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Tundo S, Mandalà G, Sella L, Favaron F, Bedre R, Kalunke RM. Xylanase Inhibitors: Defense Players in Plant Immunity with Implications in Agro-Industrial Processing. Int J Mol Sci 2022; 23:ijms232314994. [PMID: 36499321 PMCID: PMC9739030 DOI: 10.3390/ijms232314994] [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: 10/29/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022] Open
Abstract
Xylanase inhibitors (XIs) are plant cell wall proteins largely distributed in monocots that inhibit the hemicellulose degrading activity of microbial xylanases. XIs have been classified into three classes with different structures and inhibition specificities, namely Triticum aestivum xylanase inhibitors (TAXI), xylanase inhibitor proteins (XIP), and thaumatin-like xylanase inhibitors (TLXI). Their involvement in plant defense has been established by several reports. Additionally, these inhibitors have considerable economic relevance because they interfere with the activity of xylanases applied in several agro-industrial processes. Previous reviews highlighted the structural and biochemical properties of XIs and hypothesized their role in plant defense. Here, we aimed to update the information on the genomic organization of XI encoding genes, the inhibition properties of XIs against microbial xylanases, and the structural properties of xylanase-XI interaction. We also deepened the knowledge of XI regulation mechanisms in planta and their involvement in plant defense. Finally, we reported the recently studied strategies to reduce the negative impact of XIs in agro-industrial processes and mentioned their allergenicity potential.
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Affiliation(s)
- Silvio Tundo
- Department of Land, Environment, Agriculture, and Forestry (TESAF), University of Padova, 35020 Legnaro, Italy
- Correspondence:
| | - Giulia Mandalà
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Luca Sella
- Department of Land, Environment, Agriculture, and Forestry (TESAF), University of Padova, 35020 Legnaro, Italy
| | - Francesco Favaron
- Department of Land, Environment, Agriculture, and Forestry (TESAF), University of Padova, 35020 Legnaro, Italy
| | - Renesh Bedre
- Texas A&M AgriLife Research and Extension Center, Texas A&M University System, Weslaco, TX 78596, USA
| | - Raviraj M. Kalunke
- Donald Danforth Plant Science Center, 975 N Warson Rd, 7 Olivette, St. Louis, MO 63132, USA
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2
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Leys S, De Bondt Y, Schreurs L, Courtin CM. Sensitivity of the Bacillus subtilis Xyn A Xylanase and Its Mutants to Different Xylanase Inhibitors Determines Their Activity Profile and Functionality during Bread Making. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:11198-11209. [PMID: 31532988 DOI: 10.1021/acs.jafc.9b04712] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The importance of inhibition sensitivity for xylanase functionality in bread making was investigated using mutants of the wild-type Bacillus subtilis xylanase (XBSTAXI), sensitive to Triticum aestivum xylanase inhibitor (TAXI). XBSNI, a mutant with reduced sensitivity to TAXI, and XBSTI, a mutant sensitive to all wheat endogenous proteinaceous inhibitors (TAXI, Xylanase Inhibiting Protein and Thaumatin-like Xylanase Inhibitor) were used. The higher inhibition sensitivity of XBSTAXI and XBSTI compared to XBSNI was associated with a respective 7- and 53-fold increase in enzyme dosage required for a maximal increase in bread loaf volume. XBSTI and XBSTAXI were only active during the mixing phase and the beginning of fermentation, while XBSNI was able to hydrolyze arabinoxylan until the end of fermentation. In spite of this difference in activity profile, no differences in loaf volume were observed for the different xylanases at optimal concentrations. Dough extensional viscosity analysis suggests that increased water availability as a result of xylanase activity favors starch-starch and starch-gluten interactions and drives the improvement in bread loaf volume.
