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Journal articles on the topic 'Paracoccus pantotrophus'

Author: Grafiati

Published: 4 June 2021

Last updated: 18 February 2022

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1

Bartosik, Dariusz, Marta Sochacka, and Jadwiga Baj. "Identification and Characterization of Transposable Elements of Paracoccus pantotrophus." Journal of Bacteriology 185, no. 13 (July 1, 2003): 3753–63. http://dx.doi.org/10.1128/jb.185.13.3753-3763.2003.

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ABSTRACT We studied diversity and distribution of transposable elements residing in different strains (DSM 11072, DSM 11073, DSM 65, and LMD 82.5) of a soil bacterium Paracoccus pantotrophus (α-Proteobacteria). With application of a shuttle entrapment vector pMEC1, several novel insertion sequences (ISs) and transposons (Tns) have been identified. They were sequenced and subjected to detailed comparative analysis, which allowed their characterization (i.e., identification of transposase genes, terminal inverted repeats, as well as target sequences) and classification into the appropriate IS or Tn families. The frequency of transposition of these elements varied and ranged from 10−6 to 10−3 depending on the strain. The copy number, localization (plasmid or chromosome), and distribution of these elements in the Paracoccus species P. pantotrophus, P. denitrificans, P. methylutens, P. solventivorans, and P. versutus were analyzed. This allowed us to distinguish elements that are common in paracocci (ISPpa2, ISPpa3—both of the IS5 family—and ISPpa5 of IS66 family) as well as strain-specific ones (ISPpa1 of the IS256 family, ISPpa4 of the IS5 family, and Tn3434 and Tn5393 of the Tn3 family), acquired by lateral transfer events. These elements will be of a great value in the design of new genetic tools for paracocci, since only one element (IS1248 of P. denitrificans) has been described so far in this genus.

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2

Zajicek, R. S., and S. J. Ferguson. "The enigma of Paracoccus pantotrophus cytochrome cd1 activation." Biochemical Society Transactions 33, no. 1 (February 1, 2005): 147–48. http://dx.doi.org/10.1042/bst0330147.

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Paracoccus pantotrophus cytochrome cd1 nitrite reductase is isolated under aerobic conditions from anaerobically grown cells in an inactive form. This state requires reductive activation to make it catalytically competent for nitrite reduction. In this work, we discuss the methods of this reductive activation and its consequences for the cell.

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3

Bardischewsky, Frank, Jörg Fischer, Bettina Höller, and Cornelius G. Friedrich. "SoxV transfers electrons to the periplasm of Paracoccus pantotrophus – an essential reaction for chemotrophic sulfur oxidation." Microbiology 152, no. 2 (February 1, 2006): 465–72. http://dx.doi.org/10.1099/mic.0.28523-0.

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The soxVW genes are located upstream of the sox gene cluster encoding the sulfur-oxidizing ability of Paracoccus pantotrophus. SoxV is highly homologous to CcdA, which is involved in cytochrome c maturation of P. pantotrophus. SoxV was shown to function in reduction of the periplasmic SoxW, which shows a CysXaaXaaCys motif characteristic for thioredoxins. From strain GBΩV, which carries an Ω-kanamycin-resistance-encoding interposon in soxV, and complementation analysis it was evident that SoxV but not the periplasmic SoxW was essential for lithoautotrophic growth of P. pantotrophus with thiosulfate. However, the thiosulfate-oxidizing activities of cell extracts from the wild-type and from strain GBΩV were similar, demonstrating that the low thiosulfate-oxidizing activity of strain GBΩV in vivo was not due to a defect in biosynthesis or maturation of proteins of the Sox system and suggesting that SoxV is part of a regulatory or catalytic system of the Sox system. Analysis of DNA sequences available from different organisms harbouring a Sox system revealed that soxVW genes are exclusively present in sox operons harbouring the soxCD genes, encoding sulfur dehydrogenase, suggesting that SoxCD might be a redox partner of SoxV. No complementation of the ccdA mutant P. pantotrophus TP43 defective in cytochrome c maturation was achieved by expression of soxV in trans, demonstrating that the high identity of SoxV and CcdA does not correspond to functional homology.

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4

Singh, V., and A. K. Mittal. "Characterization of biofilm of a rotating biological contactor treating synthetic wastewater." Water Science and Technology 66, no. 2 (July 1, 2012): 429–37. http://dx.doi.org/10.2166/wst.2012.221.

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A four-stage rotating biological contactor (RBC) was designed and operated to treat synthetic wastewater containing 1,000 mg/l chemical oxygen demand (COD) and 112 mg/l NH4+-N. A mixed culture bacterial biofilm was developed consisting of a heterotrophic bacterium Paracoccus pantotrophus, nitrifiers and other heterotrophs. Applying the peculiar characteristics of P. pantotrophus of simultaneous heterotrophic nitrification and aerobic denitrification, high simultaneous removal of carbon and nitrogen could be achieved in the fully aerobic RBC. The microbial community structure of the RBC biofilm was categorized based on the nitrate reduction, biochemical reactions, gram staining and morphology. The presence of P. pantotrophus within the RBC biofilm was confirmed with an array of biochemical tests. Isolates from the four stages of RBC were grouped into complete denitrifiers, incomplete denitrifiers and non-denitrifiers. This categorization showed a higher relative abundance of P. pantotrophus in the first stage as compared with subsequent stages, in which other nitrifiers and heterotrophs were significantly present. High total nitrogen removal of upto 68% was in conformity with observations made using microbial categorization and biochemical tests. The high relative abundance of P. pantotrophus in the biofilm revealed that it could successfully compete with other heterotrophs and autotrophic nitrifiers in mixed bacterial biomass.

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5

Hasegawa-Kurisu, K., Y. Otani, and K. Hanaki. "Evaluation of nitrate removal by continuous culturing of an aerobic denitrifying bacterium, Paracoccus pantotrophus." Water Science and Technology 54, no. 8 (October 1, 2006): 219–28. http://dx.doi.org/10.2166/wst.2006.752.

