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Journal of Biological Inorganic... Oct 2014Iron-dependent enzymes are prevalent in nature and participate in a wide range of biological redox activities. Frequently, high-valence iron intermediates are involved... (Review)
Review
Iron-dependent enzymes are prevalent in nature and participate in a wide range of biological redox activities. Frequently, high-valence iron intermediates are involved in the catalytic events of iron-dependent enzymes, especially when the activation of peroxide or molecular oxygen is involved. Building on the fundamental framework of iron-oxygen chemistry, these reactive intermediates constantly attract significant attention from the enzymology community. During the past few decades, tremendous efforts from a number of laboratories have been dedicated to the capture and characterization of these intermediates to improve mechanistic understandings. In 2008, an unprecedented bis-Fe(IV) intermediate was reported in a c-type diheme enzyme, MauG, which is involved in the maturation of a tryptophan tryptophylquinone cofactor of methylamine dehydrogenase. This intermediate, although chemically equivalent to well-characterized high-valence iron intermediates, such as compound I, compound ES, and intermediate Q in methane monooxygenase, as well as the hypothetical Fe(V) species in Rieske non-heme oxygenases, is orders of magnitude more stable than these other high-valence species in the absence of its primary substrate. It has recently been discovered that the bis-Fe(IV) intermediate exhibits a unique near-IR absorption feature which has been attributed to a novel charge-resonance phenomenon. This review compares the properties of MauG with structurally related enzymes, summarizes the current knowledge of this new high-valence iron intermediate, including its chemical origin and structural basis, explores the formation and consequences of charge resonance, and recounts the long-range catalytic mechanism in which bis-Fe(IV) participates. Biological strategies for storing oxidizing equivalents with iron ions are also discussed.
Topics: Indolequinones; Iron Compounds; Models, Molecular; Oxidation-Reduction; Oxidoreductases Acting on CH-NH Group Donors; Paracoccus; Tryptophan
PubMed: 24722994
DOI: 10.1007/s00775-014-1123-8 -
Current Issues in Molecular Biology 2019Pd 1222 is a model methylotrophic bacterium. Its methylotrophy is based on autotrophic growth (enabled by the Calvin cycle) supported by energy from the oxidation of... (Review)
Review
Pd 1222 is a model methylotrophic bacterium. Its methylotrophy is based on autotrophic growth (enabled by the Calvin cycle) supported by energy from the oxidation of methanol or methylamine. The growing availability of genome sequence data has made it possible to investigate methylotrophy in other . The examination of a large number of spp. genomes reveals great variability in C1 metabolism, which have been shaped by different evolutionary mechanisms. Surprisingly, the methylotrophy schemes of many strains appear to have quite different genetic and biochemical bases. Besides the expected 'autotrophic methylotrophs', many strains of this genus possess another C1 assimilatory pathway, the serine cycle, which seems to have at least three independent origins. Analysis of the co-occurrence of different methylotrophic pathways indicates, on the one hand, evolutionary linkage between the Calvin cycle and the serine cycle, and, on the other hand, that genes encoding some C1 substrate-oxidizing enzymes occur more frequently in association with one or the other. This suggests that some genetic module combinations form more harmonious enzymatic sets, which act with greater efficiency in the methylotrophic process and thus undergo positive selection.
Topics: Alphaproteobacteria; Biodiversity; Biological Evolution; Genome, Bacterial; Metabolic Networks and Pathways; Methanol; Methylamines; Oxidation-Reduction; Paracoccus
PubMed: 31166188
DOI: 10.21775/cimb.033.117 -
Current Microbiology Feb 2021Strain YIM 132242, isolated from lichen collected from Pu'er, Yunnan Province, China, was short-rod-shaped, Gram-reaction-negative, aerobic, catalase- and...
