1
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Joshi S, Gangola S, Jaggi V, Sahgal M. Functional characterization and molecular fingerprinting of potential phosphate solubilizing bacterial candidates from Shisham rhizosphere. Sci Rep 2023; 13:7003. [PMID: 37117212 PMCID: PMC10147649 DOI: 10.1038/s41598-023-33217-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/10/2023] [Indexed: 04/30/2023] Open
Abstract
Phosphate solubilizing bacteria (PSB) are important role players in plant growth promotion. In the present study, we aimed to screen the functionally active phosphate solubilizing bacteria (PSB) associated with Dalbergia sissoo Roxb. (Shisham) from different provenances. Screening for phosphate solubilization was done on Pikovskaya's agar, and 18 bacteria positive for the tri-calcium phosphate (Ca3(PO4)2 solubilization showing visible dissolution halo zones were identified. All 18 isolates showed zinc solubilization, indole acetic acid (IAA), siderophore, and hydrogen cyanide (HCN) production. The morphological and biochemical characterization with 16S rDNA gene-based phylogenetic analysis identified bacterial strains as belonging to the genus Pseudomonas, Klebsiella, Streptomyces, Pantoea, Kitasatospora, Micrococcus, and Staphylococcus. Among all the isolates, one of the isolates named L4, from Lacchiwala region was the most efficient P solubilizer with a high P solubilization index (4.75 ± 0.06) and quantitative P solubilization activity (891.38 ± 18.55 μg mL-1). The validation of phosphate solubilization activity of PSB isolates was done by amplification of the Pyrroloquinoline quinone (PQQ) genes, pqqA and pqqC. Based on this study, we have selected the bacterial strains which are efficient phosphate solubilizers and could be economical and eco-friendly in plant growth promotion, disease suppression, as an antioxidant, and for subsequent enhancement of yield.
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Affiliation(s)
- Samiksha Joshi
- School of Agriculture, Graphic Era Hill University, Bhimtal, 263136, India
| | - Saurabh Gangola
- School of Agriculture, Graphic Era Hill University, Bhimtal, 263136, India
| | - Vandana Jaggi
- Department of Microbiology, GB Pant University of Agriculture and Technology, Pantnagar, 263145, India
| | - Manvika Sahgal
- Department of Microbiology, GB Pant University of Agriculture and Technology, Pantnagar, 263145, India.
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2
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Casella LG, Torres NJ, Tomlinson BR, Shepherd M, Shaw LN. The novel two-component system AmsSR governs alternative metabolic pathway usage in Acinetobacter baumannii. Front Microbiol 2023; 14:1139253. [PMID: 37082186 PMCID: PMC10112286 DOI: 10.3389/fmicb.2023.1139253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/15/2023] [Indexed: 04/22/2023] Open
Abstract
In this study, we identify a novel two-component system in Acinetobacter baumannii (herein named AmsSR for regulator of alternative metabolic systems) only present in select gammaproteobacterial and betaproteobacterial species. Bioinformatic analysis revealed that the histidine kinase, AmsS, contains 14 predicted N-terminal transmembrane domains and harbors a hybrid histidine kinase arrangement in its C-terminus. Transcriptional analysis revealed the proton ionophore CCCP selectively induces P amsSR expression. Disruption of amsSR resulted in decreased intracellular pH and increased depolarization of cytoplasmic membranes. Transcriptome profiling revealed a major reordering of metabolic circuits upon amsR disruption, with energy generation pathways typically used by bacteria growing in limited oxygen being favored. Interestingly, we observed enhanced growth rates for mutant strains in the presence of glucose, which led to overproduction of pyruvate. To mitigate the toxic effects of carbon overflow, we noted acetate overproduction in amsSR-null strains, resulting from a hyperactive Pta-AckA pathway. Additionally, due to altered expression of key metabolic genes, amsSR mutants favor an incomplete TCA cycle, relying heavily on an overactive glyoxylate shunt. This metabolic reordering overproduces NADH, which is not oxidized by the ETC; components of which were significantly downregulated upon amsSR disruption. As a result, the mutants almost exclusively rely on substrate phosphorylation for ATP production, and consequently display reduced oxygen consumption in the presence of glucose. Collectively, our data suggests that disruption of amsSR affects the function of the aerobic respiratory chain, impacting the energy status of the cell, which in turn upregulates alternative metabolic and energy generation pathways.
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Affiliation(s)
- Leila G. Casella
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, United States
| | - Nathanial J. Torres
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, United States
| | - Brooke R. Tomlinson
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, United States
| | - Mark Shepherd
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Lindsey N. Shaw
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, United States
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3
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Clark KA, Bushin LB, Seyedsayamdost MR. RaS-RiPPs in Streptococci and the Human Microbiome. ACS BIO & MED CHEM AU 2022; 2:328-339. [PMID: 35996476 PMCID: PMC9389541 DOI: 10.1021/acsbiomedchemau.2c00004] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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Radical S-adenosylmethionine (RaS) enzymes have
quickly advanced to one of the most abundant and versatile enzyme
superfamilies known. Their chemistry is predicated upon reductive
homolytic cleavage of a carbon–sulfur bond in cofactor S-adenosylmethionine forming an oxidizing carbon-based radical,
which can initiate myriad radical transformations. An emerging role
for RaS enzymes is their involvement in the biosynthesis of ribosomally
synthesized and post-translationally modified peptides (RiPPs), a
natural product family that has become known as RaS-RiPPs. These metabolites
are especially prevalent in human and mammalian microbiomes because
the complex chemistry of RaS enzymes gives rise to correspondingly
complex natural products with minimal cellular energy and genomic
fingerprint, a feature that is advantageous in microbes with small,
host-adapted genomes in competitive environments. Herein, we review
the discovery and characterization of RaS-RiPPs from the human microbiome
with a focus on streptococcal bacteria. We discuss the varied chemical
modifications that RaS enzymes introduce onto their peptide substrates
and the diverse natural products that they give rise to. The majority
of RaS-RiPPs remain to be discovered, providing an intriguing avenue
for future investigations at the intersection of metalloenzymology,
chemical ecology, and the human microbiome.
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Affiliation(s)
- Kenzie A Clark
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Leah B Bushin
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States.,Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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4
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Abstract
The widely distributed, essential redox factor pyrroloquinoline quinone (PQQ, methoxatin) (1) was discovered in the mid-1960s. The breadth and depth of its biological effects are steadily being revealed, and understanding its biosynthesis at the genomic level is a continuing process. In this review, aspects of the chemistry, biology, biosynthesis, and commercial production of 1 at the gene level, and some applications, are presented from discovery through to mid-2021.
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Affiliation(s)
- Geoffrey A Cordell
- Natural Products Inc., Evanston, Illinois 60202, United States.,Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
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5
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Benjdia A, Berteau O. Radical SAM Enzymes and Ribosomally-Synthesized and Post-translationally Modified Peptides: A Growing Importance in the Microbiomes. Front Chem 2021; 9:678068. [PMID: 34350157 PMCID: PMC8326336 DOI: 10.3389/fchem.2021.678068] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
To face the current antibiotic resistance crisis, novel strategies are urgently required. Indeed, in the last 30 years, despite considerable efforts involving notably high-throughput screening and combinatorial libraries, only few antibiotics have been launched to the market. Natural products have markedly contributed to the discovery of novel antibiotics, chemistry and drug leads, with more than half anti-infective and anticancer drugs approved by the FDA being of natural origin or inspired by natural products. Among them, thanks to their modular structure and simple biosynthetic logic, ribosomally synthesized and posttranslationally modified peptides (RiPPs) are promising scaffolds. In addition, recent studies have highlighted the pivotal role of RiPPs in the human microbiota which remains an untapped source of natural products. In this review, we report on recent developments in radical SAM enzymology and how these unique biocatalysts have been shown to install complex and sometimes unprecedented posttranslational modifications in RiPPs with a special focus on microbiome derived enzymes.
