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Author (up) Donoso, R.A.; Perez-Pantoja, D.; Gonzalez, B.
Title Strict and direct transcriptional repression of the pobA gene by benzoate avoids 4-hydroxybenzoate degradation in the pollutant degrader bacterium Cupriavidus necator JMP134 Type
Year 2011 Publication Environmental Microbiology Abbreviated Journal Environ. Microbiol.
Volume 13 Issue 6 Pages 1590-1600
Keywords
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.
Address [Donoso, Raul A.; Gonzalez, Bernardo] Univ Adolfo Ibanez, Fac Ingn & Ciencias, Santiago, Chile, Email: bernardo.gonzalez@uai.cl
Corporate Author Thesis
Publisher Wiley-Blackwell Place of Publication Editor
Language English Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1462-2912 ISBN Medium
Area Expedition Conference
Notes WOS:000291268900018 Approved
Call Number UAI @ eduardo.moreno @ Serial 147
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Author (up) Donoso, R.A.; Ruiz, D.; Garate-Castro, C.; Villegas, P.; Gonzalez-Pastor, J.E.; de Lorenzo, V.; Gonzalez, B.; Perez-Pantoja, D.
Title Identification of a self-sufficient cytochrome P450 monooxygenase from Cupriavidus pinatubonensis JMP134 involved in 2-hydroxyphenylacetic acid catabolism, via homogentisate pathway Type
Year 2021 Publication Microbial Biotechnology Abbreviated Journal Microb. Biotechnol.
Volume 14 Issue 5 Pages 1944-1960
Keywords COMPLETE GENOME SEQUENCE; ELECTRON-TRANSFER; GENE; DEGRADATION; SYSTEM; STRAIN; P450BM3; GROWTH; DOMAIN; HYDROXYLATION
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 beta-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 alpha-, beta- and gamma-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.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1751-7915 ISBN Medium
Area Expedition Conference
Notes WOS:000664134700001 Approved
Call Number UAI @ alexi.delcanto @ Serial 1426
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Author (up) Ledger, T.; Zuniga, A.; Kraiser, T.; Dasencich, P.; Donoso, R.; Perez-Pantoja, D.; Gonzalez, B.
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 (up) Lykidis, A.; Perez-Pantoja, D.; Ledger, T.; Mavromatis, K.; Anderson, I.J.; Ivanova, N.N.; Hooper, S.D.; Lapidus, A.; Lucas, S.; Gonzalez, B.; Kyrpides, N.C.
Title The Complete Multipartite Genome Sequence of Cupriavidus necator JMP134, a Versatile Pollutant Degrader Type
Year 2010 Publication Plos One Abbreviated Journal PLoS One
Volume 5 Issue 3 Pages 13 pp
Keywords
Abstract Background: Cupriavidus necator JMP134 is a Gram-negative beta-proteobacterium able to grow on a variety of aromatic and chloroaromatic compounds as its sole carbon and energy source. Methodology/ Principal Findings: Its genome consists of four replicons (two chromosomes and two plasmids) containing a total of 6631 protein coding genes. Comparative analysis identified 1910 core genes common to the four genomes compared (C. necator JMP134, C. necator H16, C. metallidurans CH34, R. solanacearum GMI1000). Although secondary chromosomes found in the Cupriavidus, Ralstonia, and Burkholderia lineages are all derived from plasmids, analyses of the plasmid partition proteins located on those chromosomes indicate that different plasmids gave rise to the secondary chromosomes in each lineage. The C. necator JMP134 genome contains 300 genes putatively involved in the catabolism of aromatic compounds and encodes most of the central ring-cleavage pathways. This strain also shows additional metabolic capabilities towards alicyclic compounds and the potential for catabolism of almost all proteinogenic amino acids. This remarkable catabolic potential seems to be sustained by a high degree of genetic redundancy, most probably enabling this catabolically versatile bacterium with different levels of metabolic responses and alternative regulation necessary to cope with a challenging environment. From the comparison of Cupriavidus genomes, it is possible to state that a broad metabolic capability is a general trait for Cupriavidus genus, however certain specialization towards a nutritional niche (xenobiotics degradation, chemolithoautotrophy or symbiotic nitrogen fixation) seems to be shaped mostly by the acquisition of “specialized” plasmids. Conclusions/Significance: The availability of the complete genome sequence for C. necator JMP134 provides the groundwork for further elucidation of the mechanisms and regulation of chloroaromatic compound biodegradation.
Address [Lykidis, Athanasios; Mavromatis, Kostantinos; Anderson, Iain J.; Ivanova, Natalia N.; Hooper, Sean D.; Lapidus, Alla; Lucas, Susan; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA, Email: alykidis@lbl.gov
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:000275894300005 Approved
Call Number UAI @ eduardo.moreno @ Serial 86
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Author (up) Marin, M.; Perez-Pantoja, D.; Donoso, R.; Wray, V.; Gonzalez, B.; Pieper, D.H.
