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  1. Article: Widespread distribution of

    Donoso, Raúl A / González-Toro, Fabián / Pérez-Pantoja, Danilo

    Computational and structural biotechnology journal

    2021  Volume 19, Page(s) 2160–2169

    Abstract: Furans represent a class of promising chemicals, since they constitute valuable intermediates in conversion of biomass into sustainable products intended to replace petroleum-derivatives. Conversely, generation of furfural and 5-hydroxymethylfurfural ( ... ...

    Abstract Furans represent a class of promising chemicals, since they constitute valuable intermediates in conversion of biomass into sustainable products intended to replace petroleum-derivatives. Conversely, generation of furfural and 5-hydroxymethylfurfural (HMF) as by-products in lignocellulosic hydrolysates is undesirable due its inhibitory effect over fermentative microorganisms. Therefore, the search for furans-metabolizing bacteria has gained increasing attention since they are valuable tools to solve these challenging issues. A few bacterial species have been described at genetic level, leading to a proposed HMF pathway encoded by a set of genes termed
    Language English
    Publishing date 2021-04-16
    Publishing country Netherlands
    Document type Journal Article
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2021.04.017
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Identification of a Phylogenetically Divergent Vanillate O-Demethylase from

    Donoso, Raúl A / Corbinaud, Ricardo / Gárate-Castro, Carla / Galaz, Sandra / Pérez-Pantoja, Danilo

    Microorganisms

    2022  Volume 11, Issue 1

    Abstract: Rieske-type two-component vanillate O-demethylases (VanODs) catalyze conversion of the lignin-derived monomer vanillate into protocatechuate in several bacterial species. Currently, VanODs have received attention because of the demand of effective lignin ...

    Abstract Rieske-type two-component vanillate O-demethylases (VanODs) catalyze conversion of the lignin-derived monomer vanillate into protocatechuate in several bacterial species. Currently, VanODs have received attention because of the demand of effective lignin valorization technologies, since these enzymes own the potential to catalyze methoxy group demethylation of distinct lignin monomers. In this work, we identified a phylogenetically divergent VanOD from
    Language English
    Publishing date 2022-12-27
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms11010078
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Comparative genomics of

    Salvà-Serra, Francisco / Pérez-Pantoja, Danilo / Donoso, Raúl A / Jaén-Luchoro, Daniel / Fernández-Juárez, Víctor / Engström-Jakobsson, Hedvig / Moore, Edward R B / Lalucat, Jorge / Bennasar-Figueras, Antoni

    Frontiers in microbiology

    2023  Volume 14, Page(s) 1159176

    Abstract: Stutzerimonas ... ...

    Abstract Stutzerimonas balearica
    Language English
    Publishing date 2023-05-15
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2023.1159176
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Complete Genome Sequence of Rhodococcus ruber R1, a Novel Strain Showing a Broad Catabolic Potential toward Lignin-Derived Aromatics.

    Farkas, Carlos / Donoso, Raúl A / Melis-Arcos, Felipe / Gárate-Castro, Carla / Pérez-Pantoja, Danilo

    Microbiology resource announcements

    2020  Volume 9, Issue 2

    Abstract: Rhodococcus ... ...

    Abstract Rhodococcus ruber
    Language English
    Publishing date 2020-01-09
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.00905-19
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Draft Genome Sequences of Two

    Farkas, Carlos / Donoso, Raúl A / Gárate-Castro, Carla / Villegas, Pamela / Durán, Roberto E / Seeger, Michael / Pérez-Pantoja, Danilo

    Microbiology resource announcements

    2020  Volume 9, Issue 2

    Abstract: ... ...

    Abstract Pseudomonas
    Language English
    Publishing date 2020-01-09
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.01131-19
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Identification of a self-sufficient cytochrome P450 monooxygenase from Cupriavidus pinatubonensis JMP134 involved in 2-hydroxyphenylacetic acid catabolism, via homogentisate pathway.

    Donoso, Raúl A / Ruiz, Daniela / Gárate-Castro, Carla / Villegas, Pamela / González-Pastor, José Eduardo / de Lorenzo, Víctor / González, Bernardo / Pérez-Pantoja, Danilo

    Microbial biotechnology

    2021  Volume 14, Issue 5, Page(s) 1944–1960

    Abstract: The self-sufficient cytochrome P450 RhF and its homologues belonging to the CYP116B subfamily have attracted considerable attention due to the potential for biotechnological applications based in their ability to catalyse an array of challenging ... ...

