1
|
Muhammad MA, Ahmad N, Akhter M, Rashid N. Structural and functional analyses of Pcal_0917, an α-glucosidase from hyperthermophilic archaeon Pyrobaculum calidifontis. Int J Biol Macromol 2023:125446. [PMID: 37330102 DOI: 10.1016/j.ijbiomac.2023.125446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/16/2023] [Accepted: 06/14/2023] [Indexed: 06/19/2023]
Abstract
Genome analysis of Pyrobaculum calidifontis revealed the presence of α-glucosidase (Pcal_0917) gene. Structural analysis affirmed the presence of signature sequences of Type II α-glucosidases in Pcal_0917. We have heterologously expressed the gene and produced recombinant Pcal_0917 in Escherichia coli. Biochemical characteristics of the recombinant enzyme resembled to that of Type I α-glucosidases, instead of Type II. Recombinant Pcal_0917 existed in a tetrameric form in solution and displayed highest activity at 95 °C and pH 6.0, independent of any metal ions. A short heat-treatment at 90 °C resulted in a 35 % increase in enzyme activity. A slight structural shift was observed by CD spectrometry at this temperature. Half-life of the enzyme was >7 h at 90 °C. Pcal_0917 exhibited apparent Vmax values of 1190 ± 5 and 3.9 ± 0.1 U/mg against p-nitrophenyl α-D-glucopyranoside and maltose, respectively. To the best of our knowledge, Pcal_0917 displayed the highest ever reported p-nitrophenyl α-D-glucopyranosidase activity among the characterized counterparts. Moreover, Pcal_0917 displayed transglycosylation activity in addition to α-glucosidase activity. Furthermore, in combination with α-amylase, Pcal_0917 was capable of producing glucose syrup from starch with >40 % glucose content. These properties make Pcal_0917 a potential candidate for starch hydrolyzing industry.
Collapse
Affiliation(s)
- Majida Atta Muhammad
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Nasir Ahmad
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Mohsina Akhter
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan.
| |
Collapse
|
2
|
Archaea as a Model System for Molecular Biology and Biotechnology. Biomolecules 2023; 13:biom13010114. [PMID: 36671499 PMCID: PMC9855744 DOI: 10.3390/biom13010114] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Archaea represents the third domain of life, displaying a closer relationship with eukaryotes than bacteria. These microorganisms are valuable model systems for molecular biology and biotechnology. In fact, nowadays, methanogens, halophiles, thermophilic euryarchaeota, and crenarchaeota are the four groups of archaea for which genetic systems have been well established, making them suitable as model systems and allowing for the increasing study of archaeal genes' functions. Furthermore, thermophiles are used to explore several aspects of archaeal biology, such as stress responses, DNA replication and repair, transcription, translation and its regulation mechanisms, CRISPR systems, and carbon and energy metabolism. Extremophilic archaea also represent a valuable source of new biomolecules for biological and biotechnological applications, and there is growing interest in the development of engineered strains. In this review, we report on some of the most important aspects of the use of archaea as a model system for genetic evolution, the development of genetic tools, and their application for the elucidation of the basal molecular mechanisms in this domain of life. Furthermore, an overview on the discovery of new enzymes of biotechnological interest from archaea thriving in extreme environments is reported.
Collapse
|
3
|
Macdonald JFH, Krohn I, Streit WR. Screening Metagenomes for Algae Cell Wall Carbohydrates Degrading Hydrolases in Enrichment Cultures. Methods Mol Biol 2023; 2555:125-137. [PMID: 36306083 DOI: 10.1007/978-1-0716-2795-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Sustainable use of natural products is one of the key challenges for the future. An increasing focus is on marine organic matter, mostly algae. New biotechnological tools for processing high amounts of micro- and macroalgae are necessary for efficient industrial degradation of marine matter. Secreted glycosyl hydrolases can be enriched and tested on the specific algae cell wall polymers of all algae groups (Rhodophyta; Phaeophyceae; Chlorophyta/Charophyta). Metagenomic analyses established new possibilities to screen algae-associated microbiomes for novel degrading enzymes in combination with sequence-based function prediction.