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Affiliation(s)
- Sofie Leys
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe) , KU Leuven , Kasteelpark Arenberg 20 , 3001 Leuven , Belgium
| | - Yamina De Bondt
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe) , KU Leuven , Kasteelpark Arenberg 20 , 3001 Leuven , Belgium
| | - Linde Schreurs
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe) , KU Leuven , Kasteelpark Arenberg 20 , 3001 Leuven , Belgium
| | - Christophe M Courtin
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe) , KU Leuven , Kasteelpark Arenberg 20 , 3001 Leuven , Belgium
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Anwar W, Javed MA, Shahid AA, Nawaz K, Akhter A, Ur Rehman MZ, Hameed U, Iftikhar S, Haider MS. Chitinase genes from Metarhizium anisopliae for the control of whitefly in cotton. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190412. [PMID: 31598241 PMCID: PMC6731705 DOI: 10.1098/rsos.190412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 08/01/2019] [Indexed: 06/01/2023]
Abstract
Entomopathogenic fungi produces endochitianses, involved in the degradation of insect chitin to facilitate the infection process. Endochitinases (Chit1) gene of family 18 glycosyl hydrolyses were amplified, cloned and characterized from genomic DNA of two isolates of Metarhizium anisopliae. Catalytic motif of family 18 glycosyl hydrolyses was found in Chit1 of M. anisopliae, while no signal peptide was found in any isolate, whereas substrate-binding motif was found in Chit1 of both isolates. Phylogenetic analysis revealed the evolutionary relationship among the fungal chitinases of Metarhizium. The Chit1 amplified were closely related to the family 18 glycosyl hydrolyses. Transient expressions of Chit1 in cotton plants using Geminivirus-mediated gene silencing vector of Cotton Leaf Crumple Virus (CLCrV) revealed the chitinase activity of Chit1 genes amplified from both of the isolates of M. anisopliae when compared with the control. Transformed cotton plants were virulent against fourth instar nymphal and adult stages of Bemisia tabaci which resulted in the mortality of both fourth instar nymphal and adult B. tabaci. Thus, the fungal chitinases expressed in cotton plants played a vital role in plant defence against B. tabaci. However, further studies are required to explore the comparative effectiveness of chitinases from different fungal strains against economically important insect pests.
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Affiliation(s)
- Waheed Anwar
- Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Asim Javed
- Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Ahmad Ali Shahid
- Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Kiran Nawaz
- Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Adnan Akhter
- Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | | | - Usman Hameed
- Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Sehrish Iftikhar
- Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
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4
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Dang Y, Liu M, Wu X. Recombinant rice xylanase-inhibiting protein inhibits GH11 endo-xylanases through competitive inhibition. Protein Expr Purif 2019; 156:17-24. [DOI: 10.1016/j.pep.2018.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 11/23/2018] [Accepted: 12/28/2018] [Indexed: 12/22/2022]
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5
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Denisenko YA, Gusakov AV, Rozhkova AM, Zorov IN, Bashirova AV, Matys VY, Nemashkalov VA, Sinitsyn AP. Protein engineering of GH10 family xylanases for gaining a resistance to cereal proteinaceous inhibitors. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.01.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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6
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Identification of proteins contained in aqueous extracts of wheat bran through a proteomic approach. J Cereal Sci 2018. [DOI: 10.1016/j.jcs.2018.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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7
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Scarafoni A, Consonni A, Pessina S, Balzaretti S, Capraro J, Galanti E, Duranti M. Structural basis of the lack of endo-glucanase inhibitory activity of Lupinus albus γ-conglutin. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 99:79-85. [PMID: 26741537 DOI: 10.1016/j.plaphy.2015.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 10/30/2015] [Accepted: 11/16/2015] [Indexed: 06/05/2023]
Abstract
Lupin γ-conglutin and soybean BG7S are two legume seed proteins strongly similar to plant endo-β-glucanases inhibitors acting against fungal GH11 and GH12 glycoside hydrolase. However these proteins lack inhibitory activity. Here we describe the conversion of lupin γ-conglutin to an active inhibitor of endo-β-glucanases belonging to GH11 family. A set of γ-conglutin mutants was designed and expressed in Pichia pastoris, along with the wild-type protein. Unexpectedly, this latter was able to inhibit a GH11 enzyme, but not GH12, whereas the mutants were able to modulate the inhibition capacity. In lupin, γ-conglutin is naturally cleaved in two subunits, whereas in P. pastoris it is not. The lack of proteolytic cleavage is one of the reasons at the basis of the inhibitory activity of recombinant γ-conglutin. The results provide new insights about structural features at the basis of the lack of inhibitory activity of wild-type γ-conglutin and its legume homologues.