Strain YIM 132242, isolated from lichen collected from Pu'er, Yunnan Province, China, was short-rod-shaped, Gram-reaction-negative, aerobic, catalase- and oxidase-positive. Growth of the strain was occurred at 10-39 °C (optimum, 28-35 °C), at pH 4.0-10.0 (optimum, pH 7.0-8.0) and at salinities of 0-8% (w/v) NaCl (optimum, 0-2%). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain YIM 132242 belonged to the genus Paracoccus and had the highest levels of sequence similarity to Paracoccus aerius KCTC 42845 (97.0% similarity), Paracoccus sediminis CMB17 (96.8% similarity), and Paracoccus fontiphilus MVW-1 (96.4% similarity). The major fatty acid was identified as C ω7c (77.6%). The predominant respiratory quinone was ubiquinone-10 (Q-10). Polar lipid analysis indicated the presence of phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidylcholine (PC), diphosphatidylglycerol (DPG), an unidentified lipid (L), and three unidentified phospholipids (PL1-PL3). Based on the draft genome sequence, the DNA G + C content of the strain was 67.1 mol%, and the values of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) of strain YIM 132242 with Paracoccus aerius KCTC 42845 were 85.4% and 29.1%, respectively. On the basis of the data from this polyphasic characterization, strain YIM 132242 represents a novel species of the genus Paracoccus, for which the name Paracoccus lichenicola sp. nov. is proposed. The type strain is YIM 132242 (= KCTC 72463 = CGMCC1.17191).
Topics: Bacterial Typing Techniques; China; DNA, Bacterial; Fatty Acids; Lichens; Paracoccus; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 33388938
DOI: 10.1007/s00284-020-02321-8 -
Journal of Bacteriology Apr 2023The periplasmic (NAP) and membrane-associated (Nar) nitrate reductases of Paracoccus denitrificans are responsible for nitrate reduction under aerobic and anaerobic...
The periplasmic (NAP) and membrane-associated (Nar) nitrate reductases of Paracoccus denitrificans are responsible for nitrate reduction under aerobic and anaerobic conditions, respectively. Expression of NAP is elevated in cells grown on a relatively reduced carbon and energy source (such as butyrate); it is believed that NAP contributes to redox homeostasis by coupling nitrate reduction to the disposal of excess reducing equivalents. Here, we show that deletion of either (one of two homologs in the P. denitrificans genome) or / (encoding a bifunctional ppGpp synthetase and hydrolase) eliminates the butyrate-dependent increase in promoter and NAP enzyme activity. We conclude that ppGpp likely signals growth on a reduced substrate and, together with DksA1, mediates increased expression of the genes encoding NAP. Support for this model comes from the observation that promoter activity is increased in cultures exposed to a protein synthesis inhibitor that is known to trigger ppGpp synthesis in other organisms. We also show that, under anaerobic growth conditions, the redox-sensing RegAB two-component pair acts as a negative regulator of NAP expression and as a positive regulator of expression of the membrane-associated nitrate reductase Nar. The and / genes are conditionally synthetically lethal; the double mutant has a null phenotype for growth on butyrate and other reduced substrates while growing normally on succinate and citrate. We also show that the second homolog () and / have roles in regulation of expression of the flavohemoglobin Hmp and in biofilm formation. Paracoccus denitrificans is a metabolically versatile Gram-negative bacterium that is used as a model for studies of respiratory metabolism. The organism can utilize nitrate as an electron acceptor for anaerobic respiration, reducing it to dinitrogen via nitrite, nitric oxide, and nitrous oxide. This pathway (known as denitrification) is important as a route for loss of fixed nitrogen from soil and as a source of the greenhouse gas nitrous oxide. Thus, it is important to understand those environmental and genetic factors that govern flux through the denitrification pathway. Here, we identify four proteins and a small molecule (ppGpp) which function as previously unknown regulators of expression of enzymes that reduce nitrate and oxidize nitric oxide.
Topics: Nitrates; Paracoccus denitrificans; Guanosine Tetraphosphate; Nitrous Oxide; Nitric Oxide; Nitrate Reductase; Nitrate Reductases; Respiration; Butyrates
PubMed: 36920204
DOI: 10.1128/jb.00027-23 -
International Journal of Systematic and... Feb 2020Two strains, designated 2251 and 3058, that were aerobic, Gram-stain-negative, non-motile, coccoid or short rod-shaped bacilli, have recently been isolated from Tibetan...
Two strains, designated 2251 and 3058, that were aerobic, Gram-stain-negative, non-motile, coccoid or short rod-shaped bacilli, have recently been isolated from Tibetan antelopes on the Qinghai-Tibet Plateau. The results of phylogenetic analyses of 16S rRNA gene sequences indicated that strains 2251 and 3058 represent a new species within the genus and are most similar to '' CUG00006 (98.9 and 99.3 %), I-41R45 (98.3 and 98.7 %) and THG-T2.31 (97.6 and 97.8 %). Results of genomic sequence-based phylogenomic analysis agreed with those from 16S rRNA gene sequence analysis. Optimal growth was achieved at pH 7.0-7.5 and 28 °C with marine medium. Cells contained C 7 as the major cellular fatty acid and ubiquinone-10 as the predominant menaquinone. The polar lipids comprised phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phospholipid, glycolipid and an unidentified lipid. The cell-wall peptidoglycan amino acids were meso-2,6-diaminopimelic acid, alanine and glutamic acid; the major cell-wall sugar was galactose. The G+C content of strain 2251 was 66.5 mol%. Both strains (2251 and 3058) had DNA-DNA relatedness values less than 50 % with all available genomes of the genus in the ncbi database. Differential genotypic inferences, together with phenotypic and biochemical characteristics, demonstrated that strains 2251 and 3058 should be classified as a novel species of the genus , for which the name sp. nov. is suggested. The type strain is 2251 (=CGMCC 1.16490=DSM 106269).