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Affiliation(s)
- Alhosna Benjdia
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Olivier Berteau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
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6
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Miah R, Nina S, Murate T, Kataoka N, Matsutani M, Matsushita K, Yakushi T. Major aldehyde dehydrogenase AldFGH of Gluconacetobacter diazotrophicus is independent of pyrroloquinoline quinone but dependent on molybdopterin for acetic acid fermentation. Appl Microbiol Biotechnol 2021; 105:2341-2350. [PMID: 33591385 DOI: 10.1007/s00253-021-11144-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/12/2021] [Accepted: 01/26/2021] [Indexed: 11/28/2022]
Abstract
Acetic acid fermentation involves the oxidation of ethanol to acetic acid via acetaldehyde as the intermediate and is catalyzed by the membrane-bound alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) of acetic acid bacteria. Although ADH depends on pyrroloquinoline quinone (PQQ), the prosthetic group associated with ALDH remains a matter of debate. This study aimed to address the dependency of ALDH of Gluconacetobacter diazotrophicus strain PAL5 on PQQ and the physiological role of ALDH in acetic acid fermentation. We constructed deletion mutant strains for both the ALDH gene clusters of PAL5, aldFGH and aldSLC. In addition, the adhAB operon for ADH was eliminated, since it shows ALDH activity. The triple-deletion derivative ΔaldFGH ΔaldSLC ΔadhAB failed to show ALDH activity, which suggested that ALDH activity in PAL5 is derived from these three enzyme complexes. Since the single-gene cluster deletion derivative ΔaldFGH lost most ALDH activity, and accumulated much higher acetaldehyde than wild type under acetic acid fermentation conditions, we concluded that AldFGH functions as the major ALDH in PAL5. Furthermore, deletion of the PQQ biosynthesis gene cluster (pqqABCDE) abolished ADH activity completely, but did not affect ALDH activity. Instead, the molybdopterin biosynthesis gene deletion derivatives lost ALDH activity. Thus, we concluded that the AldFGH and AldSLC complexes of Ga. diazotrophicus PAL5 require a form of molybdopterin but not PQQ for ALDH activity. KEY POINTS: • AldFGH is the major aldehyde dehydrogenase in Gluconacetobacter diazotrophicus PAL5. • Acetaldehyde accumulated from ethanol in the absence of AldFGH. • Molybdopterin, rather than pyrroloquinoline quinone, is required for AldFGH.
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Affiliation(s)
- Roni Miah
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Shun Nina
- Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Takeru Murate
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Naoya Kataoka
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan.,Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515, Japan.,Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Minenosuke Matsutani
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Kazunobu Matsushita
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan.,Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515, Japan.,Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Toshiharu Yakushi
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan. .,Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515, Japan. .,Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, 753-8515, Japan.
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7
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Zhu W, Klinman JP. Biogenesis of the peptide-derived redox cofactor pyrroloquinoline quinone. Curr Opin Chem Biol 2020; 59:93-103. [PMID: 32731194 PMCID: PMC7736144 DOI: 10.1016/j.cbpa.2020.05.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 12/15/2022]
Abstract
Pyrroloquinoline quinone (PQQ) is a peptide-derived redox cofactor produced by prokaryotes that also plays beneficial roles in organisms from other kingdoms. We review recent developments on the pathway of PQQ biogenesis, focusing on the mechanisms of PqqE, PqqF/G, and PqqB. These advances may shed light on other, uncharacterized biosynthetic pathways.
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Affiliation(s)
- Wen Zhu
- California Institute for Quantitative Biosciences and Department of Chemistry, University of California, Berkeley, CA, 94720-3220, USA
| | - Judith P Klinman
- California Institute for Quantitative Biosciences and Department of Chemistry, University of California, Berkeley, CA, 94720-3220, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720-3220, USA.
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8
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Alaylar B, Egamberdieva D, Gulluce M, Karadayi M, Arora NK. Integration of molecular tools in microbial phosphate solubilization research in agriculture perspective. World J Microbiol Biotechnol 2020; 36:93. [DOI: 10.1007/s11274-020-02870-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 06/12/2020] [Indexed: 01/23/2023]
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9
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Steric complementarity directs sequence promiscuous leader binding in RiPP biosynthesis. Proc Natl Acad Sci U S A 2019; 116:24049-24055. [PMID: 31719203 DOI: 10.1073/pnas.1908364116] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enzymes that generate ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products have garnered significant interest, given their ability to produce large libraries of chemically diverse scaffolds. Such RiPP biosynthetic enzymes are predicted to bind their corresponding peptide substrates through sequence-specific recognition of the leader sequence, which is removed after the installation of posttranslational modifications on the core sequence. The conservation of the leader sequence within a given RiPP class, in otherwise disparate precursor peptides, further supports the notion that strict sequence specificity is necessary for leader peptide engagement. Here, we demonstrate that leader binding by a biosynthetic enzyme in the lasso peptide class of RiPPs is directed by a minimal number of hydrophobic interactions. Biochemical and structural data illustrate how a single leader-binding domain can engage sequence-divergent leader peptides using a conserved motif that facilitates hydrophobic packing. The presence of this simple motif in noncognate peptides results in low micromolar affinity binding by binding domains from several different lasso biosynthetic systems. We also demonstrate that these observations likely extend to other RiPP biosynthetic classes. The portability of the binding motif opens avenues for the engineering of semisynthetic hybrid RiPP products.
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10
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Raghuvanshi R, Chaudhari A, Kumar GN. 2-Ketogluconic acid and pyrroloquinoline quinone secreting probiotic Escherichia coli Nissle 1917 as a dietary strategy against heavy metal induced damage in rats. J Funct Foods 2017. [DOI: 10.1016/j.jff.2017.08.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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11
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Bruender NA, Bandarian V. The Creatininase Homolog MftE from Mycobacterium smegmatis Catalyzes a Peptide Cleavage Reaction in the Biosynthesis of a Novel Ribosomally Synthesized Post-translationally Modified Peptide (RiPP). J Biol Chem 2017; 292:4371-4381. [PMID: 28077628 DOI: 10.1074/jbc.m116.762062] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 01/03/2017] [Indexed: 11/06/2022] Open
Abstract
Most ribosomally synthesized and post-translationally modified peptide (RiPP) natural products are processed by tailoring enzymes to create complex natural products that are still recognizably peptide-based. However, some tailoring enzymes dismantle the peptide en route to synthesis of small molecules. A small molecule natural product of as yet unknown structure, mycofactocin, is thought to be synthesized in this way via the mft gene cluster found in many strains of mycobacteria. This cluster harbors at least six genes, which appear to be conserved across species. We have previously shown that one enzyme from this cluster, MftC, catalyzes the oxidative decarboxylation of the C-terminal Tyr of the substrate peptide MftA in a reaction that requires the MftB protein. Herein we show that mftE encodes a creatininase homolog that catalyzes cleavage of the oxidatively decarboxylated MftA peptide to liberate its final two residues, including the C-terminal decarboxylated Tyr (VY*). Unlike MftC, which requires MftB for function, MftE catalyzes the cleavage reaction in the absence of MftB. The identification of this novel metabolite, VY*, supports the notion that the mft cluster is involved in generating a small molecule from the MftA peptide. The ability to produce VY* from MftA by in vitro reconstitution of the activities of MftB, MftC, and MftE sets the stage for identification of the novel metabolite that results from the proteins encoded by the mft cluster.