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Affiliation(s)
- Alessio Scarafoni
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Milano, Italy.
| | - Alessandro Consonni
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Milano, Italy
| | - Stefano Pessina
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Milano, Italy
| | - Silvia Balzaretti
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Milano, Italy
| | - Jessica Capraro
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Milano, Italy
| | - Elisabetta Galanti
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Milano, Italy
| | - Marcello Duranti
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Milano, Italy
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8
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Protein-protein docking with dynamic residue protonation states. PLoS Comput Biol 2014; 10:e1004018. [PMID: 25501663 PMCID: PMC4263365 DOI: 10.1371/journal.pcbi.1004018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 11/02/2014] [Indexed: 12/19/2022] Open
Abstract
Protein-protein interactions depend on a host of environmental factors. Local pH conditions influence the interactions through the protonation states of the ionizable residues that can change upon binding. In this work, we present a pH-sensitive docking approach, pHDock, that can sample side-chain protonation states of five ionizable residues (Asp, Glu, His, Tyr, Lys) on-the-fly during the docking simulation. pHDock produces successful local docking funnels in approximately half (79/161) the protein complexes, including 19 cases where standard RosettaDock fails. pHDock also performs better than the two control cases comprising docking at pH 7.0 or using fixed, predetermined protonation states. On average, the top-ranked pHDock structures have lower interface RMSDs and recover more native interface residue-residue contacts and hydrogen bonds compared to RosettaDock. Addition of backbone flexibility using a computationally-generated conformational ensemble further improves native contact and hydrogen bond recovery in the top-ranked structures. Although pHDock is designed to improve docking, it also successfully predicts a large pH-dependent binding affinity change in the Fc–FcRn complex, suggesting that it can be exploited to improve affinity predictions. The approaches in the study contribute to the goal of structural simulations of whole-cell protein-protein interactions including all the environmental factors, and they can be further expanded for pH-sensitive protein design. Protein-protein interactions are fundamental for biological function and are strongly influenced by their local environment. Cellular pH is tightly controlled and is one of the critical environmental factors that regulates protein-protein interactions. Three-dimensional structures of the protein complexes can help us understand the mechanism of the interactions. Since experimental determination of the structures of protein-protein complexes is expensive and time-consuming, computational docking algorithms are helpful to predict the structures. However, none of the current protein-protein docking algorithms account for the critical environmental pH effects. So we developed a pH-sensitive docking algorithm that can dynamically pick the favorable protonation states of the ionizable amino-acid residues. Compared to our previous standard docking algorithm, the new algorithm improves docking accuracy and generates higher-quality predictions over a large dataset of protein-protein complexes. We also use a case study to demonstrate efficacy of the algorithm in predicting a large pH-dependent binding affinity change that cannot be captured by the other methods that neglect pH effects. In principle, the approaches in the study can be used for rational design of pH-dependent protein inhibitors or industrial enzymes that are active over a wide range of pH values.
