1
|
Żebrowska J, Mucha P, Prusinowski M, Krefft D, Żylicz-Stachula A, Deptuła M, Skoniecka A, Tymińska A, Zawrzykraj M, Zieliński J, Pikuła M, Skowron PM. Development of hybrid biomicroparticles: cellulose exposing functionalized fusion proteins. Microb Cell Fact 2024; 23:81. [PMID: 38481305 PMCID: PMC10938831 DOI: 10.1186/s12934-024-02344-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 02/20/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND One of the leading current trends in technology is the miniaturization of devices to the microscale and nanoscale. The highly advanced approaches are based on biological systems, subjected to bioengineering using chemical, enzymatic and recombinant methods. Here we have utilised the biological affinity towards cellulose of the cellulose binding domain (CBD) fused with recombinant proteins. RESULTS Here we focused on fusions with 'artificial', concatemeric proteins with preprogrammed functions, constructed using DNA FACE™ technology. Such CBD fusions can be efficiently attached to micro-/nanocellulose to form functional, hybrid bionanoparticles. Microcellulose (MCC) particles were generated by a novel approach to enzymatic hydrolysis using Aspergillus sp. cellulase. The interaction between the constructs components - MCC, CBD and fused concatemeric proteins - was evaluated. Obtaining of hybrid biomicroparticles of a natural cellulose biocarrier with proteins with therapeutic properties, fused with CBD, was confirmed. Further, biological tests on the hybrid bioMCC particles confirmed the lack of their cytotoxicity on 46BR.1 N fibroblasts and human adipose derived stem cells (ASCs). The XTT analysis showed a slight inhibition of the proliferation of 46BR.1 N fibroblasts and ACSs cells stimulated with the hybrid biomicroparticles. However, in both cases no changes in the morphology of the examined cells after incubation with the hybrid biomicroparticles' MCC were detected. CONCLUSIONS Microcellulose display with recombinant proteins involves utilizing cellulose, a natural polymer found in plants, as a platform for presenting or displaying proteins. This approach harnesses the structural properties of cellulose to express or exhibit various recombinant proteins on its surface. It offers a novel method for protein expression, presentation, or immobilization, enabling various applications in biotechnology, biomedicine, and other fields. Microcellulose shows promise in biomedical fields for wound healing materials, drug delivery systems, tissue engineering scaffolds, and as a component in bio-sensors due to its biocompatibility and structural properties.
Collapse
Affiliation(s)
- Joanna Żebrowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland.
- BioVentures Institute Ltd, Poznan, 60-141, Poland.
| | - Piotr Mucha
- Department of Molecular Biochemistry, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland
| | - Maciej Prusinowski
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland
| | - Daria Krefft
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland
- BioVentures Institute Ltd, Poznan, 60-141, Poland
| | - Agnieszka Żylicz-Stachula
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland
- BioVentures Institute Ltd, Poznan, 60-141, Poland
| | - Milena Deptuła
- Laboratory of Tissue Engineering and Regenerative Medicine, Division of Embryology, Faculty of Medicine, Medical University of Gdansk, Gdansk, 80-211, Poland
| | - Aneta Skoniecka
- Laboratory of Tissue Engineering and Regenerative Medicine, Division of Embryology, Faculty of Medicine, Medical University of Gdansk, Gdansk, 80-211, Poland
| | - Agata Tymińska
- Laboratory of Tissue Engineering and Regenerative Medicine, Division of Embryology, Faculty of Medicine, Medical University of Gdansk, Gdansk, 80-211, Poland
| | - Małgorzata Zawrzykraj
- Division of Clinical Anatomy, Faculty of Medicine, Medical University of Gdansk, Gdansk, 80-211, Poland
| | - Jacek Zieliński
- Department of Oncologic Surgery, Faculty of Medicine, Medical University of Gdansk, Gdansk, 80-211, Poland
| | - Michał Pikuła
- Laboratory of Tissue Engineering and Regenerative Medicine, Division of Embryology, Faculty of Medicine, Medical University of Gdansk, Gdansk, 80-211, Poland
| | - Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland
- BioVentures Institute Ltd, Poznan, 60-141, Poland
| |
Collapse
|
2
|
Gardner JG. Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus. World J Microbiol Biotechnol 2016; 32:121. [PMID: 27263016 DOI: 10.1007/s11274-016-2068-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 04/07/2016] [Indexed: 01/10/2023]
Abstract
Study of recalcitrant polysaccharide degradation by bacterial systems is critical for understanding biological processes such as global carbon cycling, nutritional contributions of the human gut microbiome, and the production of renewable fuels and chemicals. One bacterium that has a robust ability to degrade polysaccharides is the Gram-negative saprophyte Cellvibrio japonicus. A bacterium with a circuitous history, C. japonicus underwent several taxonomy changes from an initially described Pseudomonas sp. Most of the enzymes described in the pre-genomics era have also been renamed. This review aims to consolidate the biochemical, structural, and genetic data published on C. japonicus and its remarkable ability to degrade cellulose, xylan, and pectin substrates. Initially, C. japonicus carbohydrate-active enzymes were studied biochemically and structurally for their novel polysaccharide binding and degradation characteristics, while more recent systems biology approaches have begun to unravel the complex regulation required for lignocellulose degradation in an environmental context. Also included is a discussion for the future of C. japonicus as a model system, with emphasis on current areas unexplored in terms of polysaccharide degradation and emerging directions for C. japonicus in both environmental and biotechnological applications.
Collapse
Affiliation(s)
- Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, MD, USA.