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Affiliation(s)
- Nathan A Bruender
- From the Department of Chemistry, University of Utah, Salt Lake City, Utah 84112
| | - Vahe Bandarian
- From the Department of Chemistry, University of Utah, Salt Lake City, Utah 84112
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12
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Pradhan A, Pahari A, Mohapatra S, Mishra BB. Phosphate-Solubilizing Microorganisms in Sustainable Agriculture: Genetic Mechanism and Application. ADVANCES IN SOIL MICROBIOLOGY: RECENT TRENDS AND FUTURE PROSPECTS 2017. [DOI: 10.1007/978-981-10-7380-9_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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13
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Evans RL, Latham JA, Klinman JP, Wilmot CM, Xia Y. (1)H, (13)C, and (15)N resonance assignments and secondary structure information for Methylobacterium extorquens PqqD and the complex of PqqD with PqqA. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:385-389. [PMID: 27638737 PMCID: PMC5224828 DOI: 10.1007/s12104-016-9705-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Accepted: 08/31/2016] [Indexed: 06/06/2023]
Abstract
The ribosomally synthesized and post-translationally modified peptide (RiPP), pyrroloquinoline quinone (PQQ), is a dehydrogenase cofactor synthesized by, but not exclusively used by, certain prokaryotes. RiPPs represent a rapidly expanding and diverse class of natural products-many of which have therapeutic potential-and the biosynthetic pathways for these are gaining attention. Five gene products from the pqq operon (PqqA, PqqB, PqqC, PqqD, and PqqE) are essential for PQQ biosynthesis. The substrate is the peptide PqqA, which is presented to the radical SAM enzyme PqqE by the small protein PqqD. PqqA is unstructured in solution, and only binds to PqqE when in complex with PqqD. PqqD is a member of a growing family of RiPP chaperone proteins (or domains in most cases) that present their associated peptide substrates to the initial RiPP biosynthesis enzymes. An X-ray crystal structure exists for dimeric Xanthomonas campestris PqqD (PDB ID: 3G2B), but PqqD is now known to act as a monomer under physiological conditions. In this study, the PqqD truncation from naturally fused Methylobacterium extorquens (Mex) PqqCD was overexpressed in Escherichia coli and MexPqqA was chemically synthesized. Solution NMR (1)H-,(15)N-HSQC chemical shift studies have identified the PqqD residues involved in binding PqqA, and (1)H, (13)C, and (15)N peak assignments for PqqD alone and for PqqD bound to PqqA are reported herein.
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Affiliation(s)
- Robert L Evans
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Saint Paul, MN, 55108, USA
| | - John A Latham
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80208, USA
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Carrie M Wilmot
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Saint Paul, MN, 55108, USA.
| | - Youlin Xia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Saint Paul, MN, 55108, USA
- Minnesota NMR Center, University of Minnesota, Twin Cities, Minneapolis, MN, 55455, USA
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14
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Overexpression of pyrroloquinoline quinone biosynthetic genes affects l -sorbose production in Gluconobacter oxydans WSH-003. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2016.04.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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15
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Regulation of Pyrroloquinoline Quinone-Dependent Glucose Dehydrogenase Activity in the Model Rhizosphere-Dwelling Bacterium Pseudomonas putida KT2440. Appl Environ Microbiol 2016; 82:4955-64. [PMID: 27287323 DOI: 10.1128/aem.00813-16] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/25/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Soil-dwelling microbes solubilize mineral phosphates by secreting gluconic acid, which is produced from glucose by a periplasmic glucose dehydrogenase (GDH) that requires pyrroloquinoline quinone (PQQ) as a redox coenzyme. While GDH-dependent phosphate solubilization has been observed in numerous bacteria, little is known concerning the mechanism by which this process is regulated. Here we use the model rhizosphere-dwelling bacterium Pseudomonas putida KT2440 to explore GDH activity and PQQ synthesis, as well as gene expression of the GDH-encoding gene (gcd) and PQQ biosynthesis genes (pqq operon) while under different growth conditions. We also use reverse transcription-PCR to identify transcripts from the pqq operon to more accurately map the operon structure. GDH specific activity and PQQ levels vary according to growth condition, with the highest levels of both occurring when glucose is used as the sole carbon source and under conditions of low soluble phosphate. Under these conditions, however, PQQ levels limit in vitro phosphate solubilization. GDH specific activity data correlate well with gcd gene expression data, and the levels of expression of the pqqF and pqqB genes mirror the levels of PQQ synthesized, suggesting that one or both of these genes may serve to modulate PQQ levels according to the growth conditions. The pqq gene cluster (pqqFABCDEG) encodes at least two independent transcripts, and expression of the pqqF gene appears to be under the control of an independent promoter and terminator. IMPORTANCE Plant growth promotion can be enhanced by soil- and rhizosphere-dwelling bacteria by a number of different methods. One method is by promoting nutrient acquisition from soil. Phosphorus is an essential nutrient that plants obtain through soil, but in many cases it is locked up in forms that are not available for plant uptake. Bacteria such as the model bacterium Pseudomonas putida KT2440 can solubilize insoluble soil phosphates by secreting gluconic acid. This chemical is produced from glucose by the activity of the bacterial enzyme glucose dehydrogenase, which requires a coenzyme called PQQ. Here we have studied how the glucose dehydrogenase enzyme and the PQQ coenzyme are regulated according to differences in bacterial growth conditions. We determined that glucose dehydrogenase activity and PQQ production are optimal under conditions when the bacterium is grown with glucose as the sole carbon source and under conditions of low soluble phosphate.
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16
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Ludueña LM, Anzuay MS, Angelini JG, Barros G, Luna MF, Monge MDP, Fabra A, Taurian T. Role of bacterial pyrroloquinoline quinone in phosphate solubilizing ability and in plant growth promotion on strain Serratia sp. S119. Symbiosis 2016. [DOI: 10.1007/s13199-016-0434-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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17
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Bruender NA, Bandarian V. The Radical S-Adenosyl-l-methionine Enzyme MftC Catalyzes an Oxidative Decarboxylation of the C-Terminus of the MftA Peptide. Biochemistry 2016; 55:2813-6. [PMID: 27158836 DOI: 10.1021/acs.biochem.6b00355] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ribosomally synthesized post-translationally modified peptides (RiPPs) are encoded in the genomes of a wide variety of microorganisms, in the proximity of open reading frames that encode enzymes that conduct extensive modifications, many of which are novel. Recently, members of the radical S-adenosyl-l-methionine (SAM) superfamily have been identified in these biosynthetic clusters. Herein, we demonstrate the putative radical SAM enzyme, MftC, oxidatively decarboxylates the C-terminus of the MftA peptide in the presence of the accessory protein MftB. The reaction catalyzed by MftC expands the repertoire of peptide-based radical SAM chemistry beyond the intramolecular cross-links.
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Affiliation(s)
- Nathan A Bruender
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
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18
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Maharjan S, Sakai Y, Hoseki J. Screening of dietary antioxidants against mitochondria-mediated oxidative stress by visualization of intracellular redox state. Biosci Biotechnol Biochem 2016; 80:726-34. [DOI: 10.1080/09168451.2015.1123607] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Abstract
Mitochondrial impairment and the resulting generation of reactive oxygen species (ROS) have been associated with aging and its related pathological conditions. Recently, dietary antioxidants have gained significant attention as potential preventive and therapeutic agents against ROS-generated aging and pathological conditions. We previously demonstrated that food-derived antioxidants prevented intracellular oxidative stress under proteasome inhibition conditions, which was attributed to mitochondrial dysfunction and ROS generation, followed by cell death. Here, we further screened dietary antioxidants for their activity as redox modulators by visualization of the redox state using Redoxfluor, a fluorescent protein redox probe. Direct alleviation of ROS by antioxidants, but not induction of antioxidative enzymes, prevented mitochondria-mediated intracellular oxidation. The effective antioxidants scavenged mitochondrial ROS and suppressed cell death. Our study indicates that redox visualization under mitochondria-mediated oxidative stress is useful for screening potential antioxidants to counteract mitochondrial dysfunction, which has been implicated in aging and the pathogenesis of aging-related diseases.