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Nitrate removal under aerobic conditions was investigated using pure cultures of Paracoccus pantotrophus, which is a well-known aerobic-denitrifying (AD) bacterium. When a high concentration of cultures with a high carbon/nitrogen (C/N) ratio was preserved at the beginning of batch experiments, subsequently added nitrate was completely removed. When continuous culturing was perpetuated, a high nitrate removal rate (66.5%) was observed on day 4 post-culture, although gradual decreases in AD ability with time were observed. The attenuation in AD ability was probably caused by carbon limitation, because when carbon concentration of inflow water was doubled, nitrate removal efficiency improved from 18.1% to 59.6%. Bacterial community analysis using the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) method showed that P. pantotrophus disappeared in the suspended medium on day 8 post-culture, whereas other bacterial communities dominated by Acidovorax sp. appeared. Interestingly, this replaced bacterial community also showed AD ability. As P. pantotrophus was detected as attached colonies around the membrane and bottom of the reactor, this bacterium can therefore be introduced in a fixed form for treatment of wastewater containing nitrate with a high C/N ratio.

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6

Bartosik, Dariusz, Michal Szymanik, and Jadwiga Baj. "Identification and Distribution of Insertion Sequences of Paracoccus solventivorans." Applied and Environmental Microbiology 69, no. 12 (December 2003): 7002–8. http://dx.doi.org/10.1128/aem.69.12.7002-7008.2003.

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ABSTRACT Three novel insertion sequences (ISs) (ISPso1, ISPso2, and ISPso3) of the soil bacterium Paracoccus solventivorans DSM 11592 were identified by transposition into entrapment vector pMEC1. ISPso1 (1,400 bp) carries one large open reading frame (ORF) encoding a putative basic protein (with a DDE motif conserved among transposases [Tnps] of elements belonging to the IS256 family) with the highest levels of similarity with the hypothetical Tnps of Rhodospirillum rubrum and Sphingopyxis macrogoltabida. ISPso2 (832 bp) appeared to be closely related to ISPpa2 of Paracoccus pantotrophus DSM 11072 and IS1248 of Paracoccus denitrificans PdX22, both of which belong to the IS427 group (IS5 family). These elements contain two overlapping ORFs and a putative frameshift motif (AAAAG) responsible for production of a putative transframe Tnp. ISPso3 (1,286 bp) contains a single ORF, whose putative product showed homology with Tnps of ISs classified as members of a distinct subgroup of the IS5 group of the IS5 family. The highest levels of similarity were observed with ISSsp126 of Sphingomonas sp. and IS1169 of Bacteroides fragilis. Analysis of the distribution of ISs of P. solventivorans revealed that ISPso2-like elements are the most widely spread of the elements in nine species of the genus Paracoccus. ISPso1 and ISPso3 are present in only a few paracoccal strains, which suggests that they were acquired by lateral transfer. Phylogenetic analysis of Tnps of the novel ISs and their closest relatives showed their evolutionary relationships and possible directions of lateral transfer between various bacterial hosts.

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7

Otani, Y., K. Hasegawa, and K. Hanaki. "Comparison of aerobic denitrifying activity among three cultural species with various carbon sources." Water Science and Technology 50, no. 8 (October 1, 2004): 15–22. http://dx.doi.org/10.2166/wst.2004.0477.

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Abilities of three aerobic denitrifiers such as Alcaligenes faecalis, Microvirgula aerodenitrificans and Paracoccus pantotrophus were compared from the viewpoints of nitrate removal efficiency and organic matter utilization. First, the effect of carbon source was investigated. Although nitrate reduction was observed in all strains under aerobic conditions, a change of carbon source considerably affected the denitrification ability. In the case of P. pantotrophus, nitrate and nitrite were completely removed in three days under sodium acetate or leucine as a carbon source. In the case of A. faecalis, sufficient nitrate removal was observed only when sodium acetate or ethanol was added. P. pantotrophus and A. faecalis showed a higher ability of nitrate removal than that of M. aerodenitrificans. Therefore, P. pantotrophus was selected in order to investigate the effects of concentration and repetitive addition of carbon. Sodium acetate was used as a sole carbon source. Nitrate was not reduced when the carbon concentration was below 500 mgC/L. However, when carbon source was added repeatedly, nitrate was reduced under 100 mgC/L after the optical density of the bacterium reached above 1.0. This result indicated that a high enough level of bacterial density was necessary to express aerobic denitrification activity.

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8

van Wonderen, Jessica H., Christopher Knight, Vasily S. Oganesyan, Simon J. George, Walter G. Zumft, and Myles R. Cheesman. "Activation of the Cytochrome cd1 Nitrite Reductase from Paracoccus pantotrophus." Journal of Biological Chemistry 282, no. 38 (July 10, 2007): 28207–15. http://dx.doi.org/10.1074/jbc.m701242200.

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Cytochromes cd1 are dimeric bacterial nitrite reductases, which contain two hemes per monomer. On reduction of both hemes, the distal ligand of heme d1 dissociates, creating a vacant coordination site accessible to substrate. Heme c, which transfers electrons from donor proteins into the active site, has histidine/methionine ligands except in the oxidized enzyme from Paracoccus pantotrophus where both ligands are histidine. During reduction of this enzyme, Tyr25 dissociates from the distal side of heme d1, and one heme c ligand is replaced by methionine. Activity is associated with histidine/methionine coordination at heme c, and it is believed that P. pantotrophus cytochrome cd1 is unreactive toward substrate without reductive activation. However, we report here that the oxidized enzyme will react with nitrite to yield a novel species in which heme d1 is EPR-silent. Magnetic circular dichroism studies indicate that heme d1 is low-spin FeIII but EPR-silent as a result of spin coupling to a radical species formed during the reaction with nitrite. This reaction drives the switch to histidine/methionine ligation at FeIII heme c. Thus the enzyme is activated by exposure to its physiological substrate without the necessity of passing through the reduced state. This reactivity toward nitrite is also observed for oxidized cytochrome cd1 from Pseudomonas stutzeri suggesting a more general involvement of the EPR-silent FeIII heme d1 species in nitrite reduction.

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9

Rother, Dagmar, Grazyna Orawski, Frank Bardischewsky, and Cornelius G. Friedrich. "SoxRS-mediated regulation of chemotrophic sulfur oxidation in Paracoccus pantotrophus." Microbiology 151, no. 5 (May 1, 2005): 1707–16. http://dx.doi.org/10.1099/mic.0.27724-0.