| |
Collapse
|
3
|
Chakraborty S, Fernandes VO, Dias FMV, Prates JAM, Ferreira LMA, Fontes CMGA, Goyal A, Centeno MSJ. Role of pectinolytic enzymes identified in Clostridium thermocellum cellulosome. PLoS One 2015; 10:e0116787. [PMID: 25658912 PMCID: PMC4319962 DOI: 10.1371/journal.pone.0116787] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 12/09/2014] [Indexed: 11/30/2022] Open
Abstract
The cloning, expression and characterization of three cellulosomal pectinolytic enzymes viz., two variants of PL1 (PL1A and PL1B) and PL9 from Clostridium thermocellum was carried out. The comparison of the primary sequences of PL1A, PL1B and PL9 revealed that these proteins displayed considerable sequence similarities with family 1 and 9 polysaccharide lyases, respectively. PL1A, PL1B and PL9 are the putative catalytic domains of protein sequence ABN54148.1 and ABN53381.1 respectively. These two protein sequences also contain putative carbohydrate binding module (CBM) and type-I dockerin. The associated putative CBM of PL1A showed strong homology with family 6 CBMs while those of PL1B and PL9 showed homology with family 35 CBMs. Recombinant derivatives of these three enzymes showed molecular masses of approximately 34 kDa, 40 kDa and 32 kDa for PL1A, PL1B and PL9, respectively. PL1A, PL1B and PL9 displayed high activity toward polygalacturonic acid and pectin (up to 55% methyl-esterified) from citrus fruits. However, PL1B showed relatively higher activity towards 55% and 85% methyl-esterified pectin (citrus). PL1A and PL9 showed higher activity on rhamnogalacturonan than PL1B. Both PL1A and PL9 displayed maximum activity at pH 8.5 with optimum temperature of 50°C and 60°C respectively. PL1B achieved highest activity at pH 9.8, under an optimum temperature of 50°C. PL1A, PL1B and PL9 all produced two or more unsaturated galacturonates from pectic substrates as displayed by TLC analysis confirming that they are endo-pectate lyase belonging to family 1 and 9, respectively. This report reveals that pectinolytic activity displayed by Clostridium thermocellum cellulosome is coordinated by a sub-set of at least three multi-modular enzymes.
Collapse
Affiliation(s)
- Soumyadeep Chakraborty
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Vania O. Fernandes
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
| | - Fernando M. V. Dias
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
| | - Jose A. M. Prates
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
| | - Luis M. A. Ferreira
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
| | | | - Arun Goyal
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India
- * E-mail: (AG); (MSJC)
| | - Maria S. J. Centeno
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
- * E-mail: (AG); (MSJC)
| |
Collapse
|
4
|
Hugouvieux-Cotte-Pattat N, Condemine G, Shevchik VE. Bacterial pectate lyases, structural and functional diversity. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:427-40. [PMID: 25646533 DOI: 10.1111/1758-2229.12166] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Pectate lyases are enzymes involved in plant cell wall degradation. They cleave pectin using a β-elimination mechanism, specific for acidic polysaccharides. They are mainly produced by plant pathogens and plant-associated organisms, and only rarely by animals. Pectate lyases are also commonly produced in the bacterial world, either by bacteria living in close proximity with plants or by gut bacteria that find plant material in the digestive tract of their hosts. The role of pectate lyases is essential for plant pathogens, such as Dickeya dadantii, that use a set of pectate lyases as their main virulence factor. Symbiotic bacteria produce their own pectate lyases, but they also induce plant pectate lyases to initiate the symbiosis. Pectin degradation products may act as signals affecting the plant–bacteria interactions. Bacterial pectate lyases are also essential for using the pectin of dead or living plants as a carbon source for growth. In the animal gut, Bacteroides pectate lyases degrade the pectin of ingested food, and this is particularly important for herbivores that depend on their microflora for the digestion of pectin. Some human pathogens, such as Yersinia enterocolitica, produce a few intracellular pectate lyases that can facilitate their growth in the presence of highly pectinolytic bacteria, at the plant surface, in the soil or in the animal gut.
Collapse
|
5
|
Kurokawa J, Kimura T, Ohmiya K, Sakka K. A Novel Thermophilic Pectate Lyase Containing Two Catalytic Modules ofClostridium stercorarium. Biosci Biotechnol Biochem 2014; 69:2138-45. [PMID: 16306696 DOI: 10.1271/bbb.69.2138] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The Clostridium stercorarium F-9 pel9A gene encodes a pectate lyase Pel9A consisting of 1,240 amino acids with a molecular weight of 135,171. The mature form of Pel9A is a modular enzyme composed of two family-9 catalytic modules of polysaccharide lyases, CM9-1 and CM9-2, in order from the N terminus. Pel9A showed an overall sequence similarity to the hypothetical pectate lyase PelX of Bacillus halodurans (sequence identity 53%), and CM9-2 showed moderate sequence similarities to some pectate lyases of family 9. Sequence identity between CM9-1 and CM9-2 was 21.3%. The full-length Pel9A lacking the N-terminal signal peptide was expressed, purified, and characterized. The enzyme required Ca(2+) ion for its enzyme activity and showed high activity toward polygalacturonic acid but lower activity toward pectin, indicating that Pel9A is a pectate lyase. Immunological analysis using an antiserum raised against the purified enzyme indicated that Pel9A is constitutively synthesized by C. stercorarium F-9.
Collapse
|
6
|
Li X, Wang H, Zhou C, Ma Y, Li J, Song J. Cloning, expression and characterization of a pectate lyase from Paenibacillus sp. 0602 in recombinant Escherichia coli. BMC Biotechnol 2014; 14:18. [PMID: 24612647 PMCID: PMC4007691 DOI: 10.1186/1472-6750-14-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 03/04/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biotechnological applications of microbial pectate lyases (Pels) in plant fiber processing are considered as environmentally friendly. As such, they become promising substitutes for conventional chemical degumming process. Since applications of Pels in various fields are widening, it is necessary to explore new pectolytic microorganisms and enzymes for efficient and effective usage. Here, we describe the cloning, expression, characterization and application of the recombinant Pel protein from a pectolytic bacterium of the genus Paenibacillus in Escherichia coli. RESULTS A Pel gene (pelN) was cloned using degenerate PCR and inverse PCR from the chromosomal DNA of Paenibacillus sp. 0602. The open reading frame of pelN encodes a 30 amino acid signal peptide and a 445 amino acid mature protein belonging to the polysaccharide lyase family 1. The maximum Pel activity produced by E. coli in shake flasks reached 2,467.4 U mL⁻¹, and the purified recombinant enzyme exhibits a specific activity of 2,060 U mg⁻¹ on polygalacturonic acid (PGA). The maximum activity was observed in a buffer with 5 mM Ca²⁺ at pH 9.8 and 65°C. PelN displays a half-life of around 9 h and 42 h at 50°C and 45°C, respectively. The biochemical treatment achieved the maximal reduction of percentage weight (30.5%) of the ramie bast fiber. CONCLUSIONS This work represents the first study that describes the extracellular expression of a Pel gene from Paenibacillus species in E. coli. The high yield of the extracellular overexpression, relevant thermostability and efficient degumming using combined treatments indicate its strong potential for large-scale industrial production.