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Affiliation(s)
- Sunita Maharjan
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Research Unit for Physiological Chemistry, The Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan
| | - Jun Hoseki
- Research Unit for Physiological Chemistry, The Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan
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Yang XP, Li PP, Hu XM, Ye JB, Liu Y, Ma K, Mao DB. UPLC-DAD-MS/MS Method for Analysis of PQQ in Fermentation Broth. Chromatographia 2015. [DOI: 10.1007/s10337-015-2932-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Tsurumaru H, Okubo T, Okazaki K, Hashimoto M, Kakizaki K, Hanzawa E, Takahashi H, Asanome N, Tanaka F, Sekiyama Y, Ikeda S, Minamisawa K. Metagenomic analysis of the bacterial community associated with the taproot of sugar beet. Microbes Environ 2015; 30:63-9. [PMID: 25740621 PMCID: PMC4356465 DOI: 10.1264/jsme2.me14109] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We analyzed a metagenome of the bacterial community associated with the taproot of sugar beet (Beta vulgaris L.) in order to investigate the genes involved in plant growth-promoting traits (PGPTs), namely 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, indole acetic acid (IAA), N2 fixation, phosphate solubilization, pyrroloquinoline quinone, siderophores, and plant disease suppression as well as methanol, sucrose, and betaine utilization. The most frequently detected gene among the PGPT categories encoded β-1,3-glucanase (18 per 10(5) reads), which plays a role in the suppression of plant diseases. Genes involved in phosphate solubilization (e.g., for quinoprotein glucose dehydrogenase), methanol utilization (e.g., for methanol dehydrogenase), siderophore production (e.g. isochorismate pyruvate lyase), and ACC deaminase were also abundant. These results suggested that such PGPTs are crucially involved in supporting the growth of sugar beet. In contrast, genes for IAA production (iaaM and ipdC) were less abundant (~1 per 10(5) reads). N2 fixation genes (nifHDK) were not detected; bacterial N2 -fixing activity was not observed in the (15)N2 -feeding experiment. An analysis of nitrogen metabolism suggested that the sugar beet microbiome mainly utilized ammonium and nitroalkane as nitrogen sources. Thus, N2 fixation and IAA production did not appear to contribute to sugar beet growth. Taxonomic assignment of this metagenome revealed the high abundance of Mesorhizobium, Bradyrhizobium, and Streptomyces, suggesting that these genera have ecologically important roles in the taproot of sugar beet. Bradyrhizobium-assigned reads in particular were found in almost all categories of dominant PGPTs with high abundance. The present study revealed the characteristic functional genes in the taproot-associated microbiome of sugar beet, and suggest the opportunity to select sugar beet growth-promoting bacteria.
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Klinman JP, Bonnot F. Intrigues and intricacies of the biosynthetic pathways for the enzymatic quinocofactors: PQQ, TTQ, CTQ, TPQ, and LTQ. Chem Rev 2014; 114:4343-65. [PMID: 24350630 PMCID: PMC3999297 DOI: 10.1021/cr400475g] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Judith P. Klinman
- Department of Chemistry University of California, Berkeley, California 94720, U.S.A. Supported by the National Institutes of Health (GM025765) to J.P.K
- Department of Molecular and Cell Biology University of California, Berkeley, California 94720, U.S.A. Supported by the National Institutes of Health (GM025765) to J.P.K
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, U.S.A. Supported by the National Institutes of Health (GM025765) to J.P.K
| | - Florence Bonnot
- Department of Chemistry University of California, Berkeley, California 94720, U.S.A. Supported by the National Institutes of Health (GM025765) to J.P.K
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, U.S.A. Supported by the National Institutes of Health (GM025765) to J.P.K
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22
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Broderick JB, Duffus B, Duschene KS, Shepard EM. Radical S-adenosylmethionine enzymes. Chem Rev 2014; 114:4229-317. [PMID: 24476342 PMCID: PMC4002137 DOI: 10.1021/cr4004709] [Citation(s) in RCA: 581] [Impact Index Per Article: 58.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Joan B. Broderick
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Benjamin
R. Duffus
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Kaitlin S. Duschene
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Eric M. Shepard
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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Heterologous expression of pyrroloquinoline quinone (pqq) gene cluster confers mineral phosphate solubilization ability to Herbaspirillum seropedicae Z67. Appl Microbiol Biotechnol 2014; 98:5117-29. [DOI: 10.1007/s00253-014-5610-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 02/10/2014] [Accepted: 02/11/2014] [Indexed: 11/26/2022]
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24
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Du J, Bai W, Song H, Yuan YJ. Combinational expression of sorbose/sorbosone dehydrogenases and cofactor pyrroloquinoline quinone increases 2-keto-L-gulonic acid production in Ketogulonigenium vulgare-Bacillus cereus consortium. Metab Eng 2013; 19:50-6. [PMID: 23747604 DOI: 10.1016/j.ymben.2013.05.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 05/26/2013] [Accepted: 05/30/2013] [Indexed: 11/29/2022]
Abstract
The expression levels of sorbose/sorbosone dehydrogenase genes (sdh and sndh) and the synthesis genes (pqqABCDEN) of the adjoint cofactor pyrroloquinoline quinone (PQQ) were genetically manipulated in Ketogulonigenium vulgare to increase the production of 2-keto-l-gulonic acid (2-KLG), the precursor of vitamin C, in the consortium of K. vulgare and Bacillus cereus. We found that overexpression of sdh-sndh alone in K. vulgare could not significantly enhance the production of 2-KLG, revealing the cofactor PQQ was required for the biosynthesis of 2-KLG. Various expression levels of PQQ were achieved by differential expression of pqqA, pqqABCDE and pqqABCDEN, respectively. The combinatorial expression of sdh/sndh and pqqABCDEN in K. vulgare enabled a 20% increase in the production of 2-KLG (79.1±0.6gl(-1)) than that of the parental K. vulgare (65.9±0.4gl(-1)) in shaking flasks. Our results demonstrated the balanced co-expression of both the key enzymes and the related cofactors was an efficient strategy to increase chemicals' biosynthesis.
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Affiliation(s)
- Jin Du
- Key Laboratory of Systems Bioengineering, Ministry of Education and Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, P.O. Box 6888, Tianjin 300072, PR China
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Arnison PG, Bibb MJ, Bierbaum G, Bowers AA, Bugni TS, Bulaj G, Camarero JA, Campopiano DJ, Challis GL, Clardy J, Cotter PD, Craik DJ, Dawson M, Dittmann E, Donadio S, Dorrestein PC, Entian KD, Fischbach MA, Garavelli JS, Göransson U, Gruber CW, Haft DH, Hemscheidt TK, Hertweck C, Hill C, Horswill AR, Jaspars M, Kelly WL, Klinman JP, Kuipers OP, Link AJ, Liu W, Marahiel MA, Mitchell DA, Moll GN, Moore BS, Müller R, Nair SK, Nes IF, Norris GE, Olivera BM, Onaka H, Patchett ML, Piel J, Reaney MJT, Rebuffat S, Ross RP, Sahl HG, Schmidt EW, Selsted ME, Severinov K, Shen B, Sivonen K, Smith L, Stein T, Süssmuth RD, Tagg JR, Tang GL, Truman AW, Vederas JC, Walsh CT, Walton JD, Wenzel SC, Willey JM, van der Donk WA. Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat Prod Rep 2013; 30:108-60. [PMID: 23165928 DOI: 10.1039/c2np20085f] [Citation(s) in RCA: 1452] [Impact Index Per Article: 132.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This review presents recommended nomenclature for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), a rapidly growing class of natural products. The current knowledge regarding the biosynthesis of the >20 distinct compound classes is also reviewed, and commonalities are discussed.