Collapse
Affiliation(s)
- Jascha F H Macdonald
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany.
| | - Ines Krohn
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| |
Collapse
|
4
|
High yield synthesis of nigerooligosaccharides by transglycosylation catalyzed by α-glucosidase TaAglA from Thermoplasma acidophilum. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.101582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
5
|
Cabrera MÁ, Blamey JM. Biotechnological applications of archaeal enzymes from extreme environments. Biol Res 2018; 51:37. [PMID: 30290805 PMCID: PMC6172850 DOI: 10.1186/s40659-018-0186-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 09/25/2018] [Indexed: 11/10/2022] Open
Abstract
To date, many industrial processes are performed using chemical compounds, which are harmful to nature. An alternative to overcome this problem is biocatalysis, which uses whole cells or enzymes to carry out chemical reactions in an environmentally friendly manner. Enzymes can be used as biocatalyst in food and feed, pharmaceutical, textile, detergent and beverage industries, among others. Since industrial processes require harsh reaction conditions to be performed, these enzymes must possess several characteristics that make them suitable for this purpose. Currently the best option is to use enzymes from extremophilic microorganisms, particularly archaea because of their special characteristics, such as stability to elevated temperatures, extremes of pH, organic solvents, and high ionic strength. Extremozymes, are being used in biotechnological industry and improved through modern technologies, such as protein engineering for best performance. Despite the wide distribution of archaea, exist only few reports about these microorganisms isolated from Antarctica and very little is known about thermophilic or hyperthermophilic archaeal enzymes particularly from Antarctica. This review summarizes current knowledge of archaeal enzymes with biotechnological applications, including two extremozymes from Antarctic archaea with potential industrial use, which are being studied in our laboratory. Both enzymes have been discovered through conventional screening and genome sequencing, respectively.
Collapse
Affiliation(s)
- Ma Ángeles Cabrera
- Fundación Científica y Cultural Biociencia, José Domingo Cañas, 2280, Santiago, Chile.,Facultad de Química y Biología, Universidad de Santiago de Chile, Avenida Libertador Bernardo O´Higgins, 3363, Santiago, Chile
| | - Jenny M Blamey
- Fundación Científica y Cultural Biociencia, José Domingo Cañas, 2280, Santiago, Chile. .,Facultad de Química y Biología, Universidad de Santiago de Chile, Avenida Libertador Bernardo O´Higgins, 3363, Santiago, Chile.
| |
Collapse
|
6
|
Cuebas-Irizarry MF, Irizarry-Caro RA, López-Morales C, Badillo-Rivera KM, Rodríguez-Minguela CM, Montalvo-Rodríguez R. Cloning and Molecular Characterization of an Alpha-Glucosidase (MalH) from the Halophilic Archaeon Haloquadratum walsbyi. Life (Basel) 2017; 7:life7040046. [PMID: 29160840 PMCID: PMC5745559 DOI: 10.3390/life7040046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/15/2017] [Accepted: 11/18/2017] [Indexed: 11/16/2022] Open
Abstract
We report the heterologous expression and molecular characterization of the first extremely halophilic alpha-glucosidase (EC 3.2.1.20) from the archaeon Haloquadratum walsbyi. A 2349 bp region (Hqrw_2071) from the Hqr. walsbyi C23 annotated genome was PCR-amplified and the resulting amplicon ligated into plasmid pET28b(+), expressed in E. coli Rosetta cells, and the resulting protein purified by Ni-NTA affinity chromatography. The recombinant protein showed an estimated molecular mass of 87 kDa, consistent with the expected value of the annotated protein, and an optimal activity for the hydrolysis of α-PNPG was detected at 40 °C, and at pH 6.0. Enzyme activity values were the highest in the presence of 3 M NaCl or 3-4 M KCl. However, specific activity values were two-fold higher in the presence of 3-4 M KCl when compared to NaCl suggesting a cytoplasmic localization. Phylogenetic analyses, with respect to other alpha-glucosidases from members of the class Halobacteria, showed that the Hqr. walsbyi MalH was most similar (up to 41%) to alpha-glucosidases and alpha-xylosidases of Halorubrum. Moreover, computational analyses for the detection of functional domains, active and catalytic sites, as well as 3D structural predictions revealed a close relationship with an E. coli YicI-like alpha-xylosidase of the GH31 family. However, the purified enzyme did not show alpha-xylosidase activity. This narrower substrate range indicates a discrepancy with annotations from different databases and the possibility of specific substrate adaptations of halophilic glucosidases due to high salinity. To our knowledge, this is the first report on the characterization of an alpha-glucosidase from the halophilic Archaea, which could serve as a new model to gain insights into carbon metabolism in this understudied microbial group.