Collapse
Affiliation(s)
| | | | | | - Yanhe Ma
- National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
| | | | | |
Collapse
|
7
|
Lee KJ, Dekkers BJ, Steinbrecher T, Walsh CT, Bacic A, Bentsink L, Leubner-Metzger G, Knox JP. Distinct cell wall architectures in seed endosperms in representatives of the Brassicaceae and Solanaceae. PLANT PHYSIOLOGY 2012; 160:1551-66. [PMID: 22961130 PMCID: PMC3490593 DOI: 10.1104/pp.112.203661] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 09/04/2012] [Indexed: 05/04/2023]
Abstract
In some species, a crucial role has been demonstrated for the seed endosperm during germination. The endosperm has been shown to integrate environmental cues with hormonal networks that underpin dormancy and seed germination, a process that involves the action of cell wall remodeling enzymes (CWREs). Here, we examine the cell wall architectures of the endosperms of two related Brassicaceae, Arabidopsis (Arabidopsis thaliana) and the close relative Lepidium (Lepidium sativum), and that of the Solanaceous species, tobacco (Nicotiana tabacum). The Brassicaceae species have a similar cell wall architecture that is rich in pectic homogalacturonan, arabinan, and xyloglucan. Distinctive features of the tobacco endosperm that are absent in the Brassicaceae representatives are major tissue asymmetries in cell wall structural components that reflect the future site of radicle emergence and abundant heteromannan. Cell wall architecture of the micropylar endosperm of tobacco seeds has structural components similar to those seen in Arabidopsis and Lepidium endosperms. In situ and biomechanical analyses were used to study changes in endosperms during seed germination and suggest a role for mannan degradation in tobacco. In the case of the Brassicaceae representatives, the structurally homogeneous cell walls of the endosperm can be acted on by spatially regulated CWRE expression. Genetic manipulations of cell wall components present in the Arabidopsis seed endosperm demonstrate the impact of cell wall architectural changes on germination kinetics.
Collapse
Affiliation(s)
- Kieran J.D. Lee
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom (K.J.D.L., J.P.K.); Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands (B.J.W.D., L.B.); Department of Molecular Plant Physiology, Utrecht University, 3584 CH Utrecht, The Netherlands (B.J.W.D., L.B.); University of Freiburg, Faculty of Biology, Institute for Biology II, Botany/Plant Physiology, D–79104 Freiburg, Germany (T.S., G.L.-M.); and ARC Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, Parkville, Victoria 3010, Australia (C.T.W., A.B.)
| | - Bas J.W. Dekkers
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom (K.J.D.L., J.P.K.); Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands (B.J.W.D., L.B.); Department of Molecular Plant Physiology, Utrecht University, 3584 CH Utrecht, The Netherlands (B.J.W.D., L.B.); University of Freiburg, Faculty of Biology, Institute for Biology II, Botany/Plant Physiology, D–79104 Freiburg, Germany (T.S., G.L.-M.); and ARC Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, Parkville, Victoria 3010, Australia (C.T.W., A.B.)
| | | | - Cherie T. Walsh
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom (K.J.D.L., J.P.K.); Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands (B.J.W.D., L.B.); Department of Molecular Plant Physiology, Utrecht University, 3584 CH Utrecht, The Netherlands (B.J.W.D., L.B.); University of Freiburg, Faculty of Biology, Institute for Biology II, Botany/Plant Physiology, D–79104 Freiburg, Germany (T.S., G.L.-M.); and ARC Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, Parkville, Victoria 3010, Australia (C.T.W., A.B.)
| | - Antony Bacic
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom (K.J.D.L., J.P.K.); Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands (B.J.W.D., L.B.); Department of Molecular Plant Physiology, Utrecht University, 3584 CH Utrecht, The Netherlands (B.J.W.D., L.B.); University of Freiburg, Faculty of Biology, Institute for Biology II, Botany/Plant Physiology, D–79104 Freiburg, Germany (T.S., G.L.-M.); and ARC Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, Parkville, Victoria 3010, Australia (C.T.W., A.B.)
| | - Leónie Bentsink
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom (K.J.D.L., J.P.K.); Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands (B.J.W.D., L.B.); Department of Molecular Plant Physiology, Utrecht University, 3584 CH Utrecht, The Netherlands (B.J.W.D., L.B.); University of Freiburg, Faculty of Biology, Institute for Biology II, Botany/Plant Physiology, D–79104 Freiburg, Germany (T.S., G.L.-M.); and ARC Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, Parkville, Victoria 3010, Australia (C.T.W., A.B.)
| | | | - J. Paul Knox
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom (K.J.D.L., J.P.K.); Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands (B.J.W.D., L.B.); Department of Molecular Plant Physiology, Utrecht University, 3584 CH Utrecht, The Netherlands (B.J.W.D., L.B.); University of Freiburg, Faculty of Biology, Institute for Biology II, Botany/Plant Physiology, D–79104 Freiburg, Germany (T.S., G.L.-M.); and ARC Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, Parkville, Victoria 3010, Australia (C.T.W., A.B.)
| |
Collapse
|
8
|
Vorhölter FJ, Wiggerich HG, Scheidle H, Sidhu VK, Mrozek K, Küster H, Pühler A, Niehaus K. Involvement of bacterial TonB-dependent signaling in the generation of an oligogalacturonide damage-associated molecular pattern from plant cell walls exposed to Xanthomonas campestris pv. campestris pectate lyases. BMC Microbiol 2012; 12:239. [PMID: 23082751 PMCID: PMC3551730 DOI: 10.1186/1471-2180-12-239] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 09/25/2012] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Efficient perception of attacking pathogens is essential for plants. Plant defense is evoked by molecules termed elicitors. Endogenous elicitors or damage-associated molecular patterns (DAMPs) originate from plant materials upon injury or pathogen activity. While there are comparably well-characterized examples for DAMPs, often oligogalacturonides (OGAs), generated by the activity of fungal pathogens, endogenous elicitors evoked by bacterial pathogens have been rarely described. In particular, the signal perception and transduction processes involved in DAMP generation are poorly characterized. RESULTS A mutant strain of the phytopathogenic bacterium Xanthomonas campestris pv. campestris deficient in exbD2, which encodes a component of its unusual elaborate TonB system, had impaired pectate lyase activity and caused no visible symptoms for defense on the non-host plant pepper (Capsicum annuum). A co-incubation of X. campestris pv. campestris with isolated cell wall material from C. annuum led to the release of compounds which induced an oxidative burst in cell suspension cultures of the non-host plant. Lipopolysaccharides and proteins were ruled out as elicitors by polymyxin B and heat treatment, respectively. After hydrolysis with trifluoroacetic acid and subsequent HPAE chromatography, the elicitor preparation contained galacturonic acid, the monosaccharide constituent of pectate. OGAs were isolated from this crude elicitor preparation by HPAEC and tested for their biological activity. While small OGAs were unable to induce an oxidative burst, the elicitor activity in cell suspension cultures of the non-host plants tobacco and pepper increased with the degree of polymerization (DP). Maximal elicitor activity was observed for DPs exceeding 8. In contrast to the X. campestris pv. campestris wild type B100, the exbD2 mutant was unable to generate elicitor activity from plant cell wall material or from pectin. CONCLUSIONS To our knowledge, this is the second report on a DAMP generated by bacterial features. The generation of the OGA elicitor is embedded in a complex exchange of signals within the framework of the plant-microbe interaction of C. annuum and X. campestris pv. campestris. The bacterial TonB-system is essential for the substrate-induced generation of extracellular pectate lyase activity. This is the first demonstration that a TonB-system is involved in bacterial trans-envelope signaling in the context of a pathogenic interaction with a plant.