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Affiliation(s)
- Paul G Arnison
- Prairie Plant Systems Inc, Botanical Alternatives Inc, Suite 176, 8B-3110 8th Street E, Saskatoon, SK, S7H 0W2, Canada
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26
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Lee KK, Mok IK, Yoon MH, Kim HJ, Chung DY. Mechanisms of Phosphate Solubilization by PSB (Phosphate-solubilizing Bacteria) in Soil. ACTA ACUST UNITED AC 2012. [DOI: 10.7745/kjssf.2012.45.2.169] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abstract
Ketogulonicigenium vulgare is characterized by the efficient production of 2KGA from L-sorbose. Ketogulonicigenium vulgare Y25 is known as a 2-keto-L-gulonic acid-producing strain in the vitamin C industry. Here we report the finished, annotated genome sequence of Ketogulonicigenium vulgare Y25.
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Yang XP, Zhong GF, Lin JP, Mao DB, Wei DZ. Pyrroloquinoline quinone biosynthesis in Escherichia coli through expression of the Gluconobacter oxydans pqqABCDE gene cluster. J Ind Microbiol Biotechnol 2010; 37:575-80. [DOI: 10.1007/s10295-010-0703-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Accepted: 02/12/2010] [Indexed: 11/30/2022]
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30
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Wecksler SR, Stoll S, Iavarone AT, Imsand EM, Tran H, Britt RD, Klinman JP. Interaction of PqqE and PqqD in the pyrroloquinoline quinone (PQQ) biosynthetic pathway links PqqD to the radical SAM superfamily. Chem Commun (Camb) 2010; 46:7031-3. [DOI: 10.1039/c0cc00968g] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Sashidhar B, Podile AR. Mineral phosphate solubilization by rhizosphere bacteria and scope for manipulation of the direct oxidation pathway involving glucose dehydrogenase. J Appl Microbiol 2009; 109:1-12. [PMID: 20070432 DOI: 10.1111/j.1365-2672.2009.04654.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microbial biodiversity in the soil plays a significant role in metabolism of complex molecules, helps in plant nutrition and offers countless new genes, biochemical pathways, antibiotics and other metabolites, useful molecules for agronomic productivity. Phosphorus being the second most important macro-nutrient required by the plants, next to nitrogen, its availability in soluble form in the soils is of great importance in agriculture. Microbes present in the soil employ different strategies to make use of unavailable forms of phosphate and in turn also help plants making phosphate available for plant use. Azotobacter, a free-living nitrogen fixer, is known to increase the fertility of the soil and in turn the productivity of different crops. The glucose dehydrogenase gene, the first enzyme in the direct oxidation pathway, contributes significantly to mineral phosphate solubilization ability in several Gram-negative bacteria. It is possible to enhance further the biofertilizer potential of plant growth-promoting rhizobacteria by introducing the genes involved mineral phosphate solubilization without affecting their ability to fix nitrogen or produce phytohormones for dual benefit to agricultural crops. Glucose dehydrogenases from Gram-negative bacteria can be engineered to improve their ability to use different substrates, function at higher temperatures and EDTA tolerance, etc., through site-directed mutagenesis.
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Affiliation(s)
- B Sashidhar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Central University, Hyderabad, Andhra Pradesh, India
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32
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Wecksler SR, Stoll S, Tran H, Magnusson OT, Wu SP, King D, Britt RD, Klinman JP. Pyrroloquinoline quinone biogenesis: demonstration that PqqE from Klebsiella pneumoniae is a radical S-adenosyl-L-methionine enzyme. Biochemistry 2009; 48:10151-61. [PMID: 19746930 DOI: 10.1021/bi900918b] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biogenesis of pyrroloquinoline quinone (PQQ) in Klebsiella pneumoniae requires the expression of six genes (pqqA-F). One of these genes (pqqE) encodes a 43 kDa protein (PqqE) that plays a role in the initial steps in PQQ formation [Veletrop, J. S., et al. (1995) J. Bacteriol. 177, 5088-5098]. PqqE contains two highly conserved cysteine motifs at the N- and C-termini, with the N-terminal motif comprised of a CX(3)CX(2)C consensus sequence that is unique to a family of proteins known as radical S-adenosyl-l-methionine (SAM) enzymes [Sofia, H. J., et al. (2001) Nucleic Acids Res. 29, 1097-1106]. PqqE from K. pneumoniae was cloned into Escherichia coli and expressed as the native protein and with an N-terminal His(6) tag. Anaerobic expression and purification of the His(6)-tagged PqqE results in an enzyme with a brownish-red hue indicative of Fe-S cluster formation. Spectroscopic and physical analyses indicate that PqqE contains a mixture of Fe-S clusters, with the predominant form of the enzyme containing two [4Fe-4S] clusters. PqqE isolated anaerobically yields an active enzyme capable of cleaving SAM to methionine and 5'-deoxyadenosine in an uncoupled reaction (k(obs) = 0.011 +/- 0.001 min(-1)). In this reaction, the 5'-deoxyadenosyl radical either abstracts a hydrogen atom from a solvent accessible position in the enzyme or obtains a proton and electron from buffer. The putative PQQ substrate PqqA has not yet been shown to be modified by PqqE, implying that PqqA must be modified before becoming the substrate for PqqE and/or that another protein in the biosynthetic pathway is critical for the initial steps in PQQ biogenesis.
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Affiliation(s)
- Stephen R Wecksler
- Department of Chemistry and Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
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Gliese N, Khodaverdi V, Görisch H. The PQQ biosynthetic operons and their transcriptional regulation in Pseudomonas aeruginosa. Arch Microbiol 2009; 192:1-14. [PMID: 19902179 DOI: 10.1007/s00203-009-0523-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Revised: 10/14/2009] [Accepted: 10/21/2009] [Indexed: 10/20/2022]
Abstract
Gene PA1990 of Pseudomonas aeruginosa, located downstream of pqqE and encoding a putative peptidase, was shown to be involved in excretion of PQQ into the culture supernatant. This gene is cotranscribed with the pqqABCDE cluster and was named pqqH. A PA1990::Km(r) mutant (VK3) did not show any effect in growth behaviour; however, in contrast to the wild-type, no excretion of PQQ into the culture supernatant was observed. The putative pqqF gene of P. aeruginosa was shown to be essential for PQQ biosynthesis. A pqqF::Km(r) mutant did not grow aerobically on ethanol, because of its inability to produce PQQ. Transcription of the pqqABCDEH operon was induced upon aerobic growth on ethanol, 1-propanol, 1,2-propanediol and 1-butanol, while on glycerol, succinate and acetate, transcription was low. Transcription of the pqqABCDEH operon was also found upon anoxic growth on ethanol with nitrate as electron acceptor, but no PQQ was produced. Expression of the pqqABCDEH operon is regulated at the transcriptional level. In contrast, the pqqF operon appeared to be transcribed constitutively at a very low level under all growth conditions studied.
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Affiliation(s)
- Nicole Gliese
- BioGenes GmbH, Koepenicker Strasse 325, Berlin, Germany
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34
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Guo YB, Li J, Li L, Chen F, Wu W, Wang J, Wang H. Mutations that disrupt either the pqq or the gdh gene of Rahnella aquatilis abolish the production of an antibacterial substance and result in reduced biological control of grapevine crown gall. Appl Environ Microbiol 2009; 75:6792-803. [PMID: 19734331 PMCID: PMC2772458 DOI: 10.1128/aem.00902-09] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Accepted: 08/29/2009] [Indexed: 11/20/2022] Open
Abstract
Rahnella aquatilis HX2, a biocontrol agent for grapevine crown gall caused by Agrobacterium vitis, produces an antibacterial substance that inhibits the growth of A. vitis in vitro. In this study, we show that MH15 and MH16, two Tn5-induced mutants of HX2, have lost their abilities to inhibit A. vitis and have reduced biocontrol activities; they grow in logarithmic phase at a rate similar to that of the wild type and have single Tn5 insertions. They are also impaired in producing pyrroloquinoline quinone (PQQ) or glucose dehydrogenase (GDH). Complementation of MH15 and MH16 with cosmid clones of CP465 and CP104 from an HX2 DNA library restored the antibiosis, biocontrol, and PQQ or GDH production phenotypes. A 6.7-kb BamHI fragment from CP465 that fully restored the MH15-affected phenotypes was cloned and sequenced. Sequence analysis of the mutated DNA region resulted in the identification of seven open reading frames (ORFs), six of which share significant homology with PQQ-synthesizing genes in other bacteria, designated pqqA through pqqF. Meanwhile, A 5.5-kb PstI fragment from CP104 fully complemented the MH16 mutant and contained a single ORF highly similar to that of genes coding for GDHs. An in-frame gdh deletion mutant has the same phenotypes as the Tn5 mutant of MH16. Complementation of both deletion and Tn5 gdh mutants restored the affected phenotypes to wild-type levels. Our results suggest that an antibacterial substance plays a role in biocontrol of A. vitis by HX2.