Collapse
Affiliation(s)
| | - Ricardo A Irizarry-Caro
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Carol López-Morales
- Biology Department, Box 9000, University of Puerto Rico, Mayagüez, PR 00681, USA.
| | | | | | | |
Collapse
|
7
|
Smirnova J, Fernie AR, Spahn CMT, Steup M. Photometric assay of maltose and maltose-forming enzyme activity by using 4-alpha-glucanotransferase (DPE2) from higher plants. Anal Biochem 2017; 532:72-82. [PMID: 28576440 DOI: 10.1016/j.ab.2017.05.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 05/09/2017] [Accepted: 05/26/2017] [Indexed: 12/17/2022]
Abstract
Maltose frequently occurs as intermediate of the central carbon metabolism of prokaryotic and eukaryotic cells. Various mutants possess elevated maltose levels. Maltose exists as two anomers, (α- and β-form) which are rapidly interconverted without requiring enzyme-mediated catalysis. As maltose is often abundant together with other oligoglucans, selective quantification is essential. In this communication, we present a photometric maltose assay using 4-alpha-glucanotransferase (AtDPE2) from Arabidopsis thaliana. Under in vitro conditions, AtDPE2 utilizes maltose as glucosyl donor and glycogen as acceptor releasing the other hexosyl unit as free glucose which is photometrically quantified following enzymatic phosphorylation and oxidation. Under the conditions used, DPE2 does not noticeably react with other di- or oligosaccharides. Selectivity compares favorably with that of maltase frequently used in maltose assays. Reducing end interconversion of the two maltose anomers is in rapid equilibrium and, therefore, the novel assay measures total maltose contents. Furthermore, an AtDPE2-based continuous photometric assay is presented which allows to quantify β-amylase activity and was found to be superior to a conventional test. Finally, the AtDPE2-based maltose assay was used to quantify leaf maltose contents of both Arabidopsis wild type and AtDPE2-deficient plants throughout the light-dark cycle. These data are presented together with assimilatory starch levels.
Collapse
Affiliation(s)
- Julia Smirnova
- Institute for Biochemistry and Biology, Department of Plant Physiology, University of Potsdam, Building 20, Karl-Liebknecht-Str. 20, 14461 Potsdam, Germany; Institute of Biophysics and Medical Physics of the Charité, Universitätsmedizin Berlin, Campus Berlin Mitte, 10117 Berlin, Germany; Max-Planck-Institute of Molecular Plant Physiology, Department 1 (Willmitzer), Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Department 1 (Willmitzer), Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Christian M T Spahn
- Institute of Biophysics and Medical Physics of the Charité, Universitätsmedizin Berlin, Campus Berlin Mitte, 10117 Berlin, Germany
| | - Martin Steup
- Institute for Biochemistry and Biology, Department of Plant Physiology, University of Potsdam, Building 20, Karl-Liebknecht-Str. 20, 14461 Potsdam, Germany.
| |
Collapse
|
8
|
Abstract
For modern biotechnology there is a steady need to identify novel enzymes. In biotechnological applications, however, enzymes often must function under extreme and nonnatural conditions (i.e., in the presence of solvents, high temperature and/or at extreme pH values). Cellulases have many industrial applications from the generation of bioethanol, a realistic long-term energy source, to the finishing of textiles. These industrial processes require cellulolytic activity under a wide range of pH, temperature, and ionic conditions, and they are usually carried out by mixtures of cellulases. Investigation of the broad diversity of cellulolytic enzymes involved in the natural degradation of cellulose is necessary for optimizing these processes.
Collapse
Affiliation(s)
- Nele Ilmberger
- Microbiology & Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Wolfgang R Streit
- Microbiology & Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany.