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Paracoccus pantotrophus GB17 requires thiosulfate for induction of the sulfur-oxidizing (Sox) enzyme system. The soxRS genes are divergently oriented to the soxVWXYZA–H genes. soxR predicts a transcriptional regulator of the ArsR family and soxS a periplasmic thioredoxin. The homogenote mutant GBΩS carrying a disruption of soxS by the Ω-kanamycin-resistance-encoding interposon expressed a low thiosulfate-oxidizing activity under heterotrophic and mixotrophic growth conditions. This activity was repressed by complementation with soxR, suggesting that SoxR acts as a repressor and SoxS is essential for full expression. Sequence analysis uncovered operator characteristics in the intergenic regions soxS–soxV and soxW–soxX. In each region a transcription start site was identified by primer extension analysis. Both regions were cloned into the vector pRI1 and transferred to P. pantotrophus. Strains harbouring pRI1 with soxS–soxV or soxW–soxX expressed the sox genes under heterotrophic conditions at a low rate, indicating repressor titration. Sequence analysis of SoxR suggested a helix–turn–helix (HTH) motif at position 87–108 and uncovered an invariant Cys-80 and a cysteine residue at the C-terminus. SoxR was overproduced in Escherichia coli with an N-terminal His6-tag and purified to near homogeneity. Electrophoretic gel mobility shift assays with SoxR retarded the soxS–soxV region as a single band while the soxW–soxX region revealed at least two protein–DNA complexes. These data demonstrated binding of SoxR to the relevant DNA. This is believed to be the first report of regulation of chemotrophic sulfur oxidation at the molecular level.

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10

Vikromvarasiri, Nunthaphan, Jinjuta Juntranapaporn, and Nipon Pisutpaisal. "Performance of Paracoccus pantotrophus for H2S removal in biotrickling filter." International Journal of Hydrogen Energy 42, no. 45 (November 2017): 27820–25. http://dx.doi.org/10.1016/j.ijhydene.2017.05.232.

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11

Paes de Sousa, P. M., S. R. Pauleta, M. L. Simões Gonçalves, G. W. Pettigrew, I. Moura, M. M. Correia dos Santos, and J. J. G. Moura. "Mediated catalysis of Paracoccus pantotrophus cytochrome c peroxidase by P. pantotrophus pseudoazurin: kinetics of intermolecular electron transfer." JBIC Journal of Biological Inorganic Chemistry 12, no. 5 (March 15, 2007): 691–98. http://dx.doi.org/10.1007/s00775-007-0219-9.

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12

Friedrich, Cornelius G., Armin Quentmeier, Frank Bardischewsky, Dagmar Rother, Petra Hellwig, Wolfgang Lubitz, Tresfore Dambe, and Axel Scheidig. "The sulfur-oxidizing enzyme system of paracoccus pantotrophus: proteins and reaction." Journal of Inorganic Biochemistry 96, no. 1 (July 2003): 66. http://dx.doi.org/10.1016/s0162-0134(03)80514-7.

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13

Bartosik, Dariusz, Jadwiga Baj, Ewa Piechucka, Edyta Waker, and Miroslawa Wlodarczyk. "Comparative characterization of repABC-type replicons of Paracoccus pantotrophus composite plasmids." Plasmid 48, no. 2 (September 2002): 130–41. http://dx.doi.org/10.1016/s0147-619x(02)00100-2.

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14

Friedrich, Cornelius G., Armin Quentmeier, Frank Bardischewsky, Dagmar Rother, Regine Kraft, Susanne Kostka, and Heino Prinz. "Novel Genes Coding for Lithotrophic Sulfur Oxidation of Paracoccus pantotrophus GB17." Journal of Bacteriology 182, no. 17 (September 1, 2000): 4677–87. http://dx.doi.org/10.1128/jb.182.17.4677-4687.2000.

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ABSTRACT The gene region coding for lithotrophic sulfur oxidation ofParacoccus pantotrophus GB17 is located on a 13-kb insert of plasmid pEG12. Upstream of the previously described six open reading frames (ORFs) soxABCDEF with a partial sequence ofsoxA and soxF (C. Wodara, F. Bardischewsky, and C. G. Friedrich, J. Bacteriol. 179:5014–5023, 1997), 4,350 bp were sequenced. The sequence completed soxA, and uncovered six new ORFs upstream of soxA, designated ORF1, ORF2, and ORF3, and soxXYZ. ORF1 could encode a 275-amino-acid polypeptide of 29,332 Da with a 61 to 63% similarity to LysR transcriptional regulators. ORF2 could encode a 245-amino-acid polypeptide of 26,022 Da with the potential to form six transmembrane helices and with a 48 to 51% similarity to proteins involved in redox transport in cytochrome c biogenesis. ORF3 could encode a periplasmic polypeptide of 186 amino acids of 20,638 Da with a similarity to thioredoxin-like proteins and with a putative signal peptide of 21 amino acids. Purified SoxXA, SoxYZ, and SoxB are essential for thiosulfate or sulfite-dependent cytochrome creduction in vitro. N-terminal and internal amino acid sequences identified SoxX, SoxY, SoxZ, and SoxA to be coded by the respective genes. The molecular masses of the mature proteins determined by electrospray ionization spectroscopy (SoxX, 14,834 Da; SoxY, 11,094 Da; SoxZ, 11,717 Da; and SoxA, 30,452 Da) were identical or close to those deduced from the nucleotide sequence with differences for the covalent heme moieties. SoxXA represents a novel type of periplasmicc-type cytochromes, with SoxX as a monoheme and SoxA as a hybrid diheme cytochrome c. SoxYZ is an as-yet-unprecedented soluble protein. SoxY has a putative signal peptide with a twin arginine motif and possibly cotransports SoxZ to the periplasm. SoxYZ neither contains a metal nor a complex redox center, as proposed for proteins likely to be transported via the Tat system.

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15

Vikromvarasiri, Nunthaphan, Siriorn Boonyawanich, and Nipon Pisutpaisal. "Comparative Performance of Halothiobacillus Neapolitanus and Paracoccus Pantotrophus in Sulphur Oxidation." Energy Procedia 79 (November 2015): 885–89. http://dx.doi.org/10.1016/j.egypro.2015.11.582.