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Affiliation(s)
- Yan Bin Guo
- Department of Ecological Science and Engineering, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, People's Republic of China, Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, and Key Laboratory of Plant Pathology, Ministry of Agriculture, Beijing 100193, People's Republic of China, Bureau of Fuzhou Landscape Architecture, Liuyi North Road, Fuzhou 350011, Fujian Province, People's Republic of China
| | - Jinyun Li
- Department of Ecological Science and Engineering, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, People's Republic of China, Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, and Key Laboratory of Plant Pathology, Ministry of Agriculture, Beijing 100193, People's Republic of China, Bureau of Fuzhou Landscape Architecture, Liuyi North Road, Fuzhou 350011, Fujian Province, People's Republic of China
| | - Lei Li
- Department of Ecological Science and Engineering, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, People's Republic of China, Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, and Key Laboratory of Plant Pathology, Ministry of Agriculture, Beijing 100193, People's Republic of China, Bureau of Fuzhou Landscape Architecture, Liuyi North Road, Fuzhou 350011, Fujian Province, People's Republic of China
| | - Fan Chen
- Department of Ecological Science and Engineering, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, People's Republic of China, Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, and Key Laboratory of Plant Pathology, Ministry of Agriculture, Beijing 100193, People's Republic of China, Bureau of Fuzhou Landscape Architecture, Liuyi North Road, Fuzhou 350011, Fujian Province, People's Republic of China
| | - Wenliang Wu
- Department of Ecological Science and Engineering, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, People's Republic of China, Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, and Key Laboratory of Plant Pathology, Ministry of Agriculture, Beijing 100193, People's Republic of China, Bureau of Fuzhou Landscape Architecture, Liuyi North Road, Fuzhou 350011, Fujian Province, People's Republic of China
| | - Jianhui Wang
- Department of Ecological Science and Engineering, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, People's Republic of China, Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, and Key Laboratory of Plant Pathology, Ministry of Agriculture, Beijing 100193, People's Republic of China, Bureau of Fuzhou Landscape Architecture, Liuyi North Road, Fuzhou 350011, Fujian Province, People's Republic of China
| | - Huimin Wang
- Department of Ecological Science and Engineering, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, People's Republic of China, Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, and Key Laboratory of Plant Pathology, Ministry of Agriculture, Beijing 100193, People's Republic of China, Bureau of Fuzhou Landscape Architecture, Liuyi North Road, Fuzhou 350011, Fujian Province, People's Republic of China
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Gutnick D, Avigad R, Blatt Y, Minas W, Allon R. Amphipathic microbial capsules as industrial products. ACTA ACUST UNITED AC 2008. [DOI: 10.1111/j.1365-2672.1993.tb04349.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Choi O, Kim J, Kim JG, Jeong Y, Moon JS, Park CS, Hwang I. Pyrroloquinoline quinone is a plant growth promotion factor produced by Pseudomonas fluorescens B16. PLANT PHYSIOLOGY 2008; 146:657-668. [PMID: 18055583 PMCID: PMC2245851 DOI: 10.1104/pp.107.112748] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Accepted: 11/20/2007] [Indexed: 05/25/2023]
Abstract
Pseudomonas fluorescens B16 is a plant growth-promoting rhizobacterium. To determine the factors involved in plant growth promotion by this organism, we mutagenized wild-type strain B16 using OmegaKm elements and isolated one mutant, K818, which is defective in plant growth promotion, in a rockwool culture system. A cosmid clone, pOK40, which complements the mutant K818, was isolated from a genomic library of the parent strain. Tn3-gusA mutagenesis of pOK40 revealed that the genes responsible for plant growth promotion reside in a 13.3-kb BamHI fragment. Analysis of the DNA sequence of the fragment identified 11 putative open reading frames, consisting of seven known and four previously unidentified pyrroloquinoline quinone (PQQ) biosynthetic genes. All of the pqq genes showed expression only in nutrient-limiting conditions in a PqqH-dependent manner. Electrospray ionization-mass spectrometry analysis of culture filtrates confirmed that wild-type B16 produces PQQ, whereas mutants defective in plant growth promotion do not. Application of wild-type B16 on tomato (Solanum lycopersicum) plants cultivated in a hydroponic culture system significantly increased the height, flower number, fruit number, and total fruit weight, whereas none of the strains that did not produce PQQ promoted tomato growth. Furthermore, 5 to 1,000 nm of synthetic PQQ conferred a significant increase in the fresh weight of cucumber (Cucumis sativus) seedlings, confirming that PQQ is a plant growth promotion factor. Treatment of cucumber leaf discs with PQQ and wild-type B16 resulted in the scavenging of reactive oxygen species and hydrogen peroxide, suggesting that PQQ acts as an antioxidant in plants.
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Affiliation(s)
- Okhee Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
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Hölscher T, Görisch H. Knockout and overexpression of pyrroloquinoline quinone biosynthetic genes in Gluconobacter oxydans 621H. J Bacteriol 2006; 188:7668-76. [PMID: 16936032 PMCID: PMC1636293 DOI: 10.1128/jb.01009-06] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Gluconobacter oxydans, pyrroloquinoline quinone (PQQ) serves as the cofactor for various membrane-bound dehydrogenases that oxidize sugars and alcohols in the periplasm. Proteins for the biosynthesis of PQQ are encoded by the pqqABCDE gene cluster. Our reverse transcription-PCR and promoter analysis data indicated that the pqqA promoter represents the only promoter within the pqqABCDE cluster of G. oxydans 621H. PQQ overproduction in G. oxydans was achieved by transformation with the plasmid-carried pqqA gene or the complete pqqABCDE cluster. A G. oxydans mutant unable to produce PQQ was obtained by site-directed disruption of the pqqA gene. In contrast to the wild-type strain, the pqqA mutant did not grow with d-mannitol, d-glucose, or glycerol as the sole energy source, showing that in G. oxydans 621H, PQQ is essential for growth with these substrates. Growth of the pqqA mutant, however, was found with d-gluconate as the energy source. The growth behavior of the pqqA mutant correlated with the presence or absence of the respective PQQ-dependent membrane-bound dehydrogenase activities, demonstrating the vital role of these enzymes in G. oxydans metabolism. A different PQQ-deficient mutant was generated by Tn5 transposon mutagenesis. This mutant showed a defect in a gene with high homology to the Escherichia coli tldD gene, which encodes a peptidase. Our results indicate that the tldD gene in G. oxydans 621H is involved in PQQ biosynthesis, possibly with a similar function to that of the pqqF genes found in other PQQ-synthesizing bacteria.
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Affiliation(s)
- Tina Hölscher
- FG Technische Biochemie, Sekr. GG1, TU Berlin, Seestr. 13, D-13353 Berlin, Germany.
