1
|
Yang DD, Li Q, Huang JJ, Chen M. [Diversity and enzyme-producing activity of culturable halophilic bacteria in Daishan Saltern of East China]. Ying Yong Sheng Tai Xue Bao 2012; 23:3103-3108. [PMID: 23431797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Soil and saline water samples were collected from the Daishan Saltern of East China, and the halophilic bacteria were isolated and cultured by using selective media, aimed to investigate the diversity and enzyme-producing activity of culturable halophilic bacteria in saltern environment. A total of 181 strains were isolated by culture-dependent method. Specific primers were used to amplify the 16S rRNA gene of bacteria and archaea. The operation taxonomy units (OTUs) were determined by ARDRA method, and the representative strain of each OTU was sequenced. The phylogenetic position of all the isolated strains was determined by 16S rRNA sequencing. The results showed that the isolated 181 strains displayed 21 operational taxonomic units (OTUs), of which, 12 OTUs belonged to halophilic bacteria, and the others belonged to halophilic archaea. Phylogenetic analysis indicated that there were 7 genera presented among the halophilic bacteria group, and 4 genera presented among the halophilic archaea group. The dominant halophilic strains were of Halomonas and Haloarcula, with 46.8% in halophilic bacteria and 49.1% in halophilic archaea group, respectively. Enzyme-producing analysis indicated that most strains displayed enzyme-producing activity, including the activities of producing amylase, proteinase and lipase, and the dominant strains capable of enzyme-producing were of Haloarcula. Our results showed that in the environment of Daishan Saltern, there existed a higher diversity of halophilic bacteria, being a source sink for screening enzyme-producing bacterial strains.
Collapse
Affiliation(s)
- Dan-Dan Yang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
| | | | | | | |
Collapse
|
2
|
Otto TC, Scott JR, Kauffman MA, Hodgins SM, Ditargiani RC, Hughes JH, Sarricks EP, Saturday GA, Hamilton TA, Cerasoli DM. Identification and characterization of novel catalytic bioscavengers of organophosphorus nerve agents. Chem Biol Interact 2012; 203:186-90. [PMID: 23041042 DOI: 10.1016/j.cbi.2012.09.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 09/14/2012] [Accepted: 09/18/2012] [Indexed: 11/18/2022]
Abstract
In an effort to discover novel catalytic bioscavengers of organophosphorus (OP) nerve agents, cell lysates from a diverse set of bacterial strains were screened for their capacity to hydrolyze the OP nerve agents VX, VR, and soman (GD). The library of bacterial strains was identified using both random and rational approaches. Specifically, two representative strains from eight categories of extremophiles were chosen at random. For the rational approach, the protein sequence of organophosphorus hydrolase (OPH) from Brevundimonas diminuta was searched against a non-redundant protein database using the Basic Local Alignment Search Tool to find regions of local similarity between sequences. Over 15 protein sequences with significant sequence similarity to OPH were identified from a variety of bacterial strains. Some of these matches were based on predicted protein structures derived from bacterial genome sequences rather than from bona fide proteins isolated from bacteria. Of the 25 strains selected for nerve agent testing, three bacterial strains had measurable levels of OP hydrolase activity. These strains are Ammoniphilus oxalaticus, Haloarcula sp., and Micromonospora aurantiaca. Lysates from A. oxalaticus had detectable hydrolysis of VR; Haloarcula sp. had appreciable hydrolysis of VX and VR, whereas lysates from M. aurantiaca had detectable hydrolysis of VR and GD.
Collapse
Affiliation(s)
- Tamara C Otto
- Neurobehavioral Toxicology Branch, Analytical Toxicology Division, US Army Medical Research Institute of Chemical Defense, 3100 Ricketts Point Road, Aberdeen Proving Ground, MD 21010-5400, United States.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
3
|
Korcan SE, Mutlu MB, Ciğerci IH, Güven K, Konuk M, Kutlu HM. delta-Aminolevulinic acid dehydratase of Haloarcula argentinensis isolated from Tuz Lake in Turkey. Environ Monit Assess 2010; 169:229-236. [PMID: 19757112 DOI: 10.1007/s10661-009-1164-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Accepted: 08/18/2009] [Indexed: 05/28/2023]
Abstract
The delta-aminolevulinic acid dehydratase (ALAD) enzyme of a novel record for Turkish microbial flora was studied. The isolate I-113 was obtained from Tuz Lake in Turkey and identified as Haloarcula argentinensis. The ALAD enzyme of the isolate was assayed in order to determine its requirements and to be used as biomarker for lead pollution in it's ambient. In enzymic studies, the effects of various metals (Cd, Co, Mg, Mn, Ni, Pb, and Zn), pH (3-11), temperatures (25-55 degrees C), and salinity (15-25%) conditions have been examined. The data obtained from the studies were analyzed statistically by using Kruskal-Wallis, Mann-Whitney, correlation, regression, variance analysis, and significance tests were performed by using SPSS 10.0 for Windows. Although its optimum pH was determined as 7, it was still active at pH 3-11. The optimal temperature for the enzyme was observed to be 30 degrees C. Mn and Pb inhibited its activity significantly (p < 0.05) while Zn increased it slightly. The ALAD enzyme in H. argentinensis could be used as a biomarker for Pb contamination.