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Santos CR, Hoffmam ZB, de Matos Martins VP, Zanphorlin LM, de Paula Assis LH, Honorato RV, Lopes de Oliveira PS, Ruller R, Murakami MT. Molecular mechanisms associated with xylan degradation by Xanthomonas plant pathogens. J Biol Chem 2014; 289:32186-32200. [PMID: 25266726 PMCID: PMC4231694 DOI: 10.1074/jbc.m114.605105] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 09/22/2014] [Indexed: 11/06/2022] Open
Abstract
Xanthomonas pathogens attack a variety of economically relevant plants, and their xylan CUT system (carbohydrate utilization with TonB-dependent outer membrane transporter system) contains two major xylanase-related genes, xynA and xynB, which influence biofilm formation and virulence by molecular mechanisms that are still elusive. Herein, we demonstrated that XynA is a rare reducing end xylose-releasing exo-oligoxylanase and not an endo-β-1,4-xylanase as predicted. Structural analysis revealed that an insertion in the β7-α7 loop induces dimerization and promotes a physical barrier at the +2 subsite conferring this unique mode of action within the GH10 family. A single mutation that impaired dimerization became XynA active against xylan, and high endolytic activity was achieved when this loop was tailored to match a canonical sequence of endo-β-1,4-xylanases, supporting our mechanistic model. On the other hand, the divergent XynB proved to be a classical endo-β-1,4-xylanase, despite the low sequence similarity to characterized GH10 xylanases. Interestingly, this enzyme contains a calcium ion bound nearby to the glycone-binding region, which is required for catalytic activity and structural stability. These results shed light on the molecular basis for xylan degradation by Xanthomonas and suggest how these enzymes synergistically assist infection and pathogenesis. Our findings indicate that XynB contributes to breach the plant cell wall barrier, providing nutrients and facilitating the translocation of effector molecules, whereas the exo-oligoxylanase XynA possibly participates in the suppression of oligosaccharide-induced immune responses.
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Affiliation(s)
- Camila Ramos Santos
- Biosciences National Laboratory and National Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
| | - Zaira Bruna Hoffmam
- Bioethanol Science and Technology Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
| | - Vanesa Peixoto de Matos Martins
- Biosciences National Laboratory and National Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
| | - Leticia Maria Zanphorlin
- Bioethanol Science and Technology Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
| | - Leandro Henrique de Paula Assis
- Biosciences National Laboratory and National Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
| | - Rodrigo Vargas Honorato
- Biosciences National Laboratory and National Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
| | - Paulo Sérgio Lopes de Oliveira
- Biosciences National Laboratory and National Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
| | - Roberto Ruller
- Bioethanol Science and Technology Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
| | - Mario Tyago Murakami
- Biosciences National Laboratory and National Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil.
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10
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La D, Kong M, Hoffman W, Choi YI, Kihara D. Predicting permanent and transient protein-protein interfaces. Proteins 2013; 81:805-18. [PMID: 23239312 DOI: 10.1002/prot.24235] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 11/19/2012] [Accepted: 11/28/2012] [Indexed: 11/11/2022]
Abstract
Protein-protein interactions (PPIs) are involved in diverse functions in a cell. To optimize functional roles of interactions, proteins interact with a spectrum of binding affinities. Interactions are conventionally classified into permanent and transient, where the former denotes tight binding between proteins that result in strong complexes, whereas the latter compose of relatively weak interactions that can dissociate after binding to regulate functional activity at specific time point. Knowing the type of interactions has significant implications for understanding the nature and function of PPIs. In this study, we constructed amino acid substitution models that capture mutation patterns at permanent and transient type of protein interfaces, which were found to be different with statistical significance. Using the substitution models, we developed a novel computational method that predicts permanent and transient protein binding interfaces (PBIs) in protein surfaces. Without knowledge of the interacting partner, the method uses a single query protein structure and a multiple sequence alignment of the sequence family. Using a large dataset of permanent and transient proteins, we show that our method, BindML+, performs very well in protein interface classification. A very high area under the curve (AUC) value of 0.957 was observed when predicted protein binding sites were classified. Remarkably, near prefect accuracy was achieved with an AUC of 0.991 when actual binding sites were classified. The developed method will be also useful for protein design of permanent and transient PBIs.