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38
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Young DM, Parke D, Ornston LN. OPPORTUNITIES FOR GENETIC INVESTIGATION AFFORDED BYACINETOBACTER BAYLYI, A NUTRITIONALLY VERSATILE BACTERIAL SPECIES THAT IS HIGHLY COMPETENT FOR NATURAL TRANSFORMATION. Annu Rev Microbiol 2005; 59:519-51. [PMID: 16153178 DOI: 10.1146/annurev.micro.59.051905.105823] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genetic and physiological properties of Acinetobacter baylyi strain ADP1 make it an inviting subject for investigation of the properties underlying its nutritional versatility. The organism possesses a relatively small genome in which genes for most catabolic functions are clustered in several genetic islands that, unlike pathogenicity islands, give little evidence of horizontal transfer. Coupling mutagenic polymerase chain reaction to natural transformation provides insight into how structure influences function in transporters, transcriptional regulators, and enzymes. With appropriate selection, mutants in which such molecules have acquired novel function may be obtained. The extraordinary competence of A. baylyi for natural transformation and the ease with which it expresses heterologous genes make it a promising platform for construction of novel metabolic systems. Steps toward this goal should take into account the complexity of existing pathways in which transmembrane trafficking plays a significant role.
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Affiliation(s)
- David M Young
- 1Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
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Dorrestein P, Begley TP. Oxidative cascades: a facile biosynthetic strategy for the assembly of complex molecules. Bioorg Chem 2005; 33:136-48. [PMID: 15888307 DOI: 10.1016/j.bioorg.2004.06.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2004] [Indexed: 10/26/2022]
Abstract
Electron-rich aromatic compounds undergo a facile tandem reaction sequence involving an iterative two-electron oxidation/aromatization. This review will describe the application of this motif to the synthesis of dimethylbenzimidazole, pyoverdine, actinomycin, cystodytin, pyrroloquinoline quinone, and the cataract pigment.
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Affiliation(s)
- Pieter Dorrestein
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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Magnusson OT, Toyama H, Saeki M, Schwarzenbacher R, Klinman JP. The Structure of a Biosynthetic Intermediate of Pyrroloquinoline Quinone (PQQ) and Elucidation of the Final Step of PQQ Biosynthesis. J Am Chem Soc 2004; 126:5342-3. [PMID: 15113189 DOI: 10.1021/ja0493852] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyrroloquinoline quinone (PQQ) is a tricyclic o-quinone, which serves as a cofactor in several enzyme-catalyzed redox reactions in certain bacteria. PQQ is also important for human health, and its role as a vitamin in mammals has recently been suggested. Although much is known about the function of enzymes that use PQQ as cofactor, relatively little is known about the biosynthesis of this coenzyme. Six gene products in Klebsiella pneumoniae (PqqA-F) are involved in PQQ biosynthesis, and PqqC has been shown to catalyze the last step in the pathway. The chemical structure of the substrate for PqqC has remained elusive and has hampered our understanding of the nature of this reaction. In this report we describe the purification and structure of the substrate as deduced by a number of spectroscopic and chemical methods. The substrate is 3a-(2-amino-2-carboxyethyl)-4,5-dioxo-4,5,6,7,8,9-hexahydroquinoline-7,9-dicarboxylic acid-a fully reduced derivative of PQQ, which has not undergone ring cyclization. These results show that PqqC catalyzes a novel reaction, which involves ring closure and an amazing eight-electron oxidation of the substrate.
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Affiliation(s)
- Olafur T Magnusson
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA
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41
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Rodríguez H, Fraga R. Phosphate solubilizing bacteria and their role in plant growth promotion. Biotechnol Adv 2004; 17:319-39. [PMID: 14538133 DOI: 10.1016/s0734-9750(99)00014-2] [Citation(s) in RCA: 848] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The use of phosphate solubilizing bacteria as inoculants simultaneously increases P uptake by the plant and crop yield. Strains from the genera Pseudomonas, Bacillus and Rhizobium are among the most powerful phosphate solubilizers. The principal mechanism for mineral phosphate solubilization is the production of organic acids, and acid phosphatases play a major role in the mineralization of organic phosphorous in soil. Several phosphatase-encoding genes have been cloned and characterized and a few genes involved in mineral phosphate solubilization have been isolated. Therefore, genetic manipulation of phosphate-solubilizing bacteria to improve their ability to improve plant growth may include cloning genes involved in both mineral and organic phosphate solubilization, followed by their expression in selected rhizobacterial strains. Chromosomal insertion of these genes under appropriate promoters is an interesting approach.
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Affiliation(s)
- H Rodríguez
- Department of Microbiology, Cuban Research Institute on Sugarcane By-Products (ICIDCA), P.O. Box 4026, CP 11 000, Havana, Cuba.
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42
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Kim BC, Sohn CK, Lim SK, Lee JW, Park W. Degradation of polyvinyl alcohol by Sphingomonas sp. SA3 and its symbiote. J Ind Microbiol Biotechnol 2003; 30:70-4. [PMID: 12545389 DOI: 10.1007/s10295-002-0010-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2001] [Accepted: 10/10/2002] [Indexed: 10/23/2022]
Abstract
A total of 800 samples was taken from Taegu province, Korea, where many textile factories provide a source of polyvinyl alcohol (PVA) waste. These samples were screened for PVA-degrading bacteria. A new strain, SA3, was discovered which formed yellow colonies and used PVA as the sole carbon and energy source. Strain SA3 was identified as a Sphingomonas sp., based on the partial nucleotide sequence analysis of 16S ribosomal RNA, the presence of 2-hydroxymyristic acid (14:O 2-OH) and sphingolipids with d-17:0, d-18:0, d-19:1, and d-20:1 as the main dihydrosphingosines. This genus has not previously been reported as a PVA-degrading bacterium. Sphingomonas sp. SA3 needs a symbiote strain, SA2, for PVA degradation as a growth factor producer. In mixed cultures of these strains, the optimum temperature for PVA biodegradation ranged from 30 degrees C to 35 degrees C. The optimum pH was 8.0 and the most effective nitrogen source was NH(4)(+).
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Affiliation(s)
- B C Kim
- College of Natural Sciences, Kyungpook National University, Department of Microbiology, 702-701, Taegu, Korea
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43
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Davidson VL. Pyrroloquinoline quinone (PQQ) from methanol dehydrogenase and tryptophan tryptophylquinone (TTQ) from methylamine dehydrogenase. ADVANCES IN PROTEIN CHEMISTRY 2002; 58:95-140. [PMID: 11665494 DOI: 10.1016/s0065-3233(01)58003-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- V L Davidson
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi 39216, USA
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Felder M, Gupta A, Verma V, Kumar A, Qazi GN, Cullum J. The pyrroloquinoline quinone synthesis genes of Gluconobacter oxydans. FEMS Microbiol Lett 2000; 193:231-6. [PMID: 11111029 DOI: 10.1111/j.1574-6968.2000.tb09429.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
A Tn5-induced glucose dehydrogenase (GDH) deficient mutant of Gluconobacter oxydans IFO 3293 was characterised. DNA sequencing showed that the insertion site occurred in an open reading frame with homology to the pqqE gene. It was shown that acid production could be restored by addition of the coenzyme pyrroloquinoline quinone (PQQ) to the medium. The pqq cluster of G. oxydans ATCC 9937 was cloned and sequenced. It has five genes pqqA-E. The cluster could complement the Tn5-induced mutation in IFO 3293. Pulsed-field gel electrophoresis suggested that the pqq genes are not closely linked to the ribF gene that produces the riboflavin cofactor for the gluconic acid dehydrogenase.