| |
Collapse
|
9
|
General Characteristics and Important Model Organisms. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014. [DOI: 10.1128/9781555815516.ch2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
10
|
Genome Shuffling of Aspergillus niger for Improving Transglycosylation Activity. Appl Biochem Biotechnol 2013; 172:50-61. [DOI: 10.1007/s12010-013-0421-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 07/31/2013] [Indexed: 10/26/2022]
|
11
|
Jüergensen J, Ilmberger N, Streit WR. Screening for cellulases with industrial value and their use in biomass conversion. Methods Mol Biol 2012; 834:1-16. [PMID: 22144349 DOI: 10.1007/978-1-61779-483-4_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Cellulose is an easily renewable and highly occurring resource. To take advantage of this great potential, there is a constant need of new cellulose degrading enzymes. In industrial applications enzymes have to function under extreme conditions like high temperature, very acidic or basic pH and different solvents. Cellulases have a huge area of application, for example the textile and food industry as well as the generation of bioethanol as an alternative energy source. They have the ability to yield a great energetic potential, but there is still a lack of economical technologies to conquer the stability of the cellulose structure. Via metagenomic research and well-directed screening, it is possible to detect new cellulases, which are active under tough industrial conditions.
Collapse
Affiliation(s)
- Julia Jüergensen
- Abteilung für Mikrobiologie und Biotechnologie, Universität Hamburg, Hamburg, Germany
| | | | | |
Collapse
|
12
|
Shrestha KL, Liu SW, Huang CP, Wu HM, Wang WC, Li YK. Characterization and identification of essential residues of the glycoside hydrolase family 64 laminaripentaose-producing- -1, 3-glucanase. Protein Eng Des Sel 2011; 24:617-25. [DOI: 10.1093/protein/gzr031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
13
|
Kumar L, Awasthi G, Singh B. Extremophiles: A Novel Source of Industrially Important Enzymes. ACTA ACUST UNITED AC 2011. [DOI: 10.3923/biotech.2011.121.135] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
14
|
Vuong TV, Wilson DB. Glycoside hydrolases: catalytic base/nucleophile diversity. Biotechnol Bioeng 2010; 107:195-205. [PMID: 20552664 DOI: 10.1002/bit.22838] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recent studies have shown that a number of glycoside hydrolase families do not follow the classical catalytic mechanisms, as they lack a typical catalytic base/nucleophile. A variety of mechanisms are used to replace this function, including substrate-assisted catalysis, a network of several residues, and the use of non-carboxylate residues or exogenous nucleophiles. Removal of the catalytic base/nucleophile by mutation can have a profound impact on substrate specificity, producing enzymes with completely new functions.
Collapse
Affiliation(s)
- Thu V Vuong
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | | |
Collapse
|
15
|
A high-throughput method for screening of Aspergillus niger mutants with high transglycosylation activity by detecting non-fermentable reducing sugar. World J Microbiol Biotechnol 2010; 27:1519-23. [DOI: 10.1007/s11274-010-0595-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 10/13/2010] [Indexed: 11/25/2022]
|
16
|
Song KM, Shim JH, Park JT, Kim SH, Kim YW, Boos W, Park KH. Transglycosylation properties of maltodextrin glucosidase (MalZ) from Escherichia coli and its application for synthesis of a nigerose-containing oligosaccharide. Biochem Biophys Res Commun 2010; 397:87-92. [DOI: 10.1016/j.bbrc.2010.05.073] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Accepted: 05/13/2010] [Indexed: 10/19/2022]
|
17
|
Zhou F, Chen H, Xu Y. GASdb: a large-scale and comparative exploration database of glycosyl hydrolysis systems. BMC Microbiol 2010; 10:69. [PMID: 20202206 PMCID: PMC2838879 DOI: 10.1186/1471-2180-10-69] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Accepted: 03/04/2010] [Indexed: 11/29/2022] Open
Abstract
Background The genomes of numerous cellulolytic organisms have been recently sequenced or in the pipeline of being sequenced. Analyses of these genomes as well as the recently sequenced metagenomes in a systematic manner could possibly lead to discoveries of novel biomass-degradation systems in nature. Description We have identified 4,679 and 49,099 free acting glycosyl hydrolases with or without carbohydrate binding domains, respectively, by scanning through all the proteins in the UniProt Knowledgebase and the JGI Metagenome database. Cellulosome components were observed only in bacterial genomes, and 166 cellulosome-dependent glycosyl hydrolases were identified. We observed, from our analysis data, unexpected wide distributions of two less well-studied bacterial glycosyl hydrolysis systems in which glycosyl hydrolases may bind to the cell surface directly rather than through linking to surface anchoring proteins, or cellulosome complexes may bind to the cell surface by novel mechanisms other than the other used SLH domains. In addition, we found that animal-gut metagenomes are substantially enriched with novel glycosyl hydrolases. Conclusions The identified biomass degradation systems through our large-scale search are organized into an easy-to-use database GASdb at http://csbl.bmb.uga.edu/~ffzhou/GASdb/, which should be useful to both experimental and computational biofuel researchers.