Collapse
Affiliation(s)
- S Elif Korcan
- Biology Department, Faculty of Science and Literature, Afyon Kocatepe University, ANS Campus, Gazligol Yolu, 03200, Afyonkarahisar, Turkey
| | | | | | | | | | | |
Collapse
|
4
|
Rao L, Zhao X, Pan F, Li Y, Xue Y, Ma Y, Lu JR. Solution behavior and activity of a halophilic esterase under high salt concentration. PLoS One 2009; 4:e6980. [PMID: 19759821 PMCID: PMC2736375 DOI: 10.1371/journal.pone.0006980] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Accepted: 08/01/2009] [Indexed: 11/19/2022] Open
Abstract
Background Halophiles are extremophiles that thrive in environments with very high concentrations of salt. Although the salt reliance and physiology of these extremophiles have been widely investigated, the molecular working mechanisms of their enzymes under salty conditions have been little explored. Methodology/Principal Findings A halophilic esterolytic enzyme LipC derived from archeaon Haloarcula marismortui was overexpressed from Escherichia coli BL21. The purified enzyme showed a range of hydrolytic activity towards the substrates of p-nitrophenyl esters with different alkyl chains (n = 2−16), with the highest activity being observed for p-nitrophenyl acetate, consistent with the basic character of an esterase. The optimal esterase activities were found to be at pH 9.5 and [NaCl] = 3.4 M or [KCl] = 3.0 M and at around 45°C. Interestingly, the hydrolysis activity showed a clear reversibility against changes in salt concentration. At the ambient temperature of 22°C, enzyme systems working under the optimal salt concentrations were very stable against time. Increase in temperature increased the activity but reduced its stability. Circular dichroism (CD), dynamic light scattering (DLS) and small angle neutron scattering (SANS) were deployed to determine the physical states of LipC in solution. As the salt concentration increased, DLS revealed substantial increase in aggregate sizes, but CD measurements revealed the maximal retention of the α-helical structure at the salt concentration matching the optimal activity. These observations were supported by SANS analysis that revealed the highest proportion of unimers and dimers around the optimal salt concentration, although the coexistent larger aggregates showed a trend of increasing size with salt concentration, consistent with the DLS data. Conclusions/Significance The solution α-helical structure and activity relation also matched the highest proportion of enzyme unimers and dimers. Given that all the solutions studied were structurally inhomogeneous, it is important for future work to understand how the LipC's solution aggregation affected its activity.
Collapse
Affiliation(s)
- Lang Rao
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiubo Zhao
- Biological Physics Laboratory, School of Physics and Astronomy, the University of Manchester, Manchester, United Kingdom
| | - Fang Pan
- Biological Physics Laboratory, School of Physics and Astronomy, the University of Manchester, Manchester, United Kingdom
| | - Yin Li
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yanfen Xue
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yanhe Ma
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (YM); (JRL)
| | - Jian R. Lu
- Biological Physics Laboratory, School of Physics and Astronomy, the University of Manchester, Manchester, United Kingdom
- * E-mail: (YM); (JRL)
| |
Collapse
|
5
|
Fairley DJ, Wang G, Rensing C, Pepper IL, Larkin MJ. Expression of gentisate 1,2-dioxygenase (gdoA) genes involved in aromatic degradation in two haloarchaeal genera. Appl Microbiol Biotechnol 2006; 73:691-5. [PMID: 16802151 DOI: 10.1007/s00253-006-0509-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Revised: 05/16/2006] [Accepted: 05/16/2006] [Indexed: 11/27/2022]
Abstract
Gentisate-1,2-dioxygenase genes (gdoA), with homology to a number of bacterial dioxygenases, and genes encoding a putative coenzyme A (CoA)-synthetase subunit (acdB) and a CoA-thioesterase (tieA) were identified in two haloarchaeal isolates. In Haloarcula sp. D1, gdoA was expressed during growth on 4-hydroxybenzoate but not benzoate, and acdB and tieA were not expressed during growth on any of the aromatic substrates tested. In contrast, gdoA was expressed in Haloferax sp. D1227 during growth on benzoate, 3-hydroxybenzoate, cinnamate and phenylpropionate, and both acdB and tieA were expressed during growth on benzoate, cinnamate and phenylpropionate, but not on 3-hydroxybenzoate. This pattern of induction is consistent with these genes encoding steps in a CoA-mediated benzoate pathway in this strain.