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Affiliation(s)
- David La
- Department of Biological Sciences, College of Science, Purdue University, West Lafayette, Indiana 47907, USA
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11
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Shammas S, Rogers J, Hill S, Clarke J. Slow, reversible, coupled folding and binding of the spectrin tetramerization domain. Biophys J 2012; 103:2203-14. [PMID: 23200054 PMCID: PMC3512043 DOI: 10.1016/j.bpj.2012.10.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 10/02/2012] [Accepted: 10/10/2012] [Indexed: 11/16/2022] Open
Abstract
Many intrinsically disordered proteins (IDPs) are significantly unstructured under physiological conditions. A number of these IDPs have been shown to undergo coupled folding and binding reactions whereby they can gain structure upon association with an appropriate partner protein. In general, these systems display weaker binding affinities than do systems with association between completely structured domains, with micromolar K(d) values appearing typical. One such system is the association between α- and β-spectrin, where two partially structured, incomplete domains associate to form a fully structured, three-helix bundle, the spectrin tetramerization domain. Here, we use this model system to demonstrate a method for fitting association and dissociation kinetic traces where, using typical biophysical concentrations, the association reactions are expected to be highly reversible. We elucidate the unusually slow, two-state kinetics of spectrin assembly in solution. The advantages of studying kinetics in this regime include the potential for gaining equilibrium constants as well as rate constants, and for performing experiments with low protein concentrations. We suggest that this approach would be particularly appropriate for high-throughput mutational analysis of two-state reversible binding processes.
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Affiliation(s)
| | | | | | - J. Clarke
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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12
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Yoshizawa T, Shimizu T, Hirano H, Sato M, Hashimoto H. Structural basis for inhibition of xyloglucan-specific endo-β-1,4-glucanase (XEG) by XEG-protein inhibitor. J Biol Chem 2012; 287:18710-6. [PMID: 22496365 DOI: 10.1074/jbc.m112.350520] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microorganisms such as plant pathogens secrete glycoside hydrolases (GHs) to digest the polysaccharide chains of plant cell walls. The degradation of cell walls by these enzymes is a crucial step for nutrition and invasion. To protect the cell wall from these enzymes, plants secrete glycoside hydrolase inhibitor proteins (GHIPs). Xyloglucan-specific endo-β-1,4-glucanase (XEG), a member of GH family 12 (GH12), could be a great threat to many plants because xyloglucan is a major component of the cell wall in most plants. Understanding the inhibition mechanism of XEG by GHIP is therefore of great importance in the field of plant defense, but to date the mechanism and specificity of GHIPs remain unclear. We have determined the crystal structure of XEG in complex with extracellular dermal glycoprotein (EDGP), a carrot GHIP that inhibits XEG. The structure reveals that the conserved arginines of EDGP intrude into the active site of XEG and interact with the catalytic glutamates of the enzyme. We have also determined the crystal structure of the XEG-xyloglucan complex. These structures show that EDGP closely mimics the XEG-xyloglucan interaction. Although EDGP shares structural similarity to a wheat GHIP (Triticum aestivum xylanase inhibitor-IA (TAXI-IA)) that inhibits GH11 family xylanases, the arrangement of GH and GHIP in the XEG-EDGP complex is distinct from that in the xylanase-TAXI-IA complex. Our findings imply that plants have evolved structures of GHIPs to inhibit different GH family members that attack their cell walls.
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Affiliation(s)
- Takuya Yoshizawa
- Graduate School of Nanobioscience, Yokohama City University, Tsurumi-ku, Yokohama, Kanagawa, Japan
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13
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Paës G, Berrin JG, Beaugrand J. GH11 xylanases: Structure/function/properties relationships and applications. Biotechnol Adv 2011; 30:564-92. [PMID: 22067746 DOI: 10.1016/j.biotechadv.2011.10.003] [Citation(s) in RCA: 275] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 10/06/2011] [Accepted: 10/13/2011] [Indexed: 01/02/2023]
Abstract
For technical, environmental and economical reasons, industrial demands for process-fitted enzymes have evolved drastically in the last decade. Therefore, continuous efforts are made in order to get insights into enzyme structure/function relationships to create improved biocatalysts. Xylanases are hemicellulolytic enzymes, which are responsible for the degradation of the heteroxylans constituting the lignocellulosic plant cell wall. Due to their variety, xylanases have been classified in glycoside hydrolase families GH5, GH8, GH10, GH11, GH30 and GH43 in the CAZy database. In this review, we focus on GH11 family, which is one of the best characterized GH families with bacterial and fungal members considered as true xylanases compared to the other families because of their high substrate specificity. Based on an exhaustive analysis of the sequences and 3D structures available so far, in relation with biochemical properties, we assess biochemical aspects of GH11 xylanases: structure, catalytic machinery, focus on their "thumb" loop of major importance in catalytic efficiency and substrate selectivity, inhibition, stability to pH and temperature. GH11 xylanases have for a long time been used as biotechnological tools in various industrial applications and represent in addition promising candidates for future other uses.