Collapse
Affiliation(s)
- Fengfeng Zhou
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | | | | |
Collapse
|
18
|
Abstract
Modern biotechnology has the steady need to continuously identify novel enzymes for use in biotechnological applications. In industrial applications, however, enzymes often have to function under extreme and nonnatural conditions (i.e., in the presence of solvents, high temperature and/or at extreme pH values). Cellulases have many industrial applications from the generation of bioethanol, a realistic long-term energy source, to the finishing of textiles. These industrial processes require cellulolytic activity under a range of pH, temperature, and ionic conditions, and they are usually carried out by mixtures of cellulases. Investigation of the broad diversity of cellulolytic enzymes involved in the natural degradation of cellulose is necessary for optimization of these processes.
Collapse
Affiliation(s)
- Nele Ilmberger
- Microbiology & Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | | |
Collapse
|
19
|
Alpha-mannosidases from the digestive fluid of Rhynchophorus Palmarum larvae as novel biocatalysts for transmannosylation reactions. Appl Biochem Biotechnol 2009; 162:307-20. [PMID: 20033854 DOI: 10.1007/s12010-009-8883-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Accepted: 12/02/2009] [Indexed: 10/20/2022]
Abstract
Two biological fluids, namely hemolymph and digestive fluid from the larval stage of Rhynchophorus palmarum Linneaus, a serious pest in agroecosystem exploiting oil palm, were screened for hydrolytic activities, by the use of synthetic and natural glycoside substrates. Several exo and endoglycosidase activities were observed but, the interesting alpha-mannosidase activity (0.41 +/- 0.04 UI) had attracted our attention. So, we have previously demonstrated that this activity harbours four distinctive alpha-mannosidase isoforms named RpltM, RplM1, RplM2 and RplM3. We have extended this work to determine the ability of these enzymes to catalyze synthesis reactions. Finally, we have revealed that, alpha-mannosidases from the digestive fluid of R. palmarum larvae catalyze transmannosylation reactions. The stability of the enzymes and the optimization of the transfer product yield were studied as functions of pH, enzyme unit, starting concentration of donor or acceptor and time. It was shown that, in experimental optimum conditions, average yields of 12.34 +/- 0.75, 12.15 +/- 0.79, 5.59 +/- 0.35 and 8.43 +/- 0.50% were obtained for the alpha-mannosidases RpltM, RplM1, RplM2 and RplM3, respectively. On the basis of this work, alpha-mannosidases from the digestive fluid of Rhynchophorus palmarum larvae appear to be a valuable tool for the preparation of neoglycoconjugates.
Collapse
|
20
|
Expression and characterization of an α-glucosidase from Thermoanaerobacter ethanolicus JW200 with potential for industrial application. Biologia (Bratisl) 2009. [DOI: 10.2478/s11756-009-0197-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
21
|
Alpha-glucosidase promotes hemozoin formation in a blood-sucking bug: an evolutionary history. PLoS One 2009; 4:e6966. [PMID: 19742319 PMCID: PMC2734994 DOI: 10.1371/journal.pone.0006966] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Accepted: 07/17/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Hematophagous insects digest large amounts of host hemoglobin and release heme inside their guts. In Rhodnius prolixus, hemoglobin-derived heme is detoxified by biomineralization, forming hemozoin (Hz). Recently, the involvement of the R. prolixus perimicrovillar membranes in Hz formation was demonstrated. METHODOLOGY/PRINCIPAL FINDINGS Hz formation activity of an alpha-glucosidase was investigated. Hz formation was inhibited by specific alpha-glucosidase inhibitors. Moreover, Hz formation was sensitive to inhibition by Diethypyrocarbonate, suggesting a critical role of histidine residues in enzyme activity. Additionally, a polyclonal antibody raised against a phytophagous insect alpha-glucosidase was able to inhibit Hz formation. The alpha-glucosidase inhibitors have had no effects when used 10 h after the start of reaction, suggesting that alpha-glucosidase should act in the nucleation step of Hz formation. Hz formation was seen to be dependent on the substrate-binding site of enzyme, in a way that maltose, an enzyme substrate, blocks such activity. dsRNA, constructed using the sequence of alpha-glucosidase gene, was injected into R. prolixus females' hemocoel. Gene silencing was accomplished by reduction of both alpha-glucosidase and Hz formation activities. Insects were fed on plasma or hemin-enriched plasma and gene expression and activity of alpha-glucosidase were higher in the plasma plus hemin-fed insects. The deduced amino acid sequence of alpha-glucosidase shows a high similarity to the insect alpha-glucosidases, with critical histidine and aspartic residues conserved among the enzymes. CONCLUSIONS/SIGNIFICANCE Herein the Hz formation is shown to be associated to an alpha-glucosidase, the biochemical marker from Hemipteran perimicrovillar membranes. Usually, these enzymes catalyze the hydrolysis of glycosidic bond. The results strongly suggest that alpha-glucosidase is responsible for Hz nucleation in the R. prolixus midgut, indicating that the plasticity of this enzyme may play an important role in conferring fitness to hemipteran hematophagy, for instance.