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16

Ellington, M. J. K., G. Sawers, H. J. Sears, S. Spiro, D. J. Richardson, and S. J. Ferguson. "Characterization of the expression and activity of the periplasmic nitrate reductase of Paracoccus pantotrophus in chemostat cultures." Microbiology 149, no. 6 (June 1, 2003): 1533–40. http://dx.doi.org/10.1099/mic.0.26277-0.

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The periplasmic nitrate reductase (Nap) from Paracoccus pantotrophus has a role in cellular redox balancing. Previously, transcription from the nap promoter in P. pantotrophus was shown to be responsive to the oxidation state of the carbon substrate. During batch culture, expression was higher during growth on reduced substrates such as butyrate compared to more oxidized substrates such as succinate. In the present study the effect of growth rate on nap expression in succinate-, acetate- and butyrate-limited chemostat cultures was investigated. In all three cases transcription from the nap promoter and Nap enzyme activity showed a strong correlation. At the fastest growth rates tested for the three substrates nap expression and Nap activity were highest when growth occurred on the most reduced substrate (butyrate > acetate > succinate). However, in all three cases a bell-shaped pattern of expression was observed as a function of growth rate, with the highest levels of nap expression and Nap activity being observed at intermediate growth rates. This effect was most pronounced on succinate, where an approximately fivefold variation was observed, and at intermediate dilution rates nap expression and Nap activity were comparable on all three carbon substrates. Analysis of mRNA prepared from the succinate-grown cultures revealed that different transcription initiation start sites for the nap operon were utilized as the growth rate changed. This study establishes a new regulatory feature of nap expression in P. pantotrophus that occurs at the level of transcription in response to growth rate in carbon-limited cultures.

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17

CARTRON, Michaël L., M. Dolores ROLDÁN, Stuart J. FERGUSON, Ben C. BERKS, and David J. RICHARDSON. "Identification of two domains and distal histidine ligands to the four haems in the bacterial c-type cytochrome NapC; the prototype connector between quinol/quinone and periplasmic oxido-reductases." Biochemical Journal 368, no. 2 (December 1, 2002): 425–32. http://dx.doi.org/10.1042/bj20020865.

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NapC is a tetra-haem member of a family of bacterial membrane-anchored multi-haem c-type cytochromes implicated in electron transfer between membrane quinols and periplasmic enzymes. The water-soluble tetra-haem fragment of Paracoccus pantotrophus NapC has been expressed as a periplasmic protein (NapCsol) in Paracoccus denitrificans, P. pantotrophus and Escherichia coli. Site-specific mutagenesis of NapCsol, combined with spectroscopic studies, suggests that each haem iron centre has bis-histidinyl co-ordination. Four proximal ligands arise from each of four Cys-Xaa-Xaa-Cys-His haem-binding motifs; candidates for the four distal ligands are His81, His99, His174 and His194. NapCH81A, NapCH99A, NapCH174A and NapCH194A mutants (with alanine substituted for each of the four candidate residues) have all been purified from E. coli. In each case, one of the haems has become high-spin, as judged by the presence of a broad absorption band between 620nm and 650nm for the oxidized cytochrome; this feature is absent for wild-type protein and presumably arises because of the absence of the distal histidine ligand from one of the haems. NapCH81A and NapCH174A are less well expressed in E. coli than NapCH99A and NapCH194A and cannot be detected when expressed in P. denitrificans or P. pantotrophus. In vitro and in vivo complementation studies demonstrate that the soluble periplasmic NapC can mediate electron transfer from quinols to the periplasmic nitrate reductase. This capacity was retained in vitro with the NapCH99A and NapCH194A mutants but was lost in vivo. A model for the structural organization of NapCsol into two domains, each containing a di-haem pair, is proposed. In this model, each haem pair obtains one distal haem ligand from its own domain and a second from the other domain. The suggestion of two domains is supported by observations that the 24kDa NapCsol cleaves to yield a 12kDa haem-staining band. Determination of the cleavage site showed it was between two equally sized di-haem domains predicted from sequence analysis.

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18

Quentmeier, Armin, Regine Kraft, Susanne Kostka, Reinhold Klockenkämper, and Cornelius G. Friedrich. "Characterization of a new type of sulfite dehydrogenase from Paracoccus pantotrophus GB17." Archives of Microbiology 173, no. 2 (November 29, 1999): 117–25. http://dx.doi.org/10.1007/s002039900118.

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19

Sam, Katharine A., John D. Tolland, Shirley A. Fairhurst, Christopher W. Higham, David J. Lowe, Roger N. F. Thorneley, James W. A. Allen, and Stuart J. Ferguson. "Unexpected dependence on pH of NO release from Paracoccus pantotrophus cytochrome cd1." Biochemical and Biophysical Research Communications 371, no. 4 (July 2008): 719–23. http://dx.doi.org/10.1016/j.bbrc.2008.04.149.

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20

Vikromvarasiri, Nunthaphan, Siriorn Boonyawanich, and Nipon Pisutpaisal. "Optimizing Sulfur Oxidizing Performance of Paracoccus Pantotrophus Isolated from Leather Industry Wastewater." Energy Procedia 79 (November 2015): 629–33. http://dx.doi.org/10.1016/j.egypro.2015.11.544.

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21

Ellington, M. J. K., K. K. Bhakoo, G. Sawers, D. J. Richardson, and S. J. Ferguson. "Hierarchy of Carbon Source Selection in Paracoccus pantotrophus: Strict Correlation between Reduction State of the Carbon Substrate and Aerobic Expression of the nap Operon." Journal of Bacteriology 184, no. 17 (September 1, 2002): 4767–74. http://dx.doi.org/10.1128/jb.184.17.4767-4774.2002.