Title Modified 3-Oxoadipate Pathway for the Biodegradation of Methylaromatics in Pseudomonas reinekei MT1 Type
Year 2010 Publication Journal Of Bacteriology Abbreviated Journal J. Bacteriol.
Volume 192 Issue 6 Pages 1543-1552
Keywords
Abstract Catechols are central intermediates in the metabolism of aromatic compounds. Degradation of 4-methyl-catechol via intradiol cleavage usually leads to the formation of 4-methylmuconolactone (4-ML) as a dead-end metabolite. Only a few microorganisms are known to mineralize 4-ML. The mml gene cluster of Pseudomonas reinekei MT1, which encodes enzymes involved in the metabolism of 4-ML, is shown here to encode 10 genes found in a 9.4-kb chromosomal region. Reverse transcription assays revealed that these genes form a single operon, where their expression is controlled by two promoters. Promoter fusion assays identified 4-methyl-3-oxoadipate as an inducer. Mineralization of 4-ML is initiated by the 4-methylmuconolactone methylisomerase encoded by mmlI. This reaction produces 3-ML and is followed by a rearrangement of the double bond catalyzed by the methylmuconolactone isomerase encoded by mmlJ. Deletion of mmlL, encoding a protein of the metallo-beta-lactamase superfamily, resulted in a loss of the capability of the strain MT1 to open the lactone ring, suggesting its function as a 4-methyl-3-oxoadipate enol-lactone hydrolase. Further metabolism can be assumed to occur by analogy with reactions known from the 3-oxoadipate pathway. mmlF and mmlG probably encode a 4-methyl-3-oxoadipyl-coenzyme A (CoA) transferase, and the mmlC gene product functions as a thiolase, transforming 4-methyl-3-oxoadipyl-CoA into methylsuccinyl-CoA and acetyl-CoA, as indicated by the accumulation of 4-methyl-3-oxoadipate in the respective deletion mutant. Accumulation of methylsuccinate by an mmlK deletion mutant indicates that the encoded acetyl-CoA hydrolase/transferase is crucial for channeling methylsuccinate into the central metabolism.
Address [Marin, Macarena; Pieper, Dietmar H.] Helmholtz Zentrum Infekt Forsch, Dept Microbial Pathogenesis, D-38124 Braunschweig, Germany, Email: dpi@helmholtz-hzi.de
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 0021-9193 ISBN Medium
Area Expedition Conference
Notes WOS:000274891300009 Approved
Call Number UAI @ eduardo.moreno @ Serial 84
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Author (up) Perez-Pantoja, D.; Donoso, R.; Agullo, L.; Cordova, M.; Seeger, M.; Pieper, D.H.; Gonzalez, B.
Title Genomic analysis of the potential for aromatic compounds biodegradation in Burkholderiales Type
Year 2012 Publication Environmental Microbiology Abbreviated Journal Environ. Microbiol.
Volume 14 Issue 5 Pages 1091-1117
Keywords
Abstract The relevance of the beta-proteobacterial Burkholderiales order in the degradation of a vast array of aromatic compounds, including several priority pollutants, has been largely assumed. In this review, the presence and organization of genes encoding oxygenases involved in aromatics biodegradation in 80 Burkholderiales genomes is analysed. This genomic analysis underscores the impressive catabolic potential of this bacterial lineage, comprising nearly all of the central ring-cleavage pathways reported so far in bacteria and most of the peripheral pathways involved in channelling of a broad diversity of aromatic compounds. The more widespread pathways in Burkholderiales include protocatechuate ortho ring-cleavage, catechol ortho ring-cleavage, homogentisate ring-cleavage and phenylacetyl-CoA ring-cleavage pathways found in at least 60% of genomes analysed. In general, a genus-specific pattern of positional ordering of biodegradative genes is observed in the catabolic clusters of these pathways indicating recent events in its evolutionary history. In addition, a significant bias towards secondary chromosomes, now termed chromids, is observed in the distribution of catabolic genes across multipartite genomes, which is consistent with a genus-specific character. Strains isolated from environmental sources such as soil, rhizosphere, sediment or sludge show a higher content of catabolic genes in their genomes compared with strains isolated from human, animal or plant hosts, but no significant difference is found among Alcaligenaceae, Burkholderiaceae and Comamonadaceae families, indicating that habitat is more of a determinant than phylogenetic origin in shaping aromatic catabolic versatility.
Address [Perez-Pantoja, Danilo; Donoso, Raul; Gonzalez, Bernardo] Pontificia Univ Catolica Chile, Ctr Adv Studies Ecol & Biodivers, Millennium Nucleus Plant Funct Genom, Fac Ciencias Biol, Santiago, Chile, Email: bernardo.gonzalez@uai.cl
Corporate Author Thesis
Publisher Wiley-Blackwell Place of Publication Editor
Language English Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1462-2912 ISBN Medium
Area Expedition Conference
Notes WOS:000302934000001 Approved
Call Number UAI @ eduardo.moreno @ Serial 211
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Author (up) Perez-Pantoja, D.; Donoso, R.A.; Sanchez, M.A.; Gonzalez, B.
