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  • 1
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    Online Resource
    The α- and β-Subunit Boundary at the Stem of the Mushroom-Like α 3 β 3 -Type Oxygenase Component of Rieske Non-Heme Iron Oxygenases Is the Rieske-Type Ferredoxin-Binding Site
    American Society for Microbiology ; 2022
    In:  Applied and Environmental Microbiology Vol. 88, No. 15 ( 2022-08-09)
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 88, No. 15 ( 2022-08-09)
    Abstract: Cumene dioxygenase (CumDO) is an initial enzyme in the cumene degradation pathway of Pseudomonas fluorescens IP01 and is a Rieske non-heme iron oxygenase (RO) that comprises two electron transfer components (reductase [CumDO-R] and Rieske-type ferredoxin [CumDO-F] ) and one catalytic component (α 3 β 3 -type oxygenase [CumDO-O]). Catalysis is triggered by electrons that are transferred from NAD(P)H to CumDO-O by CumDO-R and CumDO-F. To investigate the binding mode between CumDO-F and CumDO-O and to identify the key CumDO-O amino acid residues for binding, we simulated docking between the CumDO-O crystal structure and predicted model of CumDO-F and identified two potential binding sites: one is at the side-wise site and the other is at the top-wise site in mushroom-like CumDO-O. Then, we performed alanine mutagenesis of 16 surface amino acid residues at two potential binding sites. The results of reduction efficiency analyses using the purified components indicated that CumDO-F bound at the side-wise site of CumDO-O, and K117 of the α-subunit and R65 of the β-subunit were critical for the interaction. Moreover, these two positively charged residues are well conserved in α 3 β 3 -type oxygenase components of ROs whose electron donors are Rieske-type ferredoxins. Given that these residues were not conserved if the electron donors were different types of ferredoxins or reductases, the side-wise site of the mushroom-like structure is thought to be the common binding site between Rieske-type ferredoxin and α 3 β 3 -type oxygenase components in ROs. IMPORTANCE We clarified the critical amino acid residues of the oxygenase component (Oxy) of Rieske non-heme iron oxygenase (RO) for binding with Rieske-type ferredoxin (Fd). Our results showed that Rieske-type Fd-binding site is commonly located at the stem (side-wise site) of the mushroom-like α 3 β 3 quaternary structure in many ROs. The resultant binding site was totally different from those reported at the top-wise site of the doughnut-like α 3 -type Oxy, although α 3 -type Oxys correspond to the cap (α 3 subunit part) of the mushroom-like α 3 β 3 -type Oxys. Critical amino acid residues detected in this study were not conserved if the electron donors of Oxys were different types of Fds or reductases. Altogether, we can suggest that unique binding modes between Oxys and electron donors have evolved, depending on the nature of the electron donors, despite Oxy molecules having shared α 3 β 3 quaternary structures.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/aem.00835-22
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2022
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 2
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    Nucleoid-associated proteins encoded on plasmids: Occurrence and mode of function
    Elsevier BV ; 2015
    In:  Plasmid Vol. 80 ( 2015-07), p. 32-44
    Details
    In: Plasmid, Elsevier BV, Vol. 80 ( 2015-07), p. 32-44
    Type of Medium: Online Resource
    ISSN: 0147-619X
    URL: Article
    DOI: 10.1016/j.plasmid.2015.04.008
    RVK:
    WA 15000
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2015
    detail.hit.zdb_id: 1471554-5
    SSG: 12
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  • 3
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    A toxin–antitoxin system confers stability to the IncP-7 plasmid pCAR1
    Elsevier BV ; 2022
    In:  Gene Vol. 812 ( 2022-02), p. 146068-
    Details
    In: Gene, Elsevier BV, Vol. 812 ( 2022-02), p. 146068-
    Type of Medium: Online Resource
    ISSN: 0378-1119
    URL: Article
    DOI: 10.1016/j.gene.2021.146068
    RVK:
    WA 15000
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2022
    detail.hit.zdb_id: 1491012-3
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  • 4
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    Effects of Three Different Nucleoid-Associated Proteins Encoded on IncP-7 Plasmid pCAR1 on Host Pseudomonas putida KT2440
    American Society for Microbiology ; 2015
    In:  Applied and Environmental Microbiology Vol. 81, No. 8 ( 2015-04-15), p. 2869-2880
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 81, No. 8 ( 2015-04-15), p. 2869-2880