    Abstract The self-sufficient cytochrome P450 RhF and its homologues belonging to the CYP116B subfamily have attracted considerable attention due to the potential for biotechnological applications based in their ability to catalyse an array of challenging oxidative reactions without requiring additional protein partners. In this work, we showed for the first time that a CYP116B self-sufficient cytochrome P450 encoded by the ohpA gene harboured by Cupriavidus pinatubonensis JMP134, a β-proteobacterium model for biodegradative pathways, catalyses the conversion of 2-hydroxyphenylacetic acid (2-HPA) into homogentisate. Mutational analysis and HPLC metabolite detection in strain JMP134 showed that 2-HPA is degraded through the well-known homogentisate pathway requiring a 2-HPA 5-hydroxylase activity provided by OhpA, which was additionally supported by heterologous expression and enzyme assays. The ohpA gene belongs to an operon including also ohpT, coding for a substrate-binding subunit of a putative transporter, whose expression is driven by an inducible promoter responsive to 2-HPA in presence of a predicted OhpR transcriptional regulator. OhpA homologues can be found in several genera belonging to Actinobacteria and α-, β- and γ-proteobacteria lineages indicating a widespread distribution of 2-HPA catabolism via homogentisate route. These results provide first time evidence for the natural function of members of the CYP116B self-sufficient oxygenases and represent a significant input to support novel kinetic and structural studies to develop cytochrome P450-based biocatalytic processes.
    MeSH term(s) Cupriavidus/genetics ; Cytochrome P-450 Enzyme System/genetics ; Phenylacetates
    Chemical Substances Phenylacetates ; Cytochrome P-450 Enzyme System (9035-51-2) ; 2-hydroxyphenylacetic acid (UK3R9Q59AV)
    Language English
    Publishing date 2021-06-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2406063-X
    ISSN 1751-7915 ; 1751-7907
    ISSN (online) 1751-7915
    ISSN 1751-7907
    DOI 10.1111/1751-7915.13865
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Complete Multipartite Genome Sequence of the Cupriavidus basilensis Type Strain, a 2,6-Dichlorophenol-Degrading Bacterium.

    Salvà-Serra, Francisco / Donoso, Raúl A / Cho, Kyoung Hee / Yoo, Ji A / Lee, Kihyun / Yoon, Seok-Hwan / Piñeiro-Iglesias, Beatriz / Moore, Edward R B / Pérez-Pantoja, Danilo

    Microbiology resource announcements

    2021  Volume 10, Issue 19

    Abstract: We report the complete 8.94-Mb genome sequence of the type strain ... ...

    Abstract We report the complete 8.94-Mb genome sequence of the type strain of
    Language English
    Publishing date 2021-05-13
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.00134-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Quorum-Sensing Systems in the Plant Growth-Promoting Bacterium Paraburkholderia phytofirmans PsJN Exhibit Cross-Regulation and Are Involved in Biofilm Formation.

    Zúñiga, Ana / Donoso, Raúl A / Ruiz, Daniela / Ruz, Gonzalo A / González, Bernardo

    Molecular plant-microbe interactions : MPMI

    2017  Volume 30, Issue 7, Page(s) 557–565

    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. ... ...

    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.
    Language English
    Publishing date 2017-07
    Publishing country United States
    Document type Journal Article
    ZDB-ID 743331-1
    ISSN 1943-7706 ; 0894-0282
    ISSN (online) 1943-7706
    ISSN 0894-0282
    DOI 10.1094/MPMI-01-17-0008-R
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Strict and direct transcriptional repression of the pobA gene by benzoate avoids 4-hydroxybenzoate degradation in the pollutant degrader bacterium Cupriavidus necator JMP134.

    Donoso, Raúl A / Pérez-Pantoja, Danilo / González, Bernardo

    Environmental microbiology

    2011  Volume 13, Issue 6, Page(s) 1590–1600

    Abstract: As other environmental bacteria, Cupriavidus necator JMP134 uses benzoate as preferred substrate in mixtures with 4-hydroxybenzoate, strongly inhibiting its degradation. The mechanism underlying this hierarchical use was studied. A C. necator benA mutant, ...