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ABSTRACT Paracoccus pantotrophus can express a periplasmic nitrate reductase (Nap) during aerobic growth. A proposed role for this enzyme is the dissipation of excess redox energy during oxidative metabolism of reduced carbon substrates. To investigate the regulation of nap expression, a transcriptional fusion between the nap promoter region of P. pantotrophus and the lacZ gene was constructed. When this fusion was used, analyses showed that transcription from the nap promoter increases as the average reduction state of the carbon atoms increases. Thus, β-galactosidase activities increase as the carbon source changes in the order succinate-acetate-butyrate. This result was obtained regardless of which of the three carbon sources was used for culture of the inoculum. If two carbon sources were presented together, the β-galactosidase activity was always the same as it was when the least-reduced carbon source was added alone. This suggests that the regulation is dependent upon metabolism of the more-reduced carbon sources rather than just their presence in the medium. Analysis of culture medium by 1H nuclear magnetic resonance showed that for aerobic growth P. pantotrophus strictly selected its carbon source in the order succinate-acetate-butyrate. This was reflected by diauxic growth kinetics on medium containing mixed carbon substrates. The regulatory mechanism underpinning such a selection is unknown but is likely to be related to the mechanism which controls the transcription of the nap operon.

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22

Rainey, Frederick A., Donovan P. Kelly, Erko Stackebrandt, Jutta Burghardt, Akira Hiraishi, Yoko Katayama, and Ann P. Wood. "A re-evaluation of the taxonomy of Paracoccus denitrificans and a proposal for the combination Paracoccus pantotrophus comb. nov." International Journal of Systematic and Evolutionary Microbiology 49, no. 2 (April 1, 1999): 645–51. http://dx.doi.org/10.1099/00207713-49-2-645.

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23

Echalier, Aude, Celia F. Goodhew, Graham W. Pettigrew, and Vilmos Fülöp. "Activation and Catalysis of the Di-Heme Cytochrome c Peroxidase from Paracoccus pantotrophus." Structure 14, no. 1 (January 2006): 107–17. http://dx.doi.org/10.1016/j.str.2005.09.011.

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24

Juntranapaporn, Jinjuta, Nunthaphan Vikromvarasiri, Cheema Soralump, and Nipon Pisutpaisal. "Hydrogen sulfide removal from biogas in biotrickling filter system inoculated with Paracoccus pantotrophus." International Journal of Hydrogen Energy 44, no. 56 (November 2019): 29554–60. http://dx.doi.org/10.1016/j.ijhydene.2019.03.069.

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25

Gates, Andrew J., Clive S. Butler, David J. Richardson, and Julea N. Butt. "Electrocatalytic reduction of nitrate and selenate by NapAB." Biochemical Society Transactions 39, no. 1 (January 19, 2011): 236–42. http://dx.doi.org/10.1042/bst0390236.

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Bacterial cellular metabolism is renowned for its metabolic diversity and adaptability. However, certain environments present particular challenges. Aerobic metabolism of highly reduced carbon substrates by soil bacteria such as Paracoccus pantotrophus presents one such challenge since it may result in excessive electron delivery to the respiratory redox chain when compared with the availability of terminal oxidant, O2. The level of a periplasmic ubiquinol-dependent nitrate reductase, NAP, is up-regulated in the presence of highly reduced carbon substrates. NAP oxidizes ubiquinol at the periplasmic face of the cytoplasmic membrane and reduces nitrate in the periplasm. Thus its activity counteracts the accumulation of excess reducing equivalents in ubiquinol, thereby maintaining the redox poise of the ubiquinone/ubiquinol pool without contributing to the protonmotive force across the cytoplasmic membrane. Although P. pantotrophus NapAB shows a high level of substrate specificity towards nitrate, the enzyme has also been reported to reduce selenate in spectrophotometric solution assays. This transaction draws on our current knowledge concerning the bacterial respiratory nitrate reductases and extends the application of PFE (protein film electrochemistry) to resolve and quantify the selenate reductase activity of NapAB.

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26

Sabaty, Monique, Cécile Avazeri, David Pignol, and André Vermeglio. "Characterization of the Reduction of Selenate and Tellurite by Nitrate Reductases." Applied and Environmental Microbiology 67, no. 11 (November 1, 2001): 5122–26. http://dx.doi.org/10.1128/aem.67.11.5122-5126.2001.

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ABSTRACT Preliminary studies showed that the periplasmic nitrate reductase (Nap) of Rhodobacter sphaeroides and the membrane-bound nitrate reductases of Escherichia coli are able to reduce selenate and tellurite in vitro with benzyl viologen as an electron donor. In the present study, we found that this is a general feature of denitrifiers. Both the periplasmic and membrane-bound nitrate reductases of Ralstonia eutropha, Paracoccus denitrificans, and Paracoccus pantotrophus can utilize potassium selenate and potassium tellurite as electron acceptors. In order to characterize these reactions, the periplasmic nitrate reductase of R. sphaeroides f. sp. denitrificans IL106 was histidine tagged and purified. The V max andKm were determined for nitrate, tellurite, and selenate. For nitrate, values of 39 μmol · min−1 · mg−1 and 0.12 mM were obtained for V max and Km , respectively, whereas the V max values for tellurite and selenate were 40- and 140-fold lower, respectively. These low activities can explain the observation that depletion of the nitrate reductase in R. sphaeroides does not modify the MIC of tellurite for this organism.

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Kelly, Donovan P., Jean P. Euzéby, Celia F. Goodhew, and Ann P. Wood. "Redefining Paracoccus denitrificans and Paracoccus pantotrophus and the case for a reassessment of the strains held by international culture collections." International Journal of Systematic and Evolutionary Microbiology 56, no. 10 (October 1, 2006): 2495–500. http://dx.doi.org/10.1099/ijs.0.64401-0.

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Kelly, Donovan P., Jean P. Euzéby, Celia F. Goodhew, and Ann P. Wood. "Redefining Paracoccus denitrificans and Paracoccus pantotrophus and the case for a reassessment of the strains held by international culture collections." International Journal of Systematic and Evolutionary Microbiology 57, no. 1 (January 1, 2007): 198. http://dx.doi.org/10.1099/00207713-57-1-198.

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29

Mikosch, Carola A. R. M., Karin Denger, Eva-Maria Schäfer, and Alasdair M. Cook. "Anaerobic oxidations of cysteate: degradation via L-cysteate: 2-oxoglutarate aminotransferase in Paracoccus pantotrophus." Microbiology 145, no. 5 (May 1, 1999): 1153–60. http://dx.doi.org/10.1099/13500872-145-5-1153.