Collapse
Affiliation(s)
- Frank-Jörg Vorhölter
- Department of Proteome and Metabolome Research, Faculty of Biology, Universität Bielefeld, Universitätsstr 25, Bielefeld 33615, Germany.
| | | | | | | | | | | | | | | |
Collapse
|
9
|
A novel low-temperature active alkaline pectate lyase from Klebsiella sp. Y1 with potential in textile industry. Process Biochem 2011. [DOI: 10.1016/j.procbio.2011.06.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
10
|
Hervé C, Rogowski A, Blake AW, Marcus SE, Gilbert HJ, Knox JP. Carbohydrate-binding modules promote the enzymatic deconstruction of intact plant cell walls by targeting and proximity effects. Proc Natl Acad Sci U S A 2010; 107:15293-8. [PMID: 20696902 PMCID: PMC2930570 DOI: 10.1073/pnas.1005732107] [Citation(s) in RCA: 183] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cell wall degrading enzymes have a complex molecular architecture consisting of catalytic modules and noncatalytic carbohydrate-binding modules (CBMs). The function of CBMs in cell wall degrading processes is poorly understood. Here, we have evaluated the potential enzyme-targeting function of CBMs in the context of intact primary and secondary cell wall deconstruction. The capacity of a pectate lyase to degrade pectic homogalacturonan in primary cell walls was potentiated by cellulose-directed CBMs but not by xylan-directed CBMs. Conversely, the arabinofuranosidase-mediated removal of side chains from arabinoxylan in xylan-rich and cellulose-poor wheat grain endosperm cell walls was enhanced by a xylan-binding CBM but less so by a crystalline cellulose-specific module. The capacity of xylanases to degrade xylan in secondary cell walls was potentiated by both xylan- and cellulose-directed CBMs. These studies demonstrate that CBMs can potentiate the action of a cognate catalytic module toward polysaccharides in intact cell walls through the recognition of nonsubstrate polysaccharides. The targeting actions of CBMs therefore have strong proximity effects within cell wall structures, explaining why cellulose-directed CBMs are appended to many noncellulase cell wall hydrolases.
Collapse
Affiliation(s)
- Cécile Hervé
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Artur Rogowski
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HN, United Kingdom; and
| | - Anthony W. Blake
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Susan E. Marcus
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Harry J. Gilbert
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HN, United Kingdom; and
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602-4712
| | - J. Paul Knox
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| |
Collapse
|
11
|
Biochemical properties of pectate lyases produced by three different Bacillus strains isolated from fermenting cocoa beans and characterization of their cloned genes. Appl Environ Microbiol 2010; 76:5214-20. [PMID: 20543060 DOI: 10.1128/aem.00705-10] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pectinolytic enzymes play an important role in cocoa fermentation. In this study, we characterized three extracellular pectate lyases (Pels) produced by bacilli isolated from fermenting cocoa beans. These enzymes, named Pel-22, Pel-66, and Pel-90, were synthesized by Bacillus pumilus BS22, Bacillus subtilis BS66, and Bacillus fusiformis BS90, respectively. The three Pels were produced under their natural conditions and purified from the supernatants using a one-step chromatography method. The purified enzymes exhibited optimum activity at 60 degrees C, and the half-time of thermoinactivation at this temperature was approximately 30 min. Pel-22 had a low specific activity compared with the other two enzymes. However, it displayed high affinity for the substrate, about 2.5-fold higher than those of Pel-66 and Pel-90. The optimum pHs were 7.5 for Pel-22 and 8.0 for Pel-66 and Pel-90. The three enzymes trans-eliminated polygalacturonate in a random manner to generate two long oligogalacturonides, as well as trimers and dimers. A synergistic effect was observed between Pel-22 and Pel-66 and between Pel-22 and Pel-90, but not between Pel-90 and Pel-66. The Pels were also strongly active on highly methylated pectins (up to 60% for Pel-66 and Pel-90 and up to 75% for Pel-22). Fe(2+) was found to be a better cofactor than Ca(2+) for Pel-22 activity, while Ca(2+) was the best cofactor for Pel-66 and Pel-90. The amino acid sequences deduced from the cloned genes showed the characteristics of Pels belonging to Family 1. The pel-66 and pel-90 genes appear to be very similar, but they are different from the pel-22 gene. The characterized enzymes form two groups, Pel-66/Pel-90 and Pel-22; members of the different groups might cooperate to depolymerize pectin during the fermentation of cocoa beans.
Collapse
|
12
|
Marcus SE, Verhertbruggen Y, Hervé C, Ordaz-Ortiz JJ, Farkas V, Pedersen HL, Willats WGT, Knox JP. Pectic homogalacturonan masks abundant sets of xyloglucan epitopes in plant cell walls. BMC PLANT BIOLOGY 2008; 8:60. [PMID: 18498625 DOI: 10.1093/jxb/37.8.1201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Accepted: 05/22/2008] [Indexed: 05/24/2023]
Abstract
BACKGROUND Molecular probes are required to detect cell wall polymers in-situ to aid understanding of their cell biology and several studies have shown that cell wall epitopes have restricted occurrences across sections of plant organs indicating that cell wall structure is highly developmentally regulated. Xyloglucan is the major hemicellulose or cross-linking glycan of the primary cell walls of dicotyledons although little is known of its occurrence or functions in relation to cell development and cell wall microstructure. RESULTS Using a neoglycoprotein approach, in which a XXXG heptasaccharide of tamarind seed xyloglucan was coupled to BSA to produce an immunogen, we have generated a rat monoclonal antibody (designated LM15) to the XXXG structural motif of xyloglucans. The specificity of LM15 has been confirmed by the analysis of LM15 binding using glycan microarrays and oligosaccharide hapten inhibition of binding studies. The use of LM15 for the analysis of xyloglucan in the cell walls of tamarind and nasturtium seeds, in which xyloglucan occurs as a storage polysaccharide, indicated that the LM15 xyloglucan epitope occurs throughout the thickened cell walls of the tamarind seed and in the outer regions, adjacent to middle lamellae, of the thickened cell walls of the nasturtium seed. Immunofluorescence analysis of LM15 binding to sections of tobacco and pea stem internodes indicated that the xyloglucan epitope was restricted to a few cell types in these organs. Enzymatic removal of pectic homogalacturonan from equivalent sections resulted in the abundant detection of distinct patterns of the LM15 xyloglucan epitope across these organs and a diversity of occurrences in relation to the cell wall microstructure of a range of cell types. CONCLUSION These observations support ideas that xyloglucan is associated with pectin in plant cell walls. They also indicate that documented patterns of cell wall epitopes in relation to cell development and cell differentiation may need to be re-considered in relation to the potential masking of cell wall epitopes by other cell wall components.