    Abstract As other environmental bacteria, Cupriavidus necator JMP134 uses benzoate as preferred substrate in mixtures with 4-hydroxybenzoate, strongly inhibiting its degradation. The mechanism underlying this hierarchical use was studied. A C. necator benA mutant, defective in the first step of benzoate degradation, is unable to metabolize 4-hydroxybenzoate when benzoate is also included in the medium, indicating that this substrate and not one of its catabolic intermediates is directly triggering repression. Reverse transcription polymerase chain reaction analysis revealed that 4-hydroxybenzoate 3-hydroxylase-encoding pobA transcripts are nearly absent in presence of benzoate and a fusion of pobA promoter to lacZ reporter confirmed that benzoate drastically decreases the transcription of this gene. Expression of pobA driven by a heterologous promoter in C. necator benA mutant, allows growth on 4-hydroxybenzoate in presence of benzoate, overcoming its repressive effect. In contrast with other bacteria, regulators of benzoate catabolism do not participate in repression of 4-hydroxybenzoate degradation. Moreover, the effect of benzoate on pobA promoter can be observed in heterologous strains with the sole presence of PobR, the transcriptional activator of pobA gene, indicating that PobR is enough to fully reproduce the phenomenon. This novel mechanism for benzoate repression is probably mediated by direct action of benzoate over PobR.
    MeSH term(s) Anti-Infective Agents/metabolism ; Anti-Infective Agents/toxicity ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Base Sequence ; Benzoates/metabolism ; Benzoates/toxicity ; Cupriavidus necator/genetics ; Cupriavidus necator/metabolism ; Environmental Pollutants/metabolism ; Environmental Pollutants/toxicity ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Molecular Sequence Data ; Parabens/metabolism ; Transcription, Genetic
    Chemical Substances Anti-Infective Agents ; Bacterial Proteins ; Benzoates ; Environmental Pollutants ; Parabens ; 4-hydroxybenzoic acid (JG8Z55Y12H)
    Language English
    Publishing date 2011-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2020213-1
    ISSN 1462-2920 ; 1462-2912
    ISSN (online) 1462-2920
    ISSN 1462-2912
    DOI 10.1111/j.1462-2920.2011.02470.x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Strict and direct transcriptional repression of the pobA gene by benzoate avoids 4-hydroxybenzoate degradation in the pollutant degrader bacterium Cupriavidus necator JMP134

    Donoso, Raúl A / Pérez-Pantoja, Danilo / González, Bernardo

    Environmental microbiology. 2011 June, v. 13, no. 6

    2011  

    Abstract: As other environmental bacteria, Cupriavidus necator JMP134 uses benzoate as preferred substrate in mixtures with 4-hydroxybenzoate, strongly inhibiting its degradation. The mechanism underlying this hierarchical use was studied. A C. necator benA mutant, ...

    Abstract As other environmental bacteria, Cupriavidus necator JMP134 uses benzoate as preferred substrate in mixtures with 4-hydroxybenzoate, strongly inhibiting its degradation. The mechanism underlying this hierarchical use was studied. A C. necator benA mutant, defective in the first step of benzoate degradation, is unable to metabolize 4-hydroxybenzoate when benzoate is also included in the medium, indicating that this substrate and not one of its catabolic intermediates is directly triggering repression. Reverse transcription polymerase chain reaction analysis revealed that 4-hydroxybenzoate 3-hydroxylase-encoding pobA transcripts are nearly absent in presence of benzoate and a fusion of pobA promoter to lacZ reporter confirmed that benzoate drastically decreases the transcription of this gene. Expression of pobA driven by a heterologous promoter in C. necator benA mutant, allows growth on 4-hydroxybenzoate in presence of benzoate, overcoming its repressive effect. In contrast with other bacteria, regulators of benzoate catabolism do not participate in repression of 4-hydroxybenzoate degradation. Moreover, the effect of benzoate on pobA promoter can be observed in heterologous strains with the sole presence of PobR, the transcriptional activator of pobA gene, indicating that PobR is enough to fully reproduce the phenomenon. This novel mechanism for benzoate repression is probably mediated by direct action of benzoate over PobR.
    Keywords Cupriavidus necator ; bacteria ; benzoates ; genes ; metabolism ; mutants ; pollutants ; reverse transcriptase polymerase chain reaction
    Language English
    Dates of publication 2011-06
    Size p. 1590-1600.
    Publishing place Blackwell Publishing Ltd
    Document type Article
    ZDB-ID 2020213-1
    ISSN 1462-2920 ; 1462-2912
    ISSN (online) 1462-2920
    ISSN 1462-2912
    DOI 10.1111/j.1462-2920.2011.02470.x
    Database NAL-Catalogue (AGRICOLA)

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