Title Genuine genetic redundancy in maleylacetate-reductase-encoding genes involved in degradation of haloaromatic compounds by Cupriavidus necator JMP134 Type
Year 2009 Publication Microbiology-Sgm Abbreviated Journal Microbiology-(UK)
Volume 155 Issue Pages 3641-3651
Keywords
Abstract Maleylacetate reductases; (MAR) are required for biodegradation of several substituted aromatic compounds. To date, the functionality of two MAR-encoding genes (tfdF(I) and tfdF(II)) has been reported in Cupriavidus necator JMP134(pJP4), a known degrader of aromatic compounds. These two genes are located in tfd gene clusters involved in the turnover of 2,4-dichlorophenoxyacetate (2,4-D) and 3-chlorobenzoate (3-CB). The C. necator JMP134 genome comprises at least three other genes that putatively encode MAR (tcpD, hqoD and hxqD), but confirmation of their functionality and their role in the catabolism of haloaromatic compounds has not been assessed. RT-PCR expression analyses of C. necator JMP134 cells exposed to 2,4-D, 3-CB, 2,4,6-trichlorophenol (2,4,6-TCP) or 4-fluorobenzoate (4-FB) showed that tfdF(I) and tfdF(II) are induced by haloaromatics channelled to halocatechols as intermediates. In contrast, 2,4,6-TCP only induces tcpD, and any haloaromatic compounds tested did not induce hxqD and hqoD. However, the tcpD, hxqD and hqoD gene products showed MAR activity in cell extracts and provided the MAR function for 2,4-D catabolism when heterologously expressed in MAR-lacking strains. Growth tests for mutants of the five MAR-encoding genes in strain JMP134 showed that none of these genes is essential for degradation of the tested compounds. However, the role of tfdF(I)/tfdF(II) and tcpD genes in the expression of MAR activity during catabolism of 2,4-D and 2,4,6-TCP, respectively, was confirmed by enzyme activity tests in mutants. These results reveal a striking example of genetic redundancy in the degradation of aromatic compounds.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1350-0872 ISBN Medium
Area Expedition Conference
Notes WOS:000272121300019 Approved
Call Number UAI @ eduardo.moreno @ Serial 77
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Author (up) Perez-Pantoja, D.; Leiva-Novoa, P.; Donoso, R.A.; Little, C.; Godoy, M.; Pieper, D.H.; Gonzalez, B.
Title Hierarchy of Carbon Source Utilization in Soil Bacteria: Hegemonic Preference for Benzoate in Complex Aromatic Compound Mixtures Degraded by Cupriavidus pinatubonensis Strain JMP134 Type
Year 2015 Publication Applied And Environmental Microbiology Abbreviated Journal Appl. Environ. Microbiol.
Volume 81 Issue 12 Pages 3914-3924
Keywords
Abstract Cupriavidus pinatubonensis JMP134, like many other environmental bacteria, uses a range of aromatic compounds as carbon sources. Previous reports have shown a preference for benzoate when this bacterium grows on binary mixtures composed of this aromatic compound and 4-hydroxybenzoate or phenol. However, this observation has not been extended to other aromatic mixtures resembling a more archetypal context. We carried out a systematic study on the substrate preference of C. pinatubonensis JMP134 growing on representative aromatic compounds channeled through different catabolic pathways described in aerobic bacteria. Growth tests of nearly the entire set of binary combinations and in mixtures composed of 5 or 6 aromatic components showed that benzoate and phenol were always the preferred and deferred growth substrates, respectively. This pattern was supported by kinetic analyses that showed shorter times to initiate consumption of benzoate in aromatic compound mixtures. Gene expression analysis by real-time reverse transcription-PCR (RT-PCR) showed that, in all mixtures, the repression by benzoate over other catabolic pathways was exerted mainly at the transcriptional level. Additionally, inhibition of benzoate catabolism suggests that its multiple repressive actions are not mediated by a sole mechanism, as suggested by dissimilar requirements of benzoate degradation for effective repression in different aromatic compound mixtures. The hegemonic preference for benzoate over multiple aromatic carbon sources is not explained on the basis of growth rate and/or biomass yield on each single substrate or by obvious chemical or metabolic properties of these aromatic compounds.
Address [Leiva-Novoa, Pablo; Donoso, Raul A.; Little, Cedric; Gonzalez, Bernardo] Univ Adolfo Ibanez, Ctr Appl Ecol & Sustainabil, 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:000354864000002 Approved
Call Number UAI @ eduardo.moreno @ Serial 491
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