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Affiliation(s)
- Gabriel Paës
- INRA, UMR614 FARE, 2 esplanade Roland-Garros, F-51686 Reims, France.
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14
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Yoshizawa T, Shimizu T, Yamabe M, Taichi M, Nishiuchi Y, Shichijo N, Unzai S, Hirano H, Sato M, Hashimoto H. Crystal structure of basic 7S globulin, a xyloglucan-specific endo-β-1,4-glucanase inhibitor protein-like protein from soybean lacking inhibitory activity against endo-β-glucanase. FEBS J 2011; 278:1944-54. [PMID: 21457461 DOI: 10.1111/j.1742-4658.2011.08111.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
β-Linked glucans such as cellulose and xyloglucan are important components of the cell walls of most dicotyledonous plants. These β-linked glucans are constantly exposed to degradation by various endo-β-glucanases from pathogenic bacteria and fungi. To protect the cell wall from degradation by such enzymes, plants secrete proteinaceous endo-β-glucanases inhibitors, such as xyloglucan-specific endo-β-1,4-glucanase inhibitor protein (XEGIP) in tomato. XEGIPs typically inhibit xyloglucanase, a member of the glycoside hydrolase (GH)12 family. XEGIPs are also found in legumes, including soybean and lupin. To date, tomato XEGIP has been well studied, whereas XEGIPs from legumes are less well understood. Here, we determined the crystal structure of basic 7S globulin (Bg7S), a XEGIP from soybean, which represents the first three-dimensional structure of XEGIP. Bg7S formed a tetramer with pseudo-222 symmetry. Analytical centrifugation and size exclusion chromatography experiments revealed that the assembly of Bg7S in solution depended on pH. The structure of Bg7S was similar to that of a xylanase inhibitor protein from wheat (Tritinum aestivum xylanase inhibitor) that inhibits GH11 xylanase. Surprisingly, Bg7S lacked inhibitory activity against not only GH11 but also GH12 enzymes. In addition, we found that XEGIPs from azukibean, yardlongbean and mungbean also had no impact on the activity of either GH12 or GH11 enzymes, indicating that legume XEGIPs generally do not inhibit these enzymes. We reveal the structural basis of why legume XEGIPs lack this inhibitory activity. This study will provide significant clues for understanding the physiological role of Bg7S.
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Affiliation(s)
- Takuya Yoshizawa
- Graduate School of Nanobioscience, Yokohama City University, Japan
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15
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16
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Gusakov AV. Proteinaceous inhibitors of microbial xylanases. BIOCHEMISTRY (MOSCOW) 2010; 75:1185-99. [DOI: 10.1134/s0006297910100019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Rasmussen LE, Sørensen JF, Meyer AS. Kinetics and substrate selectivity of a Triticum aestivum xylanase inhibitor (TAXI) resistant D11F/R122D variant of Bacillus subtilis XynA xylanase. J Biotechnol 2010; 146:207-14. [DOI: 10.1016/j.jbiotec.2010.02.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 02/13/2010] [Accepted: 02/16/2010] [Indexed: 11/28/2022]
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Scarafoni A, Ronchi A, Duranti M. gamma-Conglutin, the Lupinus albus XEGIP-like protein, whose expression is elicited by chitosan, lacks of the typical inhibitory activity against GH12 endo-glucanases. PHYTOCHEMISTRY 2010; 71:142-148. [PMID: 19962718 DOI: 10.1016/j.phytochem.2009.11.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2009] [Revised: 11/06/2009] [Accepted: 11/10/2009] [Indexed: 05/27/2023]
Abstract