Collapse
|
22
|
Vocadlo DJ, Davies GJ. Mechanistic insights into glycosidase chemistry. Curr Opin Chem Biol 2009; 12:539-55. [PMID: 18558099 DOI: 10.1016/j.cbpa.2008.05.010] [Citation(s) in RCA: 300] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 05/19/2008] [Indexed: 11/16/2022]
Abstract
The enzymatic hydrolysis of the glycosidic bond continues to gain importance, reflecting the critically important roles complex glycans play in health and disease as well as the rekindled interest in enzymatic biomass conversion. Recent advances include the broadening of our understanding of enzyme reaction coordinates, through both computational and structural studies, improved understanding of enzyme inhibition through transition state mimicry and fascinating insights into mechanism yielded by physical organic chemistry approaches.
Collapse
Affiliation(s)
- David J Vocadlo
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, V5A 1S6, Canada.
| | | |
Collapse
|
23
|
Deoxynojirimycin enhanced the transglycosylation activity of a glycosidase from the China white jade snail. J Biotechnol 2009; 139:229-35. [DOI: 10.1016/j.jbiotec.2008.12.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Revised: 10/31/2008] [Accepted: 12/09/2008] [Indexed: 11/22/2022]
|
24
|
Bagos PG, Tsirigos KD, Plessas SK, Liakopoulos TD, Hamodrakas SJ. Prediction of signal peptides in archaea. Protein Eng Des Sel 2008; 22:27-35. [PMID: 18988691 DOI: 10.1093/protein/gzn064] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Computational prediction of signal peptides (SPs) and their cleavage sites is of great importance in computational biology; however, currently there is no available method capable of predicting reliably the SPs of archaea, due to the limited amount of experimentally verified proteins with SPs. We performed an extensive literature search in order to identify archaeal proteins having experimentally verified SP and managed to find 69 such proteins, the largest number ever reported. A detailed analysis of these sequences revealed some unique features of the SPs of archaea, such as the unique amino acid composition of the hydrophobic region with a higher than expected occurrence of isoleucine, and a cleavage site resembling more the sequences of gram-positives with almost equal amounts of alanine and valine at the position-3 before the cleavage site and a dominant alanine at position-1, followed in abundance by serine and glycine. Using these proteins as a training set, we trained a hidden Markov model method that predicts the presence of the SPs and their cleavage sites and also discriminates such proteins from cytoplasmic and transmembrane ones. The method performs satisfactorily, yielding a 35-fold cross-validation procedure, a sensitivity of 100% and specificity 98.41% with the Matthews' correlation coefficient being equal to 0.964. This particular method is currently the only available method for the prediction of secretory SPs in archaea, and performs consistently and significantly better compared with other available predictors that were trained on sequences of eukaryotic or bacterial origin. Searching 48 completely sequenced archaeal genomes we identified 9437 putative SPs. The method, PRED-SIGNAL, and the results are freely available for academic users at http://bioinformatics.biol.uoa.gr/PRED-SIGNAL/ and we anticipate that it will be a valuable tool for the computational analysis of archaeal genomes.