Collapse
Affiliation(s)
- D J Fairley
- Queen's University Environmental Science & Technology Research Centre, The Queen's University of Belfast, Belfast, Northern Ireland, UK
| | | | | | | | | |
Collapse
|
6
|
Hutcheon GW, Vasisht N, Bolhuis A. Characterisation of a highly stable alpha-amylase from the halophilic archaeon Haloarcula hispanica. Extremophiles 2005; 9:487-95. [PMID: 16075161 DOI: 10.1007/s00792-005-0471-2] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2005] [Accepted: 06/20/2005] [Indexed: 10/25/2022]
Abstract
Intracellular and extracellular proteins from halophilic archaea face very saline conditions and must be able to maintain stability and functionality at nearly saturated salt concentrations. Haloarchaeal proteins contain specific adaptations to prevent aggregation and loss of activity in such conditions, but these adaptations usually result in a lack of stability in the absence of salt. Here, we present the characterisation of a secreted alpha-amylase (AmyH) from the halophilic archaeon Haloarcula hispanica. AmyH was shown to be very halophilic but, unusually for a halophilic protein, it retained activity in the absence of salt. Intrinsic fluorescence measurements and activity assays showed that AmyH was very stable in high-salt buffer and even maintained stability upon the addition of urea. Urea-induced denaturation was only achieved in the absence of NaCl, demonstrating clearly that the stability of the protein was salt-dependent. Sequencing of the amyH gene showed an amino acid composition typical of halophilic proteins and, moreover, the presence of a signal peptide containing diagnostic features characteristic of export via the Twin-arginine translocase (Tat). Analysis of the export of AmyH showed that it was translocated post-translationally, most likely in a folded and active conformation, confirming that AmyH is a substrate of the Tat pathway.
Collapse
Affiliation(s)
- George W Hutcheon
- Department of Biological Sciences, University of Warwick, CV4 7AL, Coventry, UK
| | | | | |
Collapse
|
7
|
Mizuki T, Kamekura M, DasSarma S, Fukushima T, Usami R, Yoshida Y, Horikoshi K. Ureases of extreme halophiles of the genus Haloarcula with a unique structure of gene cluster. Biosci Biotechnol Biochem 2004; 68:397-406. [PMID: 14981304 DOI: 10.1271/bbb.68.397] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We searched for urease activities in 71 strains of extreme halophiles by a urea-phenol red-agar plate method. Positive strains were further investigated by measuring the ammonia released from urea in cell-free extracts. Only 4 strains of the genus Haloarcula, Har. aidinensis, Har. hispanica, Har. japonica, and Har. marismortui were finally shown as the urease producers. A partially purified urease from Har. hispanica was a typical halophilic enzyme in that it showed maximum activity at 18-23% NaCl and lost the activity irreversibly in the absence of NaCl. Partial genes (1596 bp) of the urease encoding from upstream of the beta subunit down to the N-terminal 139 amino acids of the alpha subunit, were PCR amplified from the four strains, as well as from five urease-negative Haloarcula strains. Strains of other genera, which were urease-negative, did not yield PCR products. The deduced amino acid sequences of the beta subunit and partial alpha subunit were similar to each other (92-100% similarities) and to those from other organisms. Analysis of the draft genome sequence of Har. marismortui, however, suggested that the order of the genes encoding the three subunits (with the total number of amino acids of 834) and four accessory proteins was beta-alpha-gamma-UreG-UreD-UreE-UreF. This order is quite unique, since in other microorganisms the order is gamma-beta-alpha-UreE-UreF-UreG-UreD in most cases. No open reading frames were detected in the PCR-amplified upstream of the beta subunit, suggesting that all Haloarcula species have the same unique structure of the urease gene cluster.