Collapse
Affiliation(s)
- Susan E Marcus
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| | | | | | | | | | | | | | | |
Collapse
|
13
|
Marcus SE, Verhertbruggen Y, Hervé C, Ordaz-Ortiz JJ, Farkas V, Pedersen HL, Willats WGT, Knox JP. Pectic homogalacturonan masks abundant sets of xyloglucan epitopes in plant cell walls. BMC PLANT BIOLOGY 2008; 8:60. [PMID: 18498625 PMCID: PMC2409341 DOI: 10.1186/1471-2229-8-60] [Citation(s) in RCA: 298] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Accepted: 05/22/2008] [Indexed: 05/17/2023]
Abstract
BACKGROUND Molecular probes are required to detect cell wall polymers in-situ to aid understanding of their cell biology and several studies have shown that cell wall epitopes have restricted occurrences across sections of plant organs indicating that cell wall structure is highly developmentally regulated. Xyloglucan is the major hemicellulose or cross-linking glycan of the primary cell walls of dicotyledons although little is known of its occurrence or functions in relation to cell development and cell wall microstructure. RESULTS Using a neoglycoprotein approach, in which a XXXG heptasaccharide of tamarind seed xyloglucan was coupled to BSA to produce an immunogen, we have generated a rat monoclonal antibody (designated LM15) to the XXXG structural motif of xyloglucans. The specificity of LM15 has been confirmed by the analysis of LM15 binding using glycan microarrays and oligosaccharide hapten inhibition of binding studies. The use of LM15 for the analysis of xyloglucan in the cell walls of tamarind and nasturtium seeds, in which xyloglucan occurs as a storage polysaccharide, indicated that the LM15 xyloglucan epitope occurs throughout the thickened cell walls of the tamarind seed and in the outer regions, adjacent to middle lamellae, of the thickened cell walls of the nasturtium seed. Immunofluorescence analysis of LM15 binding to sections of tobacco and pea stem internodes indicated that the xyloglucan epitope was restricted to a few cell types in these organs. Enzymatic removal of pectic homogalacturonan from equivalent sections resulted in the abundant detection of distinct patterns of the LM15 xyloglucan epitope across these organs and a diversity of occurrences in relation to the cell wall microstructure of a range of cell types. CONCLUSION These observations support ideas that xyloglucan is associated with pectin in plant cell walls. They also indicate that documented patterns of cell wall epitopes in relation to cell development and cell differentiation may need to be re-considered in relation to the potential masking of cell wall epitopes by other cell wall components.
Collapse
Affiliation(s)
- Susan E Marcus
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Yves Verhertbruggen
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Cécile Hervé
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - José J Ordaz-Ortiz
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Vladimir Farkas
- Slovak Academy of Sciences, Institute of Chemistry, Centre of Excellence GLYCOBIOS, Dubravska cesta 9, SK-84538 Bratislava, Slovakia
| | - Henriette L Pedersen
- Department of Biology, University of Copenhagen, Copenhagen Biocentre, Ole Maaløes Vej 5, DK-2200, Copenhagen, Denmark
| | - William GT Willats
- Department of Biology, University of Copenhagen, Copenhagen Biocentre, Ole Maaløes Vej 5, DK-2200, Copenhagen, Denmark
| | - J Paul Knox
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| |
Collapse
|
14
|
Sheldon W, Macauley M, Taylor E, Robinson C, Charnock S, Davies G, Vocadlo D, Black G. Functional analysis of a group A streptococcal glycoside hydrolase Spy1600 from family 84 reveals it is a beta-N-acetylglucosaminidase and not a hyaluronidase. Biochem J 2006; 399:241-7. [PMID: 16822234 PMCID: PMC1609908 DOI: 10.1042/bj20060307] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2006] [Revised: 06/26/2006] [Accepted: 07/06/2006] [Indexed: 11/17/2022]
Abstract
Group A streptococcus (Streptococcus pyogenes) is the causative agent of severe invasive infections such as necrotizing fasciitis (the so-called 'flesh eating disease') and toxic-shock syndrome. Spy1600, a glycoside hydrolase from family 84 of the large superfamily of glycoside hydrolases, has been proposed to be a virulence factor. In the present study we show that Spy1600 has no activity toward galactosaminides or hyaluronan, but does remove beta-O-linked N-acetylglucosamine from mammalian glycoproteins--an observation consistent with the inclusion of eukaryotic O-glycoprotein 2-acetamido-2-deoxy-beta-D-glucopyranosidases within glycoside hydrolase family 84. Proton NMR studies, structure-reactivity studies for a series of fluorinated analogues and analysis of 1,2-dideoxy-2'-methyl-alpha-D-glucopyranoso-[2,1-d]-Delta2'-thiazoline as a competitive inhibitor reveals that Spy1600 uses a double-displacement mechanism involving substrate-assisted catalysis. Family 84 glycoside hydrolases are therefore comprised of both prokaryotic and eukaryotic beta-N-acetylglucosaminidases using a conserved catalytic mechanism involving substrate-assisted catalysis. Since these enzymes do not have detectable hyaluronidase activity, many family 84 glycoside hydrolases are most likely incorrectly annotated as hyaluronidases.