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BUTLER, Clive S., John M. CHARNOCK, C. David GARNER, Andrew J. THOMSON, Stuart J. FERGUSON, Ben C. BERKS, and David J. RICHARDSON. "Thiocyanate binding to the molybdenum centre of the periplasmic nitrate reductase from Paracoccus pantotrophus." Biochemical Journal 352, no. 3 (December 15, 2000): 859. http://dx.doi.org/10.1042/0264-6021:3520859.

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BUTLER, Clive S., John M. CHARNOCK, C. David GARNER, Andrew J. THOMSON, Stuart J. FERGUSON, Ben C. BERKS, and David J. RICHARDSON. "Thiocyanate binding to the molybdenum centre of the periplasmic nitrate reductase from Paracoccus pantotrophus." Biochemical Journal 352, no. 3 (December 8, 2000): 859–64. http://dx.doi.org/10.1042/bj3520859.

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The periplasmic nitrate reductase (NAP) from Paracoccus pantotrophus is a soluble two-subunit enzyme (NapAB) that binds two haem groups, a [4FeŐ4S] cluster and a bis(molybdopterin guanine dinucleotide) (MGD) cofactor that catalyses the reduction of nitrate to nitrite. In the present study the effect of KSCN (potassium thiocyanate) as an inhibitor and Mo ligand has been investigated. Results are presented that show NAP is sensitive to SCN- (thiocyanate) inhibition, with SCN- acting as a competitive inhibitor of nitrate (Ki ≈ 4.0mM). The formation of a novel EPR Mo(V) species with an elevated gav value (gav ∼ 1.994) compared to the Mo(V) High-g (resting) species was observed upon redox cycling in the presence of SCN-. Mo K-edge EXAFS analysis of the dithionite-reduced NAP was best fitted as a mono-oxo Mo(IV) species with three MoŐS ligands at 2.35Å (1 Å = 0.1nm) and a MoŐO ligand at 2.14 Å. The addition of SCN- to the reduced Mo(IV) NAP generated a sample that was best fitted as a mono-oxo (1.70 Å) Mo(IV) species with four MoŐS ligands at 2.34 Å. Taken together, the competitive nature of SCN- inhibition of periplasmic nitrate reductase activity, the elevated Mo(V) EPR gav value following redox cycling in the presence of SCN- and the increase in sulphur co-ordination of Mo(IV) upon SCN- binding, provide strong evidence for the direct binding of SCN- via a sulphur atom to Mo.

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Wang, Jing, Xiaolin Liu, Xinbai Jiang, Libin Zhang, Cheng Hou, Guanyong Su, Lianjun Wang, Yang Mu, and Jinyou Shen. "Nitrate stimulation of N-Methylpyrrolidone biodegradation by Paracoccus pantotrophus: Metabolite mechanism and Genomic characterization." Bioresource Technology 294 (December 2019): 122185. http://dx.doi.org/10.1016/j.biortech.2019.122185.

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33

Mikosa, Malgorzata, Marta Sochacka-Pietal, Jadwiga Baj, and Dariusz Bartosik. "Identification of a transposable genomic island of Paracoccus pantotrophus DSM 11072 by its transposition to a novel entrapment vector pMMB2." Microbiology 152, no. 4 (April 1, 2006): 1063–73. http://dx.doi.org/10.1099/mic.0.28603-0.

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A novel shuttle entrapment vector, pMMB2, was used to identify a large transposable element, TnPpa1 (44·3 kb), of Paracoccus pantotrophus DSM 11072. TnPpa1 has a composite structure with divergently oriented copies of a cryptic transposon, Tn3434 (Tn3 family), located at both termini. The core region of the element contains a large set of putative genes, whose products show similarity to enzymes involved in central intermediary metabolism (e.g. tricarboxylic acid cycle or 2-methylcitrate cycle), transporters, transcriptional regulators and conserved proteins of unknown function. A 4·2 kb DNA segment of TnPpa1 is homologous to a region of chromosome cII of Rhodobacter sphaeroides 2.4.1, which exemplifies the mosaic structure of this element. TnPpa1 is bordered by 5 bp long directly repeated sequences and is located within a mega-sized replicon, pWKS5, in the DSM 11072 genome. Spontaneous inversion of the core region of TnPpa1 was detected in the host genome. Analysis of the distribution of TnPpa1 in three other strains of P. pantotrophus revealed that this element was present exclusively within DSM 11072, which suggests its relatively recent acquisition by lateral transfer. The identification of TnPpa1 (which may be considered a transposable genomic island) provides evidence for the transposition and lateral transfer of large DNA segments of chromosomal origin (carrying various housekeeping genes), which may have a great impact on the evolution of bacterial genomes.

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Luo, Wei, Jiagui Hu, Jiapeng Lu, Huili Zhang, Xiaoping Wang, Yuantao Liu, Liqing Dong, and Xiaobin Yu. "One pot cascade synthesis of L-2-aminobutyric acid employing ω-transaminase from Paracoccus pantotrophus." Molecular Catalysis 515 (October 2021): 111890. http://dx.doi.org/10.1016/j.mcat.2021.111890.

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35

Gates, Andrew J., David J. Richardson, and Julea N. Butt. "Voltammetric characterization of the aerobic energy-dissipating nitrate reductase of Paracoccus pantotrophus: exploring the activity of a redox-balancing enzyme as a function of electrochemical potential." Biochemical Journal 409, no. 1 (December 11, 2007): 159–68. http://dx.doi.org/10.1042/bj20071088.

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Paracoccus pantotrophus expresses two nitrate reductases associated with respiratory electron transport, termed NapABC and NarGHI. Both enzymes derive electrons from ubiquinol to reduce nitrate to nitrite. However, while NarGHI harnesses the energy of the quinol/nitrate couple to generate a transmembrane proton gradient, NapABC dissipates the energy associated with these reducing equivalents. In the present paper we explore the nitrate reductase activity of purified NapAB as a function of electrochemical potential, substrate concentration and pH using protein film voltammetry. Nitrate reduction by NapAB is shown to occur at potentials below approx. 0.1 V at pH 7. These are lower potentials than required for NarGH nitrate reduction. The potentials required for Nap nitrate reduction are also likely to require ubiquinol/ubiquinone ratios higher than are needed to activate the H+-pumping oxidases expressed during aerobic growth where Nap levels are maximal. Thus the operational potentials of P. pantotrophus NapAB are consistent with a productive role in redox balancing. A Michaelis constant (KM) of approx. 45 μM was determined for NapAB nitrate reduction at pH 7. This is in line with studies on intact cells where nitrate reduction by Nap was described by a Monod constant (KS) of less than 15 μM. The voltammetric studies also disclosed maximal NapAB activity in a narrow window of potential. This behaviour is resistant to change of pH, nitrate concentration and inhibitor concentration and its possible mechanistic origins are discussed.