Collapse
Affiliation(s)
- Toru Mizuki
- Department of Applied Chemistry, Faculty of Engineering, Toyo University, Kujirai, Kawagoe, Japan
| | | | | | | | | | | | | |
Collapse
|
8
|
Fukushima T, Mizuki T, Echigo A, Inoue A, Usami R. Organic solvent tolerance of halophilic alpha-amylase from a Haloarchaeon, Haloarcula sp. strain S-1. Extremophiles 2004; 9:85-9. [PMID: 15378403 DOI: 10.1007/s00792-004-0423-2] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2004] [Accepted: 08/27/2004] [Indexed: 10/26/2022]
Abstract
A halophilic archaeon, Haloarcula sp. strain S-1, produced extracellular organic solvent-tolerant alpha-amylase. Molecular mass of the enzyme was estimated to be 70 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. This amylase exhibited maximal activity at 50 degrees C in buffer containing 4.3 M NaCl, pH 7.0. Moreover, the enzyme was active and stable in various organic solvents (benzene, toluene, and chloroform, etc.). Activity was not detected at low ionic strengths, but it was detected in the presence of chloroform at low salt concentrations. On the other hand, no activity was detected in the presence of ethyl alcohol and acetone.
Collapse
Affiliation(s)
- Tadamasa Fukushima
- Department of Applied Chemistry, Faculty of Engineering, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan.
| | | | | | | | | |
Collapse
|
9
|
Santoni E, Jakopitsch C, Obinger C, Smulevich G. Manipulating the covalent link between distal side tryptophan, tyrosine, and methionine in catalase-peroxidases: an electronic absorption and resonance Raman study. Biopolymers 2004; 74:46-50. [PMID: 15137092 DOI: 10.1002/bip.20041] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Electronic absorption and resonance Raman spectroscopies have been applied to study the ferric and ferrous forms, and fluoride complexes of the Tyr249Phe and Met275Ile variants of the recombinant catalase-peroxidase (KatG) from the cyanobacterium Synechocystis PCC 6803. Both crystal structures and mass spectrometric analysis demonstrated that Tyr249 and Met275 are part of a novel KatG-specific covalent adduct including in addition a conserved tryptophan. Its role is not well established, but it has been shown to be essential for the catalase activity. In the present work we investigate the effect of mutation on the protein stability and ligand binding. The results clearly show that mutation weakens the heme binding to the protein, giving rise to a partial conversion from the 5-coordinate high spin of the wild-type protein to 6-coordinate low-spin heme. An internal ligand binds the heme iron on the distal side as a consequence of protein destabilization and partially prevents the binding of external ligand such as fluoride. The results are compared with those previously reported for the Trp122Ala and Trp122Phe variants.
Collapse
Affiliation(s)
- Elisa Santoni
- Dipartimento di Chimica, Universita' di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Florence, Italy
| | | | | | | |
Collapse
|
10
|
Abstract
The genes encoding I, K, E, C, F, A, B and D subunits of A0A1 ATP synthase were cloned from Haloarcula japonica strain TR-1. The genes were split into two clusters. Northern analysis revealed that the larger gene cluster would be transcribed as a single mRNA.
Collapse
Affiliation(s)
- R Yatsunami
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | | | | | | |
Collapse
|
11
|
Abstract
Halophilic enzymes, while performing identical enzymatic functions as their non-halophilic counterparts, have been shown to exhibit substantially different properties, among them the requirement for high salt concentrations, in the 1-4 M range, for activity and stability, and a high excess of acidic over basic amino residues. The following communication reviews the functional and structural properties of two proteins isolated from the extremely halophilic archaeon Haloarcula marismortui: the enzyme malate-dehydrogenase (hMDH) and the 2Fe-2S protein ferredoxin. It is argued that the high negative surface charge of halophilic proteins makes them more soluble and renders them more flexible at high salt concentrations, conditions under which non-halophilic proteins tend to aggregate and become rigid. This high surface charge is neutralized mainly by tightly bound water dipoles. The requirement of high salt concentration for the stabilization of halophilic enzymes, on the other hand, is due to a low affinity binding of the salt to specific sites on the surface of the folded polypeptide, thus stabilizing the active conformation of the protein.
Collapse
Affiliation(s)
- M Mevarech
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel.
| | | | | |
Collapse
|
12
|
Yatsunami R, Iwamoto M, Ihara K, Nakamura S. Molecular cloning of A1-ATPase gene from extremely halophilic archaeon Haloarcula japonica strain TR-1. Nucleic Acids Symp Ser 2000:75-6. [PMID: 10780386 DOI: 10.1093/nass/42.1.75] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The genes encoding A1-ATPase A- and B-subunits were cloned from Haloarcula japonica strain TR-1. Nucleotide sequencing analysis of the A1-ATPase gene revealed that the A- and B-subunits consisted of 586 and 473 amino acids, respectively. The deduced amino acid sequences of the A- and B-subunits of Ha. japonica showed high identities with those of Halobacterium salinarum and Haloferax volcanii. The consensus ATP-binding motif was found in the A-subunit.
Collapse
Affiliation(s)
- R Yatsunami
- Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | | | | | | |
Collapse
|