Collapse
Key Words
- β-n-acetylglucosaminidase (glcnacase)
- mammalian glycoproteins
- 1,2-dideoxy-2′-methyl-α-d-glucopyranoso-[2,1-d]-δ2′-thiazoline (nag-thiazoline)
- o-glycoprotein 2-acetamido-2-deoxy-β-d-glucopyranosidase (o-glcnacase)
- o-glycoprotein 2-acetamido-2-deoxy-β-d-glucopyranoside (o-glcnac)
- spyl600
- substrate-assisted catalysis
- glcnac, n-acetylglucosamine (2-acetamido-2-deoxy-d-glucopyranose)
- glcnacase, β-n-acetylglucosaminidase
- mgea5, meningioma expressed antigen 5
- mu, 4-methylumbelliferyl
- mu-glcnac, mu-2-acetamido-2-deoxy-β-d-glucopyranoside
- mu-glcnacf1, mu-2-deoxy-2-fluoroacetamido-β-d-glucopyranoside
- mu-glcnacf2, mu-2-deoxy-2-difluoroacetamido-β-d-glucopyranoside
- mu-glcnacf3, mu-2-deoxy-2-trifluoroacetamido-β-d-glucopyranoside
- nag-thiazoline, 1,2-dideoxy-2′-methyl-α-d-glucopyranoso-[2,1-d]-δ2′-thiazoline
- o-glcnac, o-glycoprotein 2-acetamido-2-deoxy-β-d-glucopyranoside
- o-glcnacase, o-glycoprotein 2-acetamido-2-deoxy-β-d-glucopyranosidase
- orf, open reading frame
Collapse
Affiliation(s)
- William L. Sheldon
- *Biomolecular and Biomedical Research Centre, School of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, U.K
- †School of Health, Natural and Social Sciences, University of Sunderland, Sunderland SR1 3SD, U.K
| | - Matthew S. Macauley
- ‡Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
| | - Edward J. Taylor
- §York Structural Biology Laboratory, Department of Chemistry, University of York, York YO31 5YW, U.K
| | - Charlotte E. Robinson
- *Biomolecular and Biomedical Research Centre, School of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, U.K
| | - Simon J. Charnock
- *Biomolecular and Biomedical Research Centre, School of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, U.K
| | - Gideon J. Davies
- §York Structural Biology Laboratory, Department of Chemistry, University of York, York YO31 5YW, U.K
| | - David J. Vocadlo
- ‡Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
| | - Gary W. Black
- *Biomolecular and Biomedical Research Centre, School of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, U.K
| |
Collapse
|
15
|
Shoseyov O, Shani Z, Levy I. Carbohydrate binding modules: biochemical properties and novel applications. Microbiol Mol Biol Rev 2006; 70:283-95. [PMID: 16760304 PMCID: PMC1489539 DOI: 10.1128/mmbr.00028-05] [Citation(s) in RCA: 351] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polysaccharide-degrading microorganisms express a repertoire of hydrolytic enzymes that act in synergy on plant cell wall and other natural polysaccharides to elicit the degradation of often-recalcitrant substrates. These enzymes, particularly those that hydrolyze cellulose and hemicellulose, have a complex molecular architecture comprising discrete modules which are normally joined by relatively unstructured linker sequences. This structure is typically comprised of a catalytic module and one or more carbohydrate binding modules (CBMs) that bind to the polysaccharide. CBMs, by bringing the biocatalyst into intimate and prolonged association with its substrate, allow and promote catalysis. Based on their properties, CBMs are grouped into 43 families that display substantial variation in substrate specificity, along with other properties that make them a gold mine for biotechnologists who seek natural molecular "Velcro" for diverse and unusual applications. In this article, we review recent progress in the field of CBMs and provide an up-to-date summary of the latest developments in CBM applications.
Collapse
Affiliation(s)
- Oded Shoseyov
- The Institute of Plant Science and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 76100, Israel.
| | | | | |
Collapse
|
16
|
Smith NL, Taylor EJ, Lindsay AM, Charnock SJ, Turkenburg JP, Dodson EJ, Davies GJ, Black GW. Structure of a group A streptococcal phage-encoded virulence factor reveals a catalytically active triple-stranded beta-helix. Proc Natl Acad Sci U S A 2005; 102:17652-7. [PMID: 16314578 PMCID: PMC1308890 DOI: 10.1073/pnas.0504782102] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2005] [Indexed: 11/18/2022] Open
Abstract
Streptococcus pyogenes (group A Streptococcus) causes severe invasive infections including scarlet fever, pharyngitis (streptococcal sore throat), skin infections, necrotizing fasciitis (flesh-eating disease), septicemia, erysipelas, cellulitis, acute rheumatic fever, and toxic shock. The conversion from nonpathogenic to toxigenic strains of S. pyogenes is frequently mediated by bacteriophage infection. One of the key bacteriophage-encoded virulence factors is a putative "hyaluronidase," HylP1, a phage tail-fiber protein responsible for the digestion of the S. pyogenes hyaluronan capsule during phage infection. Here we demonstrate that HylP1 is a hyaluronate lyase. The 3D structure, at 1.8-angstroms resolution, reveals an unusual triple-stranded beta-helical structure and provides insight into the structural basis for phage tail assembly and the role of phage tail proteins in virulence. Unlike the triple-stranded beta-helix assemblies of the bacteriophage T4 injection machinery and the tailspike endosialidase of the Escherichia coli K1 bacteriophage K1F, HylP1 possesses three copies of the active center on the triple-helical fiber itself without the need for an accessory catalytic domain. The triple-stranded beta-helix is not simply a structural scaffold, as previously envisaged; it is harnessed to provide a 200-angstroms-long substrate-binding groove for the optimal reduction in hyaluronan viscosity to aid phage penetration of the capsule.
Collapse
Affiliation(s)
- Nicola L Smith
- Chemical Biology Research Group, School of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, United Kingdom
| | | | | | | | | | | | | | | |
Collapse
|
17
|
Howard MB, Ekborg NA, Taylor LE, Hutcheson SW, Weiner RM. Identification and analysis of polyserine linker domains in prokaryotic proteins with emphasis on the marine bacterium Microbulbifer degradans. Protein Sci 2004; 13:1422-5. [PMID: 15075401 PMCID: PMC2286767 DOI: 10.1110/ps.03511604] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Polyserine linkers (PSLs) are interdomain, serine-rich sequences found in modular proteins. Though common among eukaryotes, their presence in prokaryotic enzymes is limited. We identified 46 extracellular proteins involved in complex carbohydrate degradation from Microbulbifer degradans that contain PSLs that separate carbohydrate-binding domains or catalytic domains from other binding domains. In nine M. degradans proteins, PSLs also separated amino-terminal lipoprotein acylation sites from the remainder of the polypeptide. Furthermore, among the 76 PSL proteins identified in sequence repositories, 65 are annotated as proteins involved in complex carbohydrate degradation. We discuss the notion that PSLs are flexible, disordered spacer regions that enhance substrate accessibility.