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Dambe, Tresfore, Armin Quentmeier, Dagmar Rother, Cornelius Friedrich, and Axel J. Scheidig. "Structure of the cytochrome complex SoxXA of Paracoccus pantotrophus, a heme enzyme initiating chemotrophic sulfur oxidation." Journal of Structural Biology 152, no. 3 (December 2005): 229–34. http://dx.doi.org/10.1016/j.jsb.2005.09.002.

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37

Rein, Ulrike, Ronnie Gueta, Karin Denger, Jürgen Ruff, Klaus Hollemeyer, and Alasdair M. Cook. "Dissimilation of cysteate via 3-sulfolactate sulfo-lyase and a sulfate exporter in Paracoccus pantotrophus NKNCYSA." Microbiology 151, no. 3 (March 1, 2005): 737–47. http://dx.doi.org/10.1099/mic.0.27548-0.

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Paracoccus pantotrophus NKNCYSA utilizes (R)-cysteate (2-amino-3-sulfopropionate) as a sole source of carbon and energy for growth, with either nitrate or molecular oxygen as terminal electron acceptor, and the specific utilization rate of cysteate is about 2 mkat (kg protein)−1. The initial degradative reaction is catalysed by an (R)-cysteate : 2-oxoglutarate aminotransferase, which yields 3-sulfopyruvate. The latter was reduced to 3-sulfolactate by an NAD-linked sulfolactate dehydrogenase [3·3 mkat (kg protein)−1]. The inducible desulfonation reaction was not detected initially in cell extracts. However, a strongly induced protein with subunits of 8 kDa (α) and 42 kDa (β) was found and purified. The corresponding genes had similarities to those encoding altronate dehydratases, which often require iron for activity. The purified enzyme could then be shown to convert 3-sulfolactate to sulfite and pyruvate and it was termed sulfolactate sulfo-lyase (Suy). A high level of sulfite dehydrogenase was also induced during growth with cysteate, and the organism excreted sulfate. A putative regulator, OrfR, was encoded upstream of suyAB on the reverse strand. Downstream of suyAB was suyZ, which was cotranscribed with suyB. The gene, an allele of tauZ, encoded a putative membrane protein with transmembrane helices (COG2855), and is a candidate to encode the sulfate exporter needed to maintain homeostasis during desulfonation. suyAB-like genes are widespread in sequenced genomes and environmental samples where, in contrast to the current annotation, several presumably encode the desulfonation of 3-sulfolactate, a component of bacterial spores.

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Bardischewsky, Frank, Armin Quentmeier, and Cornelius G. Friedrich. "The flavoprotein SoxF functions in chemotrophic thiosulfate oxidation of Paracoccus pantotrophus in vivo and in vitro." FEMS Microbiology Letters 258, no. 1 (May 2006): 121–26. http://dx.doi.org/10.1111/j.1574-6968.2006.00210.x.

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39

RASMUSSEN, Tim, Ben C. BERKS, Julea N. BUTT, and Andrew J. THOMSON. "Multiple forms of the catalytic centre, CuZ, in the enzyme nitrous oxide reductase from Paracoccus pantotrophus." Biochemical Journal 364, no. 3 (June 15, 2002): 807–15. http://dx.doi.org/10.1042/bj20020055.

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Nitrous oxide reductase catalyses the reduction of nitrous oxide to dinitrogen at a unique tetranuclear copper site, called CuZ, which has a central inorganic sulphide ligand. Limited incubation with oxygen during the preparation of nitrous oxide reductase from Paracoccus pantotrophus results in changed redox properties of the catalytic centre by comparison with anaerobic preparations. While the anaerobically purified enzyme has a catalytic centre which performs a single electron step at a midpoint potential of Em =+60mV versus the standard hydrogen electrode (n = 1), the altered centre shows no redox change under similar experimental conditions. Spectroscopic properties of this ‘redox fixed’ centre are similar to spectra of the reduced ‘redox active’ form of CuZ, although the positions and intensities of a number of transitions are changed in the optical spectrum. These observations are interpreted in terms of two forms of the catalytic centre, called CuZ and CuZ∗. The structural relationship between these forms is unclear. EPR and magnetic circular dichroism spectra suggest that the basic Cu4S structure is common to both. Curiously, steady-state activity of the aerobic enzyme preparation is slightly increased despite the fact the catalytic centre does not undergo detectable redox changes.

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ALLEN, James W. A., Christopher W. HIGHAM, Richard S. ZAJICEK, Nicholas J. WATMOUGH, and Stuart J. FERGUSON. "A novel, kinetically stable, catalytically active, all-ferric, nitrite-bound complex of Paracoccus pantotrophus cytochrome cd1." Biochemical Journal 366, no. 3 (September 15, 2002): 883–88. http://dx.doi.org/10.1042/bj20020795.

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The oxidized form of Paracoccus pantotrophus cytochrome cd1 nitrite reductase, as isolated, has bis-histidinyl co-ordination of the c haem and His/Tyr co-ordination of the d1 haem. On reduction, the haem co-ordinations change to His/Met and His/vacant respectively. If the latter form of the enzyme is reoxidized, a conformer is generated in which the ferric c haem is His/Met co-ordinated; this can revert to the ‘as isolated’ state of the enzyme over approx. 20min at room temperature. However, addition of nitrite to the enzyme after a cycle of reduction and reoxidation produces a kinetically stable, all-ferric complex with nitrite bound to the d1 haem and His/Met co-ordination of the c haem. This complex is catalytically active with the physiological electron donor protein pseudoazurin. The effective dissociation constant for nitrite is 2mM. Evidence is presented that d1 haem is optimized to bind nitrite, as opposed to other anions that are commonly good ligands to ferric haem. The all-ferric nitrite bound state of the enzyme could not be generated stoichiometrically by mixing nitrite with the ‘as isolated’ conformer of cytochrome cd1 without redox cycling.