Collapse
Affiliation(s)
- P G Bagos
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens 15701, Greece.
| | | | | | | | | |
Collapse
|
25
|
Rempel BP, Withers SG. Covalent inhibitors of glycosidases and their applications in biochemistry and biology. Glycobiology 2008; 18:570-86. [PMID: 18499865 DOI: 10.1093/glycob/cwn041] [Citation(s) in RCA: 146] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Glycoside hydrolases are important enzymes in a number of essential biological processes. Irreversible inhibitors of this class of enzyme have attracted interest as probes of both structure and function. In this review we discuss some of the compounds used to covalently modify glycosidases, their use in residue identification, structural and mechanistic investigations, and finally their applications, both in vitro and in vivo, to complex biological systems.
Collapse
Affiliation(s)
- Brian P Rempel
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | | |
Collapse
|
26
|
Soro RY, Diopoh JK, Willemot RM, Combes D. Enzymatic synthesis of polyglucosylfructosides from sucrose alone by a novel α-glucosidase isolated from the digestive juice of Archachatina ventricosa (Achatinideae). Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2007.07.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
27
|
Transformation of maltose into prebiotic isomaltooligosaccharides by a novel α-glucosidase from Xantophyllomyces dendrorhous. Process Biochem 2007. [DOI: 10.1016/j.procbio.2007.08.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
28
|
Ferrer M, Beloqui A, Golyshina OV, Plou FJ, Neef A, Chernikova TN, Fernández-Arrojo L, Ghazi I, Ballesteros A, Elborough K, Timmis KN, Golyshin PN. Biochemical and structural features of a novel cyclodextrinase from cow rumen metagenome. Biotechnol J 2007; 2:207-13. [PMID: 17238236 DOI: 10.1002/biot.200600183] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A novel enzyme, RA.04, belonging to the alpha-amylase family was obtained after expression of metagenomic DNA from rumen fluid (Ferrer et al.: Environ. Microbiol. 2005, 7, 1996-2010). The purified RA.04 has a tetrameric structure (280 kDa) and exhibited maximum activity (5000 U/mg protein) at 70 degrees C and was active within an unusually broad pH range from 5.5 to 9.0. It maintained 80% activity at pH 5.0 and 9.5 and 75 degrees C. The enzyme hydrolyzed alpha-D-(1,4) bonds 13-fold faster than alpha-D-(1,6) bonds to yield maltose and glucose as the main products, and it exhibited transglycosylation activity. Its preferred substrates, in the descending order, were maltooligosaccharides (C3-C7), cyclomaltoheptaose (beta-CD), cyclomaltohexaose (alpha-CD), cyclomaltooctaose (gamma-CD), soluble starch, amylose, pullulan and amylopectin. The biochemical properties and amino acid sequence alignments suggested that this enzyme is a cyclomaltodextrinase. However, despite the similarity in the catalytic module (with Glu359 and Asp331 being the catalytic nucleophile and substrate-binding residues, respectively), the enzyme bears a shorter N-terminal domain that may keep the active site more accessible for both starch and pullulan, compared to the other known CDases. Moreover, RA.04 lacks the well-conserved N-terminal Trp responsible for the substrate preference typical of CDases/MAases/PNases, suggesting a new residue is implicated in the preference for cyclic maltooligosaccharides. This study has demonstrated the usefulness of a metagenomic approach to gain novel debranching enzymes, important for the bread/food industries, from microbial environments with a high rate of plant polymer turnover, exemplified by the cow rumen.
Collapse
Affiliation(s)
- Manuel Ferrer
- CSIC, Institute of Catalysis, Cantoblanco, Madrid, Spain
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Ferrer M, Golyshina O, Beloqui A, Golyshin PN. Mining enzymes from extreme environments. Curr Opin Microbiol 2007; 10:207-14. [PMID: 17548239 DOI: 10.1016/j.mib.2007.05.004] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Revised: 04/09/2007] [Accepted: 05/17/2007] [Indexed: 11/21/2022]
Abstract
Current advances in metagenomics have revolutionized the research in fields of microbial ecology and biotechnology, enabling not only a glimpse into the uncultured microbial population and mechanistic understanding of possible biogeochemical cycles and lifestyles of extreme organisms but also the high-throughput discovery of new enzymes for industrial bioconversions. Nowadays, the genetic and enzymatic differences across the gradients from 'neutral and pristine' to 'extreme and polluted' environments are well documented. Yet, extremophilic organisms are possibly the least well understood because our ability to study and understand their metabolic potential has been hampered by our inability to isolate pure cultures. There are at least two obstacles for reaping the fruit of the microbial diversity of extremophiles: first, in spite of the recent progress in development of new culturing techniques most extremophiles cannot be cultured using traditional culturing technologies; and second, the problem of the very low biomass densities often occurs under the conditions hostile for life, which often do not yield enough DNA and reduces the effectiveness of cloning.