Topics: Animals; Antelopes; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Diaminopimelic Acid; Fatty Acids; Feces; Nucleic Acid Hybridization; Paracoccus; Peptidoglycan; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Tibet; Ubiquinone
PubMed: 31674893
DOI: 10.1099/ijsem.0.003807 -
Chemical Communications (Cambridge,... Apr 2015Nature's smartness and efficient assembling cascade type reactions inspired biologists and chemists all around the world. Tremendous effort has been directed towards the... (Review)
Review
Nature's smartness and efficient assembling cascade type reactions inspired biologists and chemists all around the world. Tremendous effort has been directed towards the understanding and mimicking of such networks. In recent years considerable progress has been made in developing multistep one-pot reactions combining either advantage of chemo-, regio-, and stereoselectivity of biocatalysts or promiscuity and productivity of chemocatalysts. In this context several concepts, inspired by different disciplines (biocatalysis, metabolic engineering, synthetic chemistry, and material science), have been evolved. This review will focus on major contributions in the field of cascade reactions over the last three years.
Topics: Bacillus subtilis; Bacterial Proteins; Biocatalysis; Escherichia coli; Metabolic Engineering; Mutagenesis, Site-Directed; Paracoccus denitrificans; Protein Engineering; Synthetic Biology
PubMed: 25654472
DOI: 10.1039/c4cc08752f -
Archives of Biochemistry and Biophysics Jun 2024Paracoccus denitrificans has a classical cytochrome-dependent electron transport chain and two alternative oxidases. The classical transport chain is very similar to...
Paracoccus denitrificans has a classical cytochrome-dependent electron transport chain and two alternative oxidases. The classical transport chain is very similar to that in eukaryotic mitochondria. Thus, P. denitrificans can serve as a model of the mammalian mitochondrion that may be more tractable in elucidating mechanisms of regulation of energy production than are mitochondria. In a previous publication we reported detailed studies on respiration in P. denitrificans grown aerobically on glucose or malate. We noted that P. denitrificans has large stores of lactate under various growth conditions. This is surprising because P. denitrificans lacks an NAD-dependent lactate dehydrogenase. The aim of this study was to investigate the mechanisms of lactate oxidation in P. denitrificans. We found that the bacterium grows well on either d-lactate or l-lactate. Growth on lactate supported a rate of maximum respiration that was equal to that of cells grown on glucose or malate. We report proteomic, metabolomic, and biochemical studies that establish that the metabolism of lactate by P. denitrificans is mediated by two non-NAD-dependent lactate dehydrogenases. One prefers d-lactate over l-lactate (D-iLDH) and the other prefers l-lactate (L-iLDH). We cloned and produced the D-iLDH and characterized it. The K for d-lactate was 34 μM, and for l-lactate it was 3.7 mM. Pyruvate was not a substrate, rendering the reaction unidirectional with lactate being converted to pyruvate for entry into the TCA cycle. The intracellular lactate was ∼14 mM such that both isomers could be metabolized by the enzyme. The enzyme has 1 FAD per molecule and utilizes a quinone rather than NAD as an electron acceptor. D-iLDH provides a direct entry of lactate reducing equivalents into the cytochrome chain, potentially explaining the high respiratory capacity of P. denitrificans in the presence of lactate.
Topics: Paracoccus denitrificans; Oxidation-Reduction; Lactic Acid; Glucose
PubMed: 38631502
DOI: 10.1016/j.abb.2024.109988 -
Advances in Experimental Medicine and... 2021Paracoccus carotinifaciens is an aerobic Gram-negative bacterium that exhibits motility by a peritrichous flagellum. It produces a carotenoid mixture containing...