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Allen, James W. A., Myles R. Cheesman, Christopher W. Higham, Stuart J. Ferguson, and Nicholas J. Watmough. "A Novel Conformer of Oxidized Paracoccus pantotrophus Cytochrome cd1 Observed by Freeze-Quench NIR-MCD Spectroscopy." Biochemical and Biophysical Research Communications 279, no. 2 (December 2000): 674–77. http://dx.doi.org/10.1006/bbrc.2000.4009.

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42

Epel, Boris, Kai-Oliver Schäfer, Armin Quentmeier, Cornelius Friedrich, and Wolfgang Lubitz. "Multifrequency EPR analysis of the dimanganese cluster of the putative sulfate thiohydrolase SoxB of Paracoccus pantotrophus." JBIC Journal of Biological Inorganic Chemistry 10, no. 6 (August 31, 2005): 636–42. http://dx.doi.org/10.1007/s00775-005-0015-3.

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Xie, Xiangjin, Ryan G. Hadt, Sofia R. Pauleta, Pablo J. González, Sun Un, Isabel Moura, and Edward I. Solomon. "A variable temperature spectroscopic study on Paracoccus pantotrophus pseudoazurin: Protein constraints on the blue Cu site." Journal of Inorganic Biochemistry 103, no. 10 (October 2009): 1307–13. http://dx.doi.org/10.1016/j.jinorgbio.2009.04.012.

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44

El-Tarabily, Khaled A., Abdou A. Soaud, Maher E. Saleh, and Satoshi Matsumoto. "Isolation and characterisation of sulfur-oxidising bacteria, including strains of Rhizobium, from calcareous sandy soils and their effects on nutrient uptake and growth of maize (Zea mays L.)." Australian Journal of Agricultural Research 57, no. 1 (2006): 101. http://dx.doi.org/10.1071/ar04237.

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Four sulfur-oxidising bacteria were selected among 427 bacterial isolates from calcareous sandy soils in the United Arab Emirates (UAE). These isolates were selected based on their strong ability to oxidise elemental sulfur (S°) in vitro and were identified as Paracoccus versutus CBS 114155, Paracoccus pantotrophus CBS 114154, and 2 strains as Rhizobium spp. NCCB 100053 and NCCB 100054. This is the first published report of a Rhizobium species capable of S° oxidation and also the first record of sulfur-oxidising bacteria from UAE soils. These isolates were tested in a greenhouse in the presence and absence of S° to study their effects on maize growth. Best growth was observed in the treatment with P. versutus application combined with S°, which significantly reduced soil pH, increased soil SO4 level and the uptake of N, S, Fe, Mn, and Zn in maize roots and shoots. The P and Cu uptake in the shoots of maize plants was not significant compared with the treatment that received the application of S° alone. There was no response in plant growth to treatments that included the application of S° combined with P. pantotrophus or Rhizobium strain NCCB 100053 compared with the treatment that received the application of S° alone. There was significant growth inhibition of maize plants in the treatment receiving Rhizobium strain NCCB 100054 with or without the application of S° compared with the treatment that included the application of S° alone. This growth inhibition was associated with a significant decrease in the levels of N, P, S, Fe, Mn, Zn, and Cu in roots and shoots in the absence of S°. Rhizobium strain NCCB 100054 applied with S° significantly decreased the levels of N, S, and Fe in the roots and the levels of N, P, S, Fe, Mn, and Cu in the shoots of maize, with no significant differences in the levels of P and Mn in the roots and in the levels of Zn in the shoots, compared with the treatment with S° alone. These results indicate that the treatment P. versutus combined with S° can be effective as a soil conditioner for horticultural production in calcareous sandy soils.

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Lavandera, Iván, Brigitte Höller, Alexander Kern, Ursula Ellmer, Anton Glieder, Stefaan de Wildeman, and Wolfgang Kroutil. "Asymmetric anti-Prelog reduction of ketones catalysed by Paracoccus pantotrophus and Comamonas sp. cells via hydrogen transfer." Tetrahedron: Asymmetry 19, no. 16 (August 2008): 1954–58. http://dx.doi.org/10.1016/j.tetasy.2008.08.005.

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46

Rasmussen, Tim, Thomas Brittain, Ben C. Berks, Nicholas J. Watmough, and Andrew J. Thomson. "Formation of a cytochrome c–nitrous oxide reductase complex is obligatory for N2O reduction by Paracoccus pantotrophus." Dalton Transactions, no. 21 (2005): 3501. http://dx.doi.org/10.1039/b501846c.

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Ramadhani, Atik, Miki Kawada-Matsuo, Hitoshi Komatsuzawa, and Takahiko Oho. "Recombinant Sox Enzymes from Paracoccus pantotrophus Degrade Hydrogen Sulfide, a Major Component of Oral Malodor." Microbes and Environments 32, no. 1 (2017): 54–60. http://dx.doi.org/10.1264/jsme2.me16140.

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48

Quentmeier, Armin, Petra Hellwig, Frank Bardischewsky, Gerlinde Grelle, Regine Kraft, and Cornelius G. Friedrich. "Sulfur oxidation in Paracoccus pantotrophus: interaction of the sulfur-binding protein SoxYZ with the dimanganese SoxB protein." Biochemical and Biophysical Research Communications 312, no. 4 (December 2003): 1011–18. http://dx.doi.org/10.1016/j.bbrc.2003.11.021.

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Santal, Anita Rani, Nater Pal Singh, and Baljeet Singh Saharan. "A novel application of Paracoccus pantotrophus for the decolorization of melanoidins from distillery effluent under static conditions." Journal of Environmental Management 169 (March 2016): 78–83. http://dx.doi.org/10.1016/j.jenvman.2015.12.016.

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., Angshuman Bagchi, and Tapash Ghosh . "Structural Insight into the Functionality of the Transcriptional Regulator SoxR from Paracoccus pantotrophus in Sulfur Oxidation Operon." Research Journal of Microbiology 2, no. 10 (October 1, 2007): 735–41. http://dx.doi.org/10.3923/jm.2007.735.741.

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