Collapse
Affiliation(s)
- Manuel Ferrer
- Division of Applied Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, 28049 Madrid, Spain.
| | | | | | | |
Collapse
|
30
|
Ferrer M, Golyshina OV, Beloqui A, Golyshin PN, Timmis KN. The cellular machinery of Ferroplasma acidiphilum is iron-protein-dominated. Nature 2007; 445:91-4. [PMID: 17203061 DOI: 10.1038/nature05362] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2006] [Accepted: 10/20/2006] [Indexed: 11/09/2022]
Abstract
Ferroplasma is a genus of the Archaea, one of the three branches of the tree of life, and belongs to the order Thermoplasmatales (Euryarchaeota), which contains the most acidophilic microbes yet known. Ferroplasma species live in acid mine drainage, acidic pools and environments containing sulphidic ores such as pyrite and characterized by pH values of 0-2 and high concentrations of ferrous iron and other heavy metals. F. acidiphilum strain Y(T) is a chemoautotroph that grows optimally at pH 1.7 and gains energy by oxidizing ferrous iron and carbon by the fixation of carbon dioxide. Here we show that 86% of 189 investigated cellular proteins of F. acidiphilum are iron-metalloproteins. These include proteins with deduced structural, chaperone and catalytic roles, not described as iron-metalloproteins in any other organism so far investigated. The iron atoms in the proteins seem to organize and stabilize their three-dimensional structures, to act as 'iron rivets'. Analysis of proteins of the phylogenetic neighbour Picrophilus torridus and of the habitat neighbour Acidithiobacillus ferrooxidans revealed far fewer and only typical metalloproteins. F. acidiphilum therefore has a currently unique iron-protein-dominated cellular machinery and biochemical phylogeny.
Collapse
Affiliation(s)
- Manuel Ferrer
- CSIC, Institute of Catalysis, Cantoblanco, 28049 Madrid, Spain.
| | | | | | | | | |
Collapse
|
31
|
Golyshina OV, Timmis KN. Ferroplasma and relatives, recently discovered cell wall-lacking archaea making a living in extremely acid, heavy metal-rich environments. Environ Microbiol 2005; 7:1277-88. [PMID: 16104851 DOI: 10.1111/j.1462-2920.2005.00861.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For several decades, the bacterium Acidithiobacillus (previously Thiobacillus) has been considered to be the principal acidophilic sulfur- and iron-oxidizing microbe inhabiting acidic environments rich in ores of iron and other heavy metals, responsible for the metal solubilization and leaching from such ores, and has become the paradigm of such microbes. However, during the last few years, new studies of a number of acidic environments, particularly mining waste waters, acidic pools, etc., in diverse geographical locations have revealed the presence of new cell wall-lacking archaea related to the recently described, acidophilic, ferrous-iron oxidizing Ferroplasma acidiphilum. These mesophilic and moderately thermophilic microbes, representing the family Ferroplasmaceae, were numerically significant members of the microbial consortia of the habitats studied, are able to mobilize metals from sulfide ores, e.g. pyrite, arsenopyrite and copper-containing sulfides, and are more acid-resistant than iron and sulfur oxidizing bacteria exhibiting similar eco-physiological properties. Ferroplasma cell membranes contain novel caldarchaetidylglycerol tetraether lipids, which have extremely low proton permeabilities, as a result of the bulky isoprenoid core, and which are probably a major contributor to the extreme acid tolerance of these cell wall-less microbes. Surprisingly, several intracellular enzymes, including an ATP-dependent DNA ligase have pH optima close to that of the external environment rather than of the cytoplasm. Ferroplasma spp. are probably the major players in the biogeochemical cycling of sulfur and sulfide metals in highly acidic environments, and may have considerable potential for biotechnological applications such as biomining and biocatalysis under extreme conditions.
Collapse
Affiliation(s)
- Olga V Golyshina
- Division of Microbiology, GBF - German Research Centre for Biotechnology, Mascheroder Weg 1, 38124 Braunschweig, Germany.
| | | |
Collapse
|