Paracoccus carotinifaciens is an aerobic Gram-negative bacterium that exhibits motility by a peritrichous flagellum. It produces a carotenoid mixture containing astaxanthin as the main component. Selective breeding of P. carotinifaciens has been performed using classical techniques for mutation induction, such as chemical treatment and ultraviolet irradiation, and not using genetic engineering technology. The commercial production of astaxanthin with P. carotinifaciens has been established by optimizing fermentation medium and conditions in the process. Dehydrated P. carotinifaciens is used as a coloring agent for farmed fish and egg yolks. Compared with the administration of chemically synthesized astaxanthin, dehydrated P. carotinifaciens imparts more natural coloration, which is favored by consumers. In addition, astaxanthin-rich carotenoid extracts (ARE) derived from P. carotinifaciens are developed for human nutrition. Animal and clinical studies with ARE for evaluating its efficacy have been conducted and suggested that ARE would be useful for preventing anxiety, stomach ulcer, and retinal damage, as well as improving cognitive function. The efficacy is anticipated to result from not only astaxanthin but also other carotenoids in ARE, such as adonirubin and adonixanthin, in some studies. Hence, astaxanthin commercially produced with P. carotinifaciens has been applied widely in animals and humans.
Topics: Animals; Anxiety; Humans; Paracoccus; Xanthophylls
PubMed: 33783727
DOI: 10.1007/978-981-15-7360-6_2 -
Bioresource Technology Jun 2024The construction of aerobic denitrification (AD) systems in an antibiotic-stressed environment is a serious challenge. This study investigated strategy of cyclic stress... (Review)
Review
The construction of aerobic denitrification (AD) systems in an antibiotic-stressed environment is a serious challenge. This study investigated strategy of cyclic stress with concentration gradient (5-30 mg/L) of sulfamethoxazole (SMX) in a sequencing batch reactor (SBR), to achieve operation of AD. Total nitrogen removal efficiency of system increased from about 10 % to 95 %. Original response of abundant-rare genera to antibiotics was changed by SMX stress, particularly conditionally rare or abundant taxa (CRAT). AD process depends on synergistic effect of heterotrophic nitrifying aerobic denitrification bacteria (Paracoccus, Thauera, Hypomicrobium, etc). AmoABC, napA, and nirK were functionally co-expressed with multiple antibiotic resistance genes (ARGs) (acrR, ereAB, and mdtO), facilitating AD process. ARGs and TCA cycling synergistically enhance the antioxidant and electron transport capacities of AD process. Antibiotic efflux pump mechanism played an important role in operation of AD. The study provides strong support for regulating activated sludge to achieve in situ AD function.
Topics: Denitrification; Sulfamethoxazole; Bioreactors; Aerobiosis; Sewage; Anti-Bacterial Agents; Nitrogen; Bacteria; Stress, Physiological
PubMed: 38710419
DOI: 10.1016/j.biortech.2024.130801 -
Molecules (Basel, Switzerland) Feb 2020Methomyl is a broad-spectrum oxime carbamate commonly used to control arthropods, nematodes, flies, and crop pests. However, extensive use of this pesticide in... (Review)
Review
Methomyl is a broad-spectrum oxime carbamate commonly used to control arthropods, nematodes, flies, and crop pests. However, extensive use of this pesticide in agricultural practices has led to environmental toxicity and human health issues. Oxidation, incineration, adsorption, and microbial degradation methods have been developed to remove insecticidal residues from soil/water environments. Compared with physicochemical methods, biodegradation is considered to be a cost-effective and ecofriendly approach to the removal of pesticide residues. Therefore, micro-organisms have become a key component of the degradation and detoxification of methomyl through catabolic pathways and genetic determinants. Several species of methomyl-degrading bacteria have been isolated and characterized, including , , , , , , , , and . The degradation pathways of methomyl and the fate of several metabolites have been investigated. Further in-depth studies based on molecular biology and genetics are needed to elaborate their role in the evolution of novel catabolic pathways and the microbial degradation of methomyl. In this review, we highlight the mechanism of microbial degradation of methomyl along with metabolic pathways and genes/enzymes of different genera.
Topics: Adsorption; Alcaligenes; Bacillus; Biodegradation, Environmental; Cholinesterase Inhibitors; Flavobacterium; Humans; Incineration; Insecticides; Metabolic Networks and Pathways; Methomyl; Oxidation-Reduction; Paracoccus; Pseudomonas; Serratia; Soil Pollutants; Trametes; Water Pollutants, Chemical
PubMed: 32046287
DOI: 10.3390/molecules25030738