Collapse
Affiliation(s)
- Michael B Howard
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA
| | | | | | | | | |
Collapse
|
18
|
Pagès S, Valette O, Abdou L, Bélaïch A, Bélaïch JP. A rhamnogalacturonan lyase in the Clostridium cellulolyticum cellulosome. J Bacteriol 2003; 185:4727-33. [PMID: 12896991 PMCID: PMC166469 DOI: 10.1128/jb.185.16.4727-4733.2003] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clostridium cellulolyticum secretes large multienzymatic complexes with plant cell wall-degrading activities named cellulosomes. Most of the genes encoding cellulosomal components are located in a large gene cluster: cipC-cel48F-cel8C-cel9G-cel9E-orfX-cel9H-cel9J-man5K-cel9M. Downstream of the cel9M gene, a new open reading frame was discovered and named rgl11Y. Amino acid sequence analysis indicates that this gene encodes a multidomain pectinase, Rgl11Y, containing an N-terminal signal sequence, a catalytic domain belonging to family 11 of the polysaccharide lyases, and a C-terminal dockerin domain. The present report describes the biochemical characterization of a recombinant form of Rgl11Y. Rgl11Y cleaves the alpha-L-Rhap-(1-->4)-alpha-D-GalpA glycosidic bond in the backbone of rhamnogalacturonan I (RGI) via a beta-elimination mechanism. Its specific activity on potato pectic galactan and rhamnogalacturonan was found to be 28 and 3.6 IU/mg, respectively, indicating that Rgl11Y requires galactan decoration of the RGI backbone. The optimal pH of Rgl11Y is 8.5 and calcium is required for its activity. Rgl11Y was shown to be incorporated in the C. cellulolyticum cellulosome through a typical cohesin-dockerin interaction. Rgl11Y from C. cellulolyticum is the first cellulosomal rhamnogalacturonase characterized.
Collapse
Affiliation(s)
- Sandrine Pagès
- Laboratoire de Bioénergétique et Ingénierie des Protéines, IBSM, Centre National de la Recherche Scientifique, Marseille, France.
| | | | | | | | | |
Collapse
|
19
|
Howard MB, Ekborg NA, Taylor LE, Weiner RM, Hutcheson SW. Genomic analysis and initial characterization of the chitinolytic system of Microbulbifer degradans strain 2-40. J Bacteriol 2003; 185:3352-60. [PMID: 12754233 PMCID: PMC155392 DOI: 10.1128/jb.185.11.3352-3360.2003] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2002] [Accepted: 03/04/2003] [Indexed: 11/20/2022] Open
Abstract
The marine bacterium Microbulbifer degradans strain 2-40 produces at least 10 enzyme systems for degrading insoluble complex polysaccharides (ICP). The draft sequence of the 2-40 genome allowed a genome-wide analysis of the chitinolytic system of strain 2-40. The chitinolytic system includes three secreted chitin depolymerases (ChiA, ChiB, and ChiC), a secreted chitin-binding protein (CbpA), periplasmic chitooligosaccharide-modifying enzymes, putative sugar transporters, and a cluster of genes encoding cytoplasmic proteins involved in N-acetyl-D-glucosamine (GlcNAc) metabolism. Each chitin depolymerase was detected in culture supernatants of chitin-grown strain 2-40 and was active against chitin and glycol chitin. The chitin depolymerases also had a specific pattern of activity toward the chitin analogs 4-methylumbelliferyl-beta-D-N,N'-diacetylchitobioside (MUF-diNAG) and 4-methylumbelliferyl-beta-D-N,N',N"-triacetylchitotrioside (MUF-triNAG). The depolymerases were modular in nature and contained glycosyl hydrolase family 18 domains, chitin-binding domains, and polycystic kidney disease domains. ChiA and ChiB each possessed polyserine linkers of up to 32 consecutive serine residues. In addition, ChiB and CbpA contained glutamic acid-rich domains. At 1,271 amino acids, ChiB is the largest bacterial chitinase reported to date. A chitodextrinase (CdxA) with activity against chitooligosaccharides (degree of polymerization of 5 to 7) was identified. The activities of two apparent periplasmic (HexA and HexB) N-acetyl-beta-D-glucosaminidases and one cytoplasmic (HexC) N-acetyl-beta-D-glucosaminidase were demonstrated. Genes involved in GlcNAc metabolism, similar to those of the Escherichia coli K-12 NAG utilization operon, were identified. NagA from strain 2-40, a GlcNAc deacetylase, was shown to complement a nagA mutation in E. coli K-12. Except for the GlcNAc utilization cluster, genes for all other components of the chitinolytic system were dispersed throughout the genome. Further examination of this system may provide additional insight into the mechanisms by which marine bacteria degrade chitin and provide a basis for future research on the ICP-degrading systems of strain 2-40.
Collapse
Affiliation(s)
- Michael B Howard
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA
| | | | | | | | | |
Collapse
|
20
|
Sánchez-Torres P, Visser J, Benen JAE. Identification of amino acid residues critical for catalysis and stability in Aspergillus niger family 1 pectin lyase A. Biochem J 2003; 370:331-7. [PMID: 12418964 PMCID: PMC1223150 DOI: 10.1042/bj20021071] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2002] [Revised: 09/11/2002] [Accepted: 11/06/2002] [Indexed: 11/17/2022]
Abstract
Site-directed-mutagenesis studies were performed on family 1 pectin lyase A (PL1A) from Aspergillus niger to gain insight into the reaction mechanism for the pectin lyase-catalysed beta-elimination cleavage of methylesterified polygalacturonic acid and to stabilize the enzyme at slightly basic pH. On the basis of the three-dimensional structures of PL1A [Mayans, Scott, Connerton, Gravesen, Benen, Visser, Pickersgill and Jenkins (1997) Structure 5, 677-689] and the modelled enzyme-substrate complex of PL1B [Herron, Benen, Scavetta, Visser and Jurnak (2000) Proc. Natl. Acad. Sci. U.S.A. 97, 8762-8769], Asp154, Arg176, Arg236 and Lys239 were mutagenized. Substituting Arg236 with alanine or lysine rendered the enzyme completely inactive, and mutagenesis of Arg176 and Lys239 severely affected catalysis. The Asp154-->Arg and Asp154-->Glu mutant enzymes were only moderately impaired in respect of catalysis. The results strongly indicate that Arg236, which is sandwiched between Arg176 and Lys239, would initiate the reaction upon enzyme-substrate interaction, through the abstraction of the proton at C5 of the galacturonopyranose ring. The positively charged residues Arg176 and Lys239 are responsible for lowering the p K a of Arg236. Arg176 and Lys239 are maintained in a charged state by interacting with Asp154 or bulk solvent respectively. The deprotonation of the Asp186-Asp221 pair was proposed to be responsible for a pH-driven conformational change of PL1A [Mayans, Scott, Connerton, Gravesen, Benen, Visser, Pickersgill and Jenkins (1997) Structure 5, 677-689]. Substitution of Asp186 and Asp221 by Asn186 and Asn221 was expected to stabilize the enzyme. However, the Asp186-->Asn/Asp221-->Asn enzyme appeared less stable than the wild-type enzyme, even at pH 6.0, as evidenced by fluorescence studies. This demonstrates that the pH-dependent conformational change is not driven by deprotonation of the Asp186-Asp221 pair.
