-growth-promoting traits and is necessary for efficient rhizosphere colonization. Wildtype B. phytofirmans but not the iacC mutant in IAA mineralization is able to restore promotion effects in roots of A. thaliana in the presence of exogenously added IAA, indicating the importance of this trait for promoting primary root length. Using a transgenic A. thaliana line with suppressed auxin signaling (miR393) and analyzing the expression of auxin receptors in wild-type inoculated plants, we provide evidence that auxin signaling in plants is necessary for the growth promotion effects produced by B. phytofirmans. The interplay between ethylene and auxin signaling was also confirmed by the response of the plant to a 1-aminocyclopropane-1-carboxylate deaminase bacterial mutant strain.  
  Address Univ Adolfo Ibanez, Fac Ingn & Ciencias, Santiago, Chile, Email: bernardo.gonzalez@uai.cl  
  Corporate Author Thesis  
  Publisher Amer Phytopathological Soc Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0894-0282 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000317875400008 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 277  
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