gamma-Conglutin, a glycoprotein from Lupinus albus seed, has been characterized at molecular level but its physiological function is still unknown. gamma-Conglutin shares a high structural similarity with xyloglucan-specific endo-beta-1,4-glucanase inhibitor proteins (XEGIPs) and Triticum aestivum xylanase inhibitor (TAXI-I), which act specifically against fungal glycosyl hydrolase belonging to families 12 and 11, respectively. To assess the possible involvement of gamma-conglutin in plant defense, germinating lupin seeds were incubated with chitosan. The relative quantification of gamma-conglutin mRNA extracted from cotyledons was then carried out by RT-qPCR and indicated that chitosan strongly elicited the expression of gamma-conglutin. Moreover, biochemical trials aimed to test the inhibitory capacity of the protein have been also carried out. gamma-Conglutin failed to inhibit representative fungal endo-glucanases and other cell wall-degrading enzymes. To explain the lack of inhibitory capacity we investigated the possible structural differences between gamma-conglutin and XEGIPs and TAXI-I, including the construction of a predictive 3D model of the protein. Bioinformatic analysis suggests that the lack of inhibitory activity of gamma-conglutin can be attributed to sequence differences in the inhibitor interaction domains, and in particular to a sequence deletion in one of the functional loops.
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Affiliation(s)
- Alessio Scarafoni
- Dipartimento di Scienze Molecolari Agroalimentari, Università degli Studi di Milano, via G. Celoria 2, 20133 Milano, Italy.
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Lagaert S, Beliën T, Volckaert G. Plant cell walls: Protecting the barrier from degradation by microbial enzymes. Semin Cell Dev Biol 2009; 20:1064-73. [DOI: 10.1016/j.semcdb.2009.05.008] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Accepted: 05/25/2009] [Indexed: 10/20/2022]
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Pollet A, Sansen S, Raedschelders G, Gebruers K, Rabijns A, Delcour JA, Courtin CM. Identification of structural determinants for inhibition strength and specificity of wheat xylanase inhibitors TAXI-IA and TAXI-IIA. FEBS J 2009; 276:3916-27. [PMID: 19769747 DOI: 10.1111/j.1742-4658.2009.07105.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Triticum aestivum xylanase inhibitor (TAXI)-type inhibitors are active against microbial xylanases from glycoside hydrolase family 11, but the inhibition strength and the specificity towards different xylanases differ between TAXI isoforms. Mutational and biochemical analyses of TAXI-I, TAXI-IIA and Bacillus subtilis xylanase A showed that inhibition strength and specificity depend on the identity of only a few key residues of inhibitor and xylanase [Fierens K et al. (2005) FEBS J 272, 5872-5882; Raedschelders G et al. (2005) Biochem Biophys Res Commun335, 512-522; Sorensen JF & Sibbesen O (2006) Protein Eng Des Sel 19, 205-210; Bourgois TM et al. (2007) J Biotechnol 130, 95-105]. Crystallographic analysis of the structures of TAXI-IA and TAXI-IIA in complex with glycoside hydrolase family 11 B. subtilis xylanase A now provides a substantial explanation for these observations and a detailed insight into the structural determinants for inhibition strength and specificity. Structures of the xylanaseinhibitor complexes show that inhibition is established by loop interactions with active-site residues and substrate-mimicking contacts in the binding subsites. The interaction of residues Leu292 of TAXI-IA and Pro294 of TAXI-IIA with the -2 glycon subsite of the xylanase is shown to be critical for both inhibition strength and specificity. Also, detailed analysis of the interaction interfaces of the complexes illustrates that the inhibition strength of TAXI is related to the presence of an aspartate or asparagine residue adjacent to the acid/base catalyst of the xylanase, and therefore to the pH optimum of the xylanase. The lower the pH optimum of the xylanase, the stronger will be the interaction between enzyme and inhibitor, and the stronger the resulting inhibition.