Collapse
Affiliation(s)
- Paloma Sánchez-Torres
- Section Molecular Genetics of Industrial Microorganisms, Wageningen University, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands
| | | | | |
Collapse
|
21
|
Abstract
Many researchers have acknowledged the fact that there exists an immense potential for the application of the cellulose-binding domains (CBDs) in the field of biotechnology. This becomes apparent when the phrase "cellulose-binding domain" is used as the key word for a computerized patent search; more then 150 hits are retrieved. Cellulose is an ideal matrix for large-scale affinity purification procedures. This chemically inert matrix has excellent physical properties as well as low affinity for nonspecific protein binding. It is available in a diverse range of forms and sizes, is pharmaceutically safe, and relatively inexpensive. Present studies into the application of CBDs in industry have established that they can be applied in the modification of physical and chemical properties of composite materials and the development of modified materials with improved properties. In agro-biotechnology, CBDs can be used to modify polysaccharide materials both in vivo and in vitro. The CBDs exert nonhydrolytic fiber disruption on cellulose-containing materials. The potential applications of "CBD technology" range from modulating the architecture of individual cells to the modification of an entire organism. Expressing these genes under specific promoters and using appropriate trafficking signals, can be used to alter the nutritional value and texture of agricultural crops and their final products.
Collapse
Affiliation(s)
- Ilan Levy
- Institute of Plant Science and Genetics in Agriculture and Otto Warburg Centre for Agricultural Biotechnology, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, PO Box 12, Rehovot 76100, Israel
| | | |
Collapse
|
22
|
Charnock SJ, Brown IE, Turkenburg JP, Black GW, Davies GJ. Convergent evolution sheds light on the anti-beta -elimination mechanism common to family 1 and 10 polysaccharide lyases. Proc Natl Acad Sci U S A 2002; 99:12067-72. [PMID: 12221284 PMCID: PMC129399 DOI: 10.1073/pnas.182431199] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2002] [Accepted: 07/19/2002] [Indexed: 11/18/2022] Open
Abstract
Enzyme-catalyzed beta-elimination of sugar uronic acids, exemplified by the degradation of plant cell wall pectins, plays an important role in a wide spectrum of biological processes ranging from the recycling of plant biomass through to pathogen virulence. The three-dimensional crystal structure of the catalytic module of a "family PL-10" polysaccharide lyase, Pel10Acm from Cellvibrio japonicus, solved at a resolution of 1.3 A, reveals a new polysaccharide lyase fold and is the first example of a polygalacturonic acid lyase that does not exhibit the "parallel beta-helix" topology. The "Michaelis" complex of an inactive mutant in association with the substrate trigalacturonate/Ca2+ reveals the catalytic machinery harnessed by this polygalacturonate lyase, which displays a stunning resemblance, presumably through convergent evolution, to the tetragalacturonic acid complex observed for a structurally unrelated polygalacturonate lyase from family PL-1. Common coordination of the -1 and +1 subsite saccharide carboxylate groups by a protein-liganded Ca2+ ion, the positioning of an arginine catalytic base in close proximity to the alpha-carbon hydrogen and numerous other conserved enzyme-substrate interactions, considered in light of mutagenesis data for both families, suggest a generic polysaccharide anti-beta-elimination mechanism.
Collapse
Affiliation(s)
- Simon J Charnock
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, United Kingdom
| | | | | | | | | |
Collapse
|
23
|
McKie VA, Vincken JP, Voragen AG, van den Broek LA, Stimson E, Gilbert HJ. A new family of rhamnogalacturonan lyases contains an enzyme that binds to cellulose. Biochem J 2001; 355:167-77. [PMID: 11256961 PMCID: PMC1221724 DOI: 10.1042/0264-6021:3550167] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Pseudomonas cellulosa is an aerobic bacterium that synthesizes an extensive array of modular cellulases and hemicellulases, which have a modular architecture consisting of catalytic domains and distinct non-catalytic carbohydrate-binding modules (CBMs). To investigate whether the main-chain-cleaving pectinases from this bacterium also have a modular structure, a library of P. cellulosa genomic DNA, constructed in lambdaZAPII, was screened for pectinase-encoding sequences. A recombinant phage that attacked arabinan, galactan and rhamnogalacturonan was isolated. The encoded enzyme, designated Rgl11A, had a modular structure comprising an N-terminal domain that exhibited homology to Bacillus and Streptomyces proteins of unknown function, a middle domain that exhibited sequence identity to fibronectin-3 domains, and a C-terminal domain that was homologous to family 2a CBMs. Expression of the three modules of the Pseudomonas protein in Escherichia coli showed that its C-terminal module was a functional cellulose-binding domain, and the N-terminal module consisted of a catalytic domain that hydrolysed rhamnogalacturonan-containing substrates. The activity of Rgl11A against apple- and potato-derived rhamnogalacturonan substrates indicated that the enzyme had a strong preference for rhamnogalacturonans that contained galactose side chains, and which were not esterified. The enzyme had an absolute requirement for calcium, a high optimum pH, and catalysis was associated with an increase in absorbance at 235 nm, indicating that glycosidic bond cleavage was mediated via a beta-elimination mechanism. These data indicate that Rgl11A is a rhamnogalacturonan lyase and, together with the homologous Bacillus and Streptomyces proteins, comprise a new family of polysaccharide lyases. The presence of a family 2a CBM in Rgl11A, and in a P. cellulosa pectate lyase described in the accompanying paper [Brown, Mallen, Charnock, Davies and Black (2001) Biochem. J. 355, 155-165] suggests that the capacity to bind cellulose plays an important role in the activity of main-chain-cleaving Pseudomonas pectinases, in addition to cellulases and hemicellulases.
Collapse
Affiliation(s)
- V A McKie
- Department of Biological and Nutritional Sciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, U.K
| | | | | | | | | | | |
Collapse
|