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Affiliation(s)
- M Felder
- LB Genetik, Universität Kaiserlautern, Postfach 3049, Germany
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Nagy I, De Mot R. Sequence analysis of the oxidase/reductase genes upstream of the Rhodococcus erythropolis aldehyde dehydrogenase gene thcA reveals a gene organisation different from Mycobacterium tuberculosis. DNA SEQUENCE : THE JOURNAL OF DNA SEQUENCING AND MAPPING 2000; 10:61-6. [PMID: 10565547 DOI: 10.3109/10425179909033938] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The sequence of the DNA region upstream of the thiocarbamate-inducible aldehyde dehydrogenase gene thcA of Rhodococcus erythropolis NI86/21 was determined. Most of the predicted ORFs are related to various oxidases/reductases, including short-chain oxidases/reductases, GMC oxidoreductases, alpha-hydroxy acid oxidases (subfamily 1 flavin oxidases/dehydrogenases), and subfamily 2 flavin oxidases/dehydrogenases. One ORF is related to enzymes involved in biosynthesis of PQQ or molybdopterin cofactors. In addition, a putative member of the TetR family of regulatory proteins was identified. The substantial sequence divergence from functionally characterized enzymes precludes a reliable prediction about the probable function of these proteins at this stage. In Mycobacterium tuberculosis H37Rv, most of these ORFs have homologs that are also clustered in the genome, but some striking differences in gene organization were observed between Rhodococcus and Mycobacterium.
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Affiliation(s)
- I Nagy
- F.A. Janssens Laboratory of Genetics, Catholic University of Leuven, Heverlee, Belgium
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Stites TE, Mitchell AE, Rucker RB. Physiological importance of quinoenzymes and the O-quinone family of cofactors. J Nutr 2000; 130:719-27. [PMID: 10736320 DOI: 10.1093/jn/130.4.719] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
O-quinone cofactors derived from tyrosine and tryptophan are involved in novel biological reactions that range from oxidative deaminations to free-radical redox reactions. The formation of each of these cofactors appears to involve post-translational modifications of either tyrosine or tryptophan residues. The modifications result in cofactors, such as topaquinone (TPQ), tryptophan tryptophylquinone (TTQ), lysine tyrosylquinone (LTQ) or the copper-complexed cysteinyl-tyrosyl radical from metal-catalyzed reactions. Pyrroloquinoline quinone (PQQ) appears to be formed from the annulation of peptidyl glutamic acid and tyrosine residues stemming from their modification as components of a precursor peptide substrate. PQQ, a primary focus of this review, has invoked considerable interest because of its presence in foods, antioxidant properties and role as a growth-promoting factor. Although no enzymes in animals have been identified that exclusively utilize PQQ, oral supplementation of PQQ in nanomolar amounts increases the responsiveness of B- and T-cells to mitogens and improves neurologic function and reproductive outcome in rodents. Regarding TPQ and LTQ, a case may be made that the formation of TPQ and LTQ is also influenced by nutritional status, specifically dietary copper. For at least one of the amine oxidases, lysyl oxidase, enzymatic activity correlates directly with copper intake. TPQ and LTQ are generated following the incorporation of copper by a process that involves the two-step oxidation of a specified tyrosyl residue to first peptidyl dopa and then peptidyl topaquinone to generate active enzymes, generally classed as "quinoenzymes." Limited attention is also paid to TTQ and the copper-complexed cysteinyl-tyrosyl radical, cofactors important to fungal and bacterial redox processes.
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Affiliation(s)
- T E Stites
- Department of Nutrition, University of California, Davis, Davis, CA 95616, USA
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47
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Van Spanning RJ, de Vries S, Harms N. Coping with formaldehyde during C1 metabolism of Paracoccus denitrificans. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s1381-1177(99)00065-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Szameit C, Miech C, Balleininger M, Schmidt B, von Figura K, Dierks T. The iron sulfur protein AtsB is required for posttranslational formation of formylglycine in the Klebsiella sulfatase. J Biol Chem 1999; 274:15375-81. [PMID: 10336424 DOI: 10.1074/jbc.274.22.15375] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The catalytic residue of eukaryotic and prokaryotic sulfatases is a alpha-formylglycine. In the sulfatase of Klebsiella pneumoniae the formylglycine is generated by posttranslational oxidation of serine 72. We cloned the atsBA operon of K. pneumoniae and found that the sulfatase was expressed in inactive form in Escherichia coli transformed with the structural gene (atsA). Coexpression of the atsB gene, however, led to production of high sulfatase activity, indicating that the atsB gene product plays a posttranslational role that is essential for the sulfatase to gain its catalytic activity. This was verified after purification of the sulfatase from the periplasm of the cells. Peptide analysis of the protein expressed in the presence of AtsB revealed that half of the polypeptides carried the formylglycine at position 72, while the remaining polypeptides carried the encoded serine. The inactive sulfatase expressed in the absence of AtsB carried exclusively serine 72, demonstrating that the atsB gene is required for formylglycine modification. This gene encodes a 395-amino acid residue iron sulfur protein that has a cytosolic localization and is supposed to directly or indirectly catalyze the oxidation of the serine to formylglycine.
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Affiliation(s)
- C Szameit
- Institut für Biochemie und Molekulare Zellbiologie, Abteilung Biochemie II, Universität Göttingen, Gosslerstrasse 12d, 37073 Göttingen, Germany
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McIntire WS. Newly discovered redox cofactors: possible nutritional, medical, and pharmacological relevance to higher animals. Annu Rev Nutr 1998; 18:145-77. [PMID: 9706222 DOI: 10.1146/annurev.nutr.18.1.145] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Research spurred by the discovery of pyrroloquinoline quinone (PPQ) in 1979 led to the discovery of four additional oxidation-reduction (redox) cofactors, all of which result from transmogrification of amino acyl side chains in respective enzymes. These cofactors are (a) topa quinone in copper-containing amine oxidases, enzymes found in nearly all forms of life, including human; (b) lysyl topa quinone of the copper protein lysyl oxidase, an enzyme required for proper cross-linking of collagen and elastin; (c) tryptophan tryptophylquinone of alkylamine dehydrogenases from gram-negative soil bacteria; and (d) the copper-complexed cysteinyltyrosyl radical of fungal galactose oxidase. Originally, PQQ was thought to be a covalently bound cofactor in numerous enzymes from eukaryotes and prokaryotes. Today, PQQ is only found as a noncovalent cofactor in bacterial enzymes. The ubiquity of PQQ in the environment and its steady accessibility in the human diet has raised questions concerning its role as a vitamin, or an essential or helpful nutrient. The relevance to nutrition, medicine, and pharmacology of PQQ, topa quinone, lysyl topa quinone, tryptophan trytophylquinone, the galactose oxidase cofactor, and the enzymes harboring these cofactors are discussed in this review.
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Affiliation(s)
- W S McIntire
- Department of Veterans Affairs Medical Center, San Francisco, California 94121, USA.
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50
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Kim KY, Jordan D, Krishnan HB. Expression of genes from Rahnella aquatilis that are necessary for mineral phosphate solubilization in Escherichia coli. FEMS Microbiol Lett 1998; 159:121-7. [PMID: 9485602 DOI: 10.1111/j.1574-6968.1998.tb12850.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Rahnella aquatilis is a Gram-negative bacterium that can fix atmospheric nitrogen and also has the ability to solubilize mineral phosphate. We have cloned the genes that confer the mineral phosphate solubilizing (Mps) trait from this organism by mobilizing a cosmid library of R. aquatilis into Escherichia coli HB101. A 7.0-kb EcoRI fragment from a cosmid, when transferred into E. coli strains HB101 and DH5 alpha, conferred the ability to solubilize hydroxyapatite and the production of gluconic acid to E. coli. The relative amounts of soluble phosphate and gluconic acid produced by the cloned 7.0-kb EcoRI fragment in E. coli were significantly higher than those of R. aquatilis. Nucleotide sequence analysis revealed two complete open reading frames (ORF1 and ORF2) and a partial ORF, ORF1 and ORF2 encoded proteins of molecular mass 10 kDa and 44 kDa. The 44-kDa protein showed extensive sequence similarity to pqqE of Erwinia herbicola, Klebsiella pneumoniae and A. Acinetobacter calcoaceticus. The 10-kDa protein revealed strong similarity to the pqqD of K. pneumoniae and A. calcoaceticus.
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Affiliation(s)
- K Y Kim
- Department of Plant Pathology, University of Missouri, Columbia 65211, USA
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