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Affiliation(s)
- Annick Pollet
- Laboratory of Food Chemistry and Biochemistry, Katholieke Universiteit Leuven, Belgium
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Fierens E, Gebruers K, Voet AR, De Maeyer M, Courtin CM, Delcour JA. Biochemical and structural characterization of TLXI, the Triticum aestivum L. thaumatin-like xylanase inhibitor. J Enzyme Inhib Med Chem 2009; 24:646-54. [DOI: 10.1080/14756360802321831] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Ellen Fierens
- Laboratory of Food Chemistry and Biochemistry, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, Box 24633001, Leuven, Belgium
| | - Kurt Gebruers
- Laboratory of Food Chemistry and Biochemistry, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, Box 24633001, Leuven, Belgium
| | - Arnout R.D. Voet
- Laboratory of Biomolecular Modelling and BioMacS, Katholieke Universiteit Leuven, Celestijnenlaan 200G3001, Leuven, Belgium
| | - Marc De Maeyer
- Laboratory of Biomolecular Modelling and BioMacS, Katholieke Universiteit Leuven, Celestijnenlaan 200G3001, Leuven, Belgium
| | - Christophe M. Courtin
- Laboratory of Food Chemistry and Biochemistry, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, Box 24633001, Leuven, Belgium
| | - Jan A. Delcour
- Laboratory of Food Chemistry and Biochemistry, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, Box 24633001, Leuven, Belgium
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Rombouts S, Fierens E, Vandermarliere E, Voet A, Gebruers K, Beaugrand J, Courtin CM, Delcour JA, de Maeyer M, Rabijns A, Van Campenhout S, Volckaert G. His22 of TLXI plays a critical role in the inhibition of glycoside hydrolase family 11 xylanases. J Enzyme Inhib Med Chem 2008; 24:38-46. [DOI: 10.1080/14756360701841913] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Sigrid Rombouts
- Laboratory of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, B-3001 Leuven, Belgium
| | - Ellen Fierens
- Laboratory of Food Chemistry and Biochemistry, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Elien Vandermarliere
- Laboratory for Biocrystallography, Katholieke Universiteit Leuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Arnout Voet
- Laboratory of Biomolecular Modeling and BioMacS, Katholieke Universiteit Leuven, Celestijnenlaan 200G, B-3001 Leuven, Belgium
| | - Kurt Gebruers
- Laboratory of Food Chemistry and Biochemistry, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Johnny Beaugrand
- Laboratory of Food Chemistry and Biochemistry, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Christophe M. Courtin
- Laboratory of Food Chemistry and Biochemistry, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Jan A. Delcour
- Laboratory of Food Chemistry and Biochemistry, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Marc de Maeyer
- Laboratory of Biomolecular Modeling and BioMacS, Katholieke Universiteit Leuven, Celestijnenlaan 200G, B-3001 Leuven, Belgium
| | - Anja Rabijns
- Laboratory for Biocrystallography, Katholieke Universiteit Leuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Steven Van Campenhout
- Laboratory of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, B-3001 Leuven, Belgium
| | - Guido Volckaert
- Laboratory of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, B-3001 Leuven, Belgium
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Gebruers K, Mokrane H, Nadjemi B, Beaugrand J, Fierens K, Proost P, Courtin CM, Delcour JA. Sorghum (Sorghum bicolor L. Moench) contains a XIP-type xylanase inhibitor but none of the TAXI- and TLXI-types. J Cereal Sci 2008. [DOI: 10.1016/j.jcs.2007.09.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Beaugrand J, Gebruers K, Ververken C, Fierens E, Dornez E, Goddeeris BM, Delcour JA, Courtin CM. Indirect enzyme-antibody sandwich enzyme-linked immunosorbent assay for quantification of TAXI and XIP type xylanase inhibitors in wheat and other cereals. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2007; 55:7682-8. [PMID: 17715986 DOI: 10.1021/jf071087b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
To quantify Triticum aestivum xylanase inhibitor (TAXI) and xylanase inhibiting protein (XIP) type proteins in cereals in general and wheat ( T. aestivum) in particular, a robust enzyme-linked immunosorbent assay (ELISA) using an uncommon enzyme-antibody sandwich format was developed. Bacillus subtilis glycoside hydