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Yang T, Tedersoo L, Lin X, Fitzpatrick MC, Jia Y, Liu X, Ni Y, Shi Y, Lu P, Zhu J, Chu H. Distinct fungal successional trajectories following wildfire between soil horizons in a cold-temperate forest. THE NEW PHYTOLOGIST 2020; 227:572-587. [PMID: 32155671 DOI: 10.1111/nph.16531] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/02/2020] [Indexed: 06/10/2023]
Abstract
Soil fungi represent a major component of below-ground biodiversity that determines the succession and recovery of forests after disturbance. However, their successional trajectories and driving mechanisms following wildfire remain unclear. We examined fungal biomass, richness, composition and enzymes across three soil horizons (Oe, A1 and A2) along a near-complete fire chronosequence (1, 2, 8, 14, 30, 49 and c. 260 yr) in cold-temperate forests of the Great Khingan Mountains, China. The importance of soil properties, spatial distance and tree composition were also tested. Ectomycorrhizal fungal richness and β-glucosidase activity were strongly reduced by burning and significantly increased with 'time since fire' in the Oe horizon but not in the mineral horizons. Time since fire and soil C : N ratio were the primary drivers of fungal composition in the Oe and A1/A2 horizons, respectively. Ectomycorrhizal fungal composition was remarkably sensitive to fire history in the Oe horizon, while saprotroph community was strongly affected by time since fire in the deeper soil horizon and this effect emerged 18 years after fire in the A2 horizon. Our study demonstrates pronounced horizon-dependent successional trajectories following wildfire and indicates interactive effects of time since fire, soil stoichiometry and spatial distance in the reassembly of below-ground fungal communities in a cold and fire-prone region.
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Affiliation(s)
- Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Leho Tedersoo
- Natural History Museum, University of Tartu, 14a Ravila, Tartu, 50411, Estonia
| | - Xingwu Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Matthew C Fitzpatrick
- Appalachian Laboratory, University of Maryland Centre for Environmental Science, Frostburg, MD, 21531, USA
| | - Yunsheng Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Xu Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Yingying Ni
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Pengpeng Lu
- Microbiology Institute of Shaanxi, Shaanxi Academy of Sciences, Xiying Road 76, Xi'an, 710043, China
| | - Jianguo Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
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Inhibition of urease activity by different compounds provides insight into the modulation and association of bacterial nickel import and ureolysis. Sci Rep 2020; 10:8503. [PMID: 32444844 PMCID: PMC7244745 DOI: 10.1038/s41598-020-65107-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 04/28/2020] [Indexed: 01/29/2023] Open
Abstract
The nickel-dependent urease enzyme is responsible for the hydrolysis of urea to ammonia and carbon dioxide. A number of bacteria produce urease (ureolytic bacteria) and are associated with various infectious diseases and ammonia emissions from agriculture. We report the first comprehensive comparison of the inhibition of urease activity by compounds analysed under the same conditions. Thus, 71 commercially available compounds were screened for their anti-ureolytic properties against both the ureolytic bacterium Klebsiella pneumoniae and purified jack bean urease. Of the tested compounds, 30 showed more than 25% inhibition of the ureolytic activity of Klebsiella pneumoniae or jack bean urease, and among these, carbon disulfide, N-phenylmaleimide, diethylenetriaminepentaacetic acid, sodium pyrrolidinedithiocarbamate, 1,2,4-butanetricarboxylic acid, tannic acid, and gallic acid have not previously been reported to possess anti-ureolytic properties. The diverse effects of metal ion chelators on ureolysis were investigated using a cellular nickel uptake assay. Ethylenediaminetetraacetic acid (EDTA) and dimethylglyoxime (DMG) clearly reduced the nickel import and ureolytic activity of cells, oxalic acid stimulated nickel import but reduced the ureolytic activity of cells, 1,2,4-butanetricarboxylic acid strongly stimulated nickel import and slightly increased the ureolytic activity of cells, while L-cysteine had no effect on nickel import but efficiently reduced the ureolytic activity of cells.
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Hu S, Gao Y, Wu Y, Guo X, Ying Y, Wen Y, Yang H. Raman tracking the activity of urease in saliva for healthcare. Biosens Bioelectron 2019; 129:24-28. [PMID: 30682685 DOI: 10.1016/j.bios.2018.12.059] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 12/25/2018] [Accepted: 12/27/2018] [Indexed: 10/27/2022]
Abstract
The detection of urease activity in the oral cavity is considered to be an efficient way to prevent dental caries and also to screen for helicobacter pylori infection. Herein, a rapid surface enhanced Raman scattering (SERS) method is proposed to determine the activity of urease by using inositol hexaphosphate (IP6) stabilized silver nanoparticles (AgNPs@IP6) as an efficient SERS-active substrate. The determination was achieved by monitoring the SERS peak intensity of urea at 1003 cm-1. With urease increase, the response of urea at 1003 cm-1 decreases gradually, indicating the two has good correlation. A linear relationship between the absolute value of signal drop and urease concentration is observed in a range from 2.35 to 37.5 μg/mL. In addition, the rapid SERS method was used to evaluate the activity of urease in real sample of saliva without any pretreatment, exhibiting a promising potential for biomedical application.
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Affiliation(s)
- Sen Hu
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Key Laboratory of Rare Earth Functional Materials, Shanghai Municipal Education Committee Key Laboratory of Molecular Imaging Probes and Sensors, College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200234, China
| | - Yun Gao
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Key Laboratory of Rare Earth Functional Materials, Shanghai Municipal Education Committee Key Laboratory of Molecular Imaging Probes and Sensors, College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200234, China
| | - Yiping Wu
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Key Laboratory of Rare Earth Functional Materials, Shanghai Municipal Education Committee Key Laboratory of Molecular Imaging Probes and Sensors, College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200234, China.
| | - Xiaoyu Guo
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Key Laboratory of Rare Earth Functional Materials, Shanghai Municipal Education Committee Key Laboratory of Molecular Imaging Probes and Sensors, College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200234, China
| | - Ye Ying
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Key Laboratory of Rare Earth Functional Materials, Shanghai Municipal Education Committee Key Laboratory of Molecular Imaging Probes and Sensors, College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200234, China
| | - Ying Wen
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Key Laboratory of Rare Earth Functional Materials, Shanghai Municipal Education Committee Key Laboratory of Molecular Imaging Probes and Sensors, College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200234, China
| | - Haifeng Yang
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Key Laboratory of Rare Earth Functional Materials, Shanghai Municipal Education Committee Key Laboratory of Molecular Imaging Probes and Sensors, College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200234, China.
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Konieczna I, Zarnowiec P, Kwinkowski M, Kolesinska B, Fraczyk J, Kaminski Z, Kaca W. Bacterial urease and its role in long-lasting human diseases. Curr Protein Pept Sci 2013; 13:789-806. [PMID: 23305365 PMCID: PMC3816311 DOI: 10.2174/138920312804871094] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 07/15/2012] [Accepted: 09/03/2012] [Indexed: 02/07/2023]
Abstract
Urease is a virulence factor found in various pathogenic bacteria. It is essential in colonization of a host organism and in maintenance of bacterial cells in tissues. Due to its enzymatic activity, urease has a toxic effect on human cells. The presence of ureolytic activity is an important marker of a number of bacterial infections. Urease is also an immunogenic protein and is recognized by antibodies present in human sera. The presence of such antibodies is connected with progress of several long-lasting diseases, like rheumatoid arthritis, atherosclerosis or urinary tract infections. In bacterial ureases, motives with a sequence and/or structure similar to human proteins may occur. This phenomenon, known as molecular mimicry, leads to the appearance of autoantibodies, which take part in host molecules destruction. Detection of antibodies-binding motives (epitopes) in bacterial proteins is a complex process. However, organic chemistry tools, such as synthetic peptide libraries, are helpful in both, epitope mapping as well as in serologic investigations. In this review, we present a synthetic report on a molecular organization of bacterial ureases - genetic as well as structural. We characterize methods used in detecting urease and ureolytic activity, including techniques applied in disease diagnostic processes and in chemical synthesis of urease epitopes. The review also provides a summary of knowledge about a toxic effect of bacterial ureases on human body and about occurrence of anti-urease antibodies in long-lasting diseases.
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Affiliation(s)
- Iwona Konieczna
- Department of Microbiology, Institute of Biology, The Jan Kochanowski University, ul. Swietokrzyska 15, 25-406 Kielce, Poland.
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Temperature- and pressure-dependent stopped-flow kinetic studies of jack bean urease. Implications for the catalytic mechanism. J Biol Inorg Chem 2012; 17:1123-34. [PMID: 22890689 PMCID: PMC3442171 DOI: 10.1007/s00775-012-0926-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 07/14/2012] [Indexed: 12/03/2022]
Abstract
Abstract Urease, a Ni-containing metalloenzyme, features an activity that has profound medical and agricultural implications. The mechanism of this activity, however, has not been as yet thoroughly established. Accordingly, to improve its understanding, in this study we analyzed the steady-state kinetic parameters of the enzyme (jack bean), KM and kcat, measured at different temperatures and pressures. Such an analysis is useful as it provides information on the molecular nature of the intermediate and transition states of the catalytic reaction. We measured the parameters in a noninteracting buffer using a stopped-flow technique in the temperature range 15–35 °C and in the pressure range 5–132 MPa, the pressure-dependent measurements being the first of their kind performed for urease. While temperature enhanced the activity of urease, pressure inhibited the enzyme; the inhibition was biphasic. Analyzing KM provided the characteristics of the formation of the ES complex, and analyzing kcat, the characteristics of the activation of ES. From the temperature-dependent measurements, the energetic parameters were derived, i.e. thermodynamic ΔHo and ΔSo for ES formation, and kinetic ΔH≠ and ΔS≠ for ES activation, while from the pressure-dependent measurements, the binding ΔVb and activation \documentclass[12pt]{minimal}
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\begin{document}$$ \Updelta V_{\rm cat}^{ \ne } $$\end{document} volumes were determined. The thermodynamic and activation parameters obtained are discussed in terms of the current proposals for the mechanism of the urease reaction, and they are found to support the mechanism proposed by Benini et al. (Structure 7:205–216; 1999), in which the Ni–Ni bridging hydroxide—not the terminal hydroxide—is the nucleophile in the catalytic reaction. Graphical abstract ![]()
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Astaurova OB, Bass IA, Khmel IA. Suggested interrelationships of RNA-polymerase sigma S subunit and nitrogen control system in Pseudomonas chlororaphis. RUSS J GENET+ 2007. [DOI: 10.1134/s1022795407080029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Affiliation(s)
- E B Harris
- Laboratory Research Branch, LSU, U.S. Public Health Service, Baton Rouge 70894-5072, USA.
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Abstract
Urease (urea amidohydrolase; EC 3.5.1.5) catalyzes the hydrolysis of urea to yield ammonia and carbamate. The latter compound spontaneously decomposes to yield another molecule of ammonia and carbonic acid. The urease phenotype is widely distributed across the bacterial kingdom, and the gene clusters encoding this enzyme have been cloned from numerous bacterial species. The complete nucleotide sequence, ranging from 5.15 to 6.45 kb, has been determined for five species including Bacillus sp. strain TB-90, Klebsiella aerogenes, Proteus mirabilis, Helicobacter pylori, and Yersinia enterocolitica. Sequences for selected genes have been determined for at least 10 other bacterial species and the jack bean enzyme. Urease synthesis can be nitrogen regulated, urea inducible, or constitutive. The crystal structure of the K. aerogenes enzyme has been determined. When combined with chemical modification studies, biophysical and spectroscopic analyses, site-directed mutagenesis results, and kinetic inhibition experiments, the structure provides important insight into the mechanism of catalysis. Synthesis of active enzyme requires incorporation of both carbon dioxide and nickel ions into the protein. Accessory genes have been shown to be required for activation of urease apoprotein, and roles for the accessory proteins in metallocenter assembly have been proposed. Urease is central to the virulence of P. mirabilis and H. pylori. Urea hydrolysis by P. mirabilis in the urinary tract leads directly to urolithiasis (stone formation) and contributes to the development of acute pyelonephritis. The urease of H. pylori is necessary for colonization of the gastric mucosa in experimental animal models of gastritis and serves as the major antigen and diagnostic marker for gastritis and peptic ulcer disease in humans. In addition, the urease of Y. enterocolitica has been implicated as an arthritogenic factor in the development of infection-induced reactive arthritis. The significant progress in our understanding of the molecular biology of microbial ureases is reviewed.
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Affiliation(s)
- H L Mobley
- Division of Infectious Diseases, University of Maryland School of Medicine, Baltimore 21201, USA
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Dubois A, Fiala N, Heman-Ackah LM, Drazek ES, Tarnawski A, Fishbein WN, Perez-Perez GI, Blaser MJ. Natural gastric infection with Helicobacter pylori in monkeys: a model for spiral bacteria infection in humans. Gastroenterology 1994; 106:1405-17. [PMID: 8194685 DOI: 10.1016/0016-5085(94)90392-1] [Citation(s) in RCA: 101] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND/AIMS There is no generally accepted model for Helicobacter pylori infection in humans. The aim of this study was to examine the natural history and effect of treatment in rhesus monkeys and sequentially define the immune response to H. pylori in relation to treatment. METHODS Infection and gastritis were graded blindly by histological analysis and culture of biopsy specimens harvested during gastroduodenoscopies in 26 anesthetized colony-bred monkeys. Plasma H. pylori-specific immunoglobulin (Ig) G levels were determined by enzyme-linked immunosorbent assay. RESULTS H. pylori and Gastrospirilum hominis-like organisms were present in 13 and 9 monkeys, respectively; 3 animals harbored both organisms, whereas 4 monkeys were not infected. Gastritis score was < or = 1.5 in animals uninfected or infected only with G. hominis-like organisms and > or = 2.0 in all H. pylori-infected animals. IgG ratios were > or = 0.5 in 12 of 13 H. pylori-infected animals and in 2 of 13 H. pylori-negative animals (P < 0.001). One monkey became infected with H. pylori during the observation period, with concurrent increase of gastritis and plasma IgG levels. In untreated animals, infection, gastritis, and plasma IgG levels remained unchanged over 7-15 months. Triple therapy eradicated H. pylori at 6 months in 4 of 6 animals while suppressing gastritis and plasma IgG levels. CONCLUSIONS Rhesus monkeys harboring H. pylori are persistently infected and have gastritis and elevated specific IgG levels, all of which may respond to appropriate therapy, whereas G. hominis infection is associated with little inflammation.
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Affiliation(s)
- A Dubois
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland
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Abstract
Microbial ureases hydrolyze urea to ammonia and carbon dioxide. Urease activity of an infectious microorganism can contribute to the development of urinary stones, pyelonephritis, gastric ulceration, and other diseases. In contrast to these harmful effects, urease activity of ruminal and gastrointestinal microorganisms can benefit both the microbe and host by recycling (thereby conserving) urea nitrogen. Microbial ureases also play an important role in utilization of environmental nitrogenous compounds and urea-based fertilizers. Urease is a high-molecular-weight, multimeric, nickel-containing enzyme. Its cytoplasmic location requires that urea enter the cell for utilization, and in some species energy-dependent urea uptake systems have been detected. Eucaryotic microorganisms possess a homopolymeric urease, analogous to the well-studied plant enzyme composed of six identical subunits. Gram-positive bacteria may also possess homopolymeric ureases, but the evidence for this is not conclusive. In contrast, ureases from gram-negative bacteria studied thus far clearly possess three distinct subunits with Mrs of 65,000 to 73,000 (alpha), 10,000 to 12,000 (beta), and 8,000 to 10,000 (gamma). Tightly bound nickel is present in all ureases and appears to participate in catalysis. Urease genes have been cloned from several species, and nickel-containing recombinant ureases have been characterized. Three structural genes are transcribed on a single messenger ribonucleic acid and translated in the order gamma, beta, and then alpha. In addition to these genes, several other peptides are encoded in the urease operon of some species. The roles for these other genes are not firmly established, but may involve regulation, urea transport, nickel transport, or nickel processing.
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Abstract
Although referred to as "urinary calculus disease", the formation of stone in the urinary tract is not caused by a single etiological agent. As such, diverse clinical investigations to diagnose the cause of stone formation must be carried out and the course of management after diagnosis must inevitably be different in each case. This review will cover all aspects of calculus formation, but will give particular attention to calculi caused by infection of the urinary tract with urease-producing bacteria. This is a recurrent, potentially life-threatening disease which has led clinicians to refer to the condition as "stone cancer". Because the etiology of infection stones is so different from stones caused by metabolic disorders, the two disease patterns should be considered separately, a fact often overlooked in epidemiological studies of stone formation. The importance of analysis of calculi as an aid to management is thus emphasized; identification of stone type will help to indicate appropriate therapy. A review of methods of analysis will be covered, particularly crystallographic analysis. Inhibition of bacterial urease as a means of management of infection stones will be discussed together with problems encountered and brighter hopes for the future.
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Fishbein WN. Formamide: the minimum-structure substrate for urease. BIOCHIMICA ET BIOPHYSICA ACTA 1977; 484:433-42. [PMID: 20965 DOI: 10.1016/0005-2744(77)90099-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Kominami E, Kobayashi K, Kominami S, Katunuma N. Properties of a Specific Protease for Pyridoxal Enzymes and Its Biological Role. J Biol Chem 1972. [DOI: 10.1016/s0021-9258(19)44663-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Magaña-Plaza I, Montes C, Ruiz-Herrera J. Purification and biochemical characteristics of urease from Proteus rettgeri. BIOCHIMICA ET BIOPHYSICA ACTA 1971; 242:230-7. [PMID: 5001086 DOI: 10.1016/0005-2744(71)90103-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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