    Abstract: Nucleoid-associated proteins (NAPs), which fold bacterial DNA and influence gene transcription, are considered to be global transcriptional regulators of genes on both plasmids and the host chromosome. Incompatibility P-7 group plasmid pCAR1 carries genes encoding three NAPs: H-NS family protein Pmr, NdpA-like protein Pnd, and HU-like protein Phu. In this study, the effects of single or double disruption of pmr , pnd , and phu were assessed in host Pseudomonas putida KT2440. When pmr and pnd or pmr and phu were simultaneously disrupted, both the segregational stability and the structural stability of pCAR1 were markedly decreased, suggesting that Pmr, Pnd, and Phu act as plasmid-stabilizing factors in addition to their established roles in replication and partition systems. The transfer frequency of pCAR1 was significantly decreased in these double mutants. The segregational and structural instability of pCAR1 in the double mutants was recovered by complementation of pmr , whereas no recovery of transfer deficiency was observed. Comprehensive phenotype comparisons showed that the host metabolism of carbon compounds, which was reduced by pCAR1 carriage, was restored by disruption of the NAP gene(s). Transcriptome analyses of mutants indicated that transcription of genes for energy production, conversion, inorganic ion transport, and metabolism were commonly affected; however, how their products altered the phenotypes of mutants was not clear. The findings of this study indicated that Pmr, Pnd, and Phu act synergistically to affect pCAR1 replication, maintenance, and transfer, as well as to alter the host metabolic phenotype.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.00023-15
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2015
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 5
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    MvaT Family Proteins Encoded on IncP-7 Plasmid pCAR1 and the Host Chromosome Regulate the Host Transcriptome Cooperatively but Differently
    American Society for Microbiology ; 2016
    In:  Applied and Environmental Microbiology Vol. 82, No. 3 ( 2016-02), p. 832-842
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 82, No. 3 ( 2016-02), p. 832-842
    Abstract: MvaT proteins are members of the H-NS family of proteins in pseudomonads. The IncP-7 conjugative plasmid pCAR1 carries an mvaT -homologous gene, pmr . In Pseudomonas putida KT2440 bearing pCAR1, pmr and the chromosomally carried homologous genes, turA and turB , are transcribed at high levels, and Pmr interacts with TurA and TurB in vitro . In the present study, we clarified how the three MvaT proteins regulate the transcriptome of P. putida KT2440(pCAR1). Analyses performed by a modified chromatin immunoprecipitation assay with microarray technology (ChIP-chip) suggested that the binding regions of Pmr, TurA, and TurB in the P. putida KT2440(pCAR1) genome are almost identical; nevertheless, transcriptomic analyses using mutants with deletions of the genes encoding the MvaT proteins during the log and early stationary growth phases clearly suggested that their regulons were different. Indeed, significant regulon dissimilarity was found between Pmr and the other two proteins. Transcription of a larger number of genes was affected by Pmr deletion during early stationary phase than during log phase, suggesting that Pmr ameliorates the effects of pCAR1 on host fitness more effectively during the early stationary phase. Alternatively, the similarity of the TurA and TurB regulons implied that they might play complementary roles as global transcriptional regulators in response to plasmid carriage.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.03071-15
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2016
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
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  • 6
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    Structural similarities and differences in H‐ NS family proteins revealed by the N‐terminal structure of TurB in Pseudomonas putida KT 2440
    Wiley ; 2016
    In:  FEBS Letters Vol. 590, No. 20 ( 2016-10), p. 3583-3594
    Details
    In: FEBS Letters, Wiley, Vol. 590, No. 20 ( 2016-10), p. 3583-3594
    Abstract: H‐ NS family proteins play key roles in bacterial nucleoid compaction and global transcription. MvaT homologues in Pseudomonas have almost negligible amino acid sequence identity with H‐ NS , but can complement an hns ‐related phenotype of Escherichia coli . Here, we report the crystal structure of the N‐terminal dimerization/oligomerization domain of TurB, an MvaT homologue in Pseudomonas putida KT 2440. Our data identify two dimerization sites; the structure of the central dimerization site is almost the same as the corresponding region of H‐ NS , whereas the terminal dimerization sites are different. Our results reveal similarities and differences in dimerization and oligomerization mechanisms between H‐ NS and TurB.
    Type of Medium: Online Resource
    ISSN: 0014-5793 , 1873-3468
    URL: Issue
    URL: Article
    DOI: 10.1002/feb2.2016.590.issue-20
    DOI: 10.1002/1873-3468.12425
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2016
    detail.hit.zdb_id: 1460391-3
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  • 7
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    A Novel Gene Cluster Is Involved in the Degradation of Lignin-Derived Monoaromatics in Thermus oshimai JL-2
    American Society for Microbiology ; 2021
    In:  Applied and Environmental Microbiology Vol. 87, No. 11 ( 2021-05-11)
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 87, No. 11 ( 2021-05-11)
    Abstract: A novel gene cluster involved in the degradation of lignin-derived monoaromatics such as p -hydroxybenzoate, vanillate, and ferulate has been identified in the thermophilic nitrate reducer Thermus oshimai JL-2. Based on conserved domain analyses and metabolic pathway mapping, the cluster was classified into upper- and peripheral-pathway operons. The upper-pathway genes, responsible for the degradation of p -hydroxybenzoate and vanillate, are located on a 0.27-Mb plasmid, whereas the peripheral-pathway genes, responsible for the transformation of ferulate, are spread throughout the plasmid and the chromosome. In addition, a lower-pathway operon was also identified in the plasmid that corresponds to the meta- cleavage pathway of catechol. Spectrophotometric and gene induction data suggest that the upper and lower operons are induced by p -hydroxybenzoate, which the strain can degrade completely within 4 days of incubation, whereas the peripheral genes are expressed constitutively. The upper degradation pathway follows a less common route, proceeding via the decarboxylation of protocatechuate to form catechol, and involves a novel thermostable γ-carboxymuconolactone decarboxylase homolog, identified as protocatechuate decarboxylase based on gene deletion experiments. This gene cluster is conserved in only a few members of the Thermales and shows traces of vertical expansion of catabolic pathways in these organisms toward lignoaromatics. IMPORTANCE High-temperature steam treatment of lignocellulosic biomass during the extraction of cellulose and hemicellulose fractions leads to the release of a wide array of lignin-derived aromatics into the natural ecosystem, some of which can have detrimental effects on the environment. Not only will identifying organisms capable of using such aromatics aid in environmental cleanup, but thermostable enzymes, if characterized, can also be used for efficient lignin valorization. However, no thermophilic lignin degraders have been reported thus far. The present study reports T. oshimai JL-2 as a thermophilic bacterium with the potential to use lignin-derived aromatics. The identification of a novel thermostable protocatechuate decarboxylase gene in the strain further adds to its significance, as such an enzyme can be efficiently used in the biosynthesis of cis , cis -muconate, an important intermediate in the commercial production of plastics.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.01589-20
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2021
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 8
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    Online Resource
    Transcriptional heterogeneity of catabolic genes on the plasmid pCAR1 causes host-specific carbazole degradation
    American Society for Microbiology ; 2024
    In:  Applied and Environmental Microbiology Vol. 90, No. 2 ( 2024-02-21)
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 90, No. 2 ( 2024-02-21)
    Abstract: Horizontally acquired genes increase the competitiveness of host bacteria under selective conditions, although unregulated expression of foreign genes may impose fitness costs. The “appropriate” host for a plasmid is empirically known to maximize the expression of plasmid-borne traits. In the case of pCAR1-harboring Pseudomonas strains, P. resinovorans CA10 exhibits strong carbazole-degrading capacity, whereas P. putida KT2440 harboring pCAR1 exhibits low degradation capacity. Our results suggest that a chromosomally encoded transcription factor affects transcriptional and metabolic fluctuations in host cells, resulting in different carbazole-degrading capacities as a population. This study may provide a clue for determining appropriate hosts for a plasmid and for regulating the expression of plasmid-borne traits, such as the degradation of xenobiotics and antibiotic resistance.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/aem.01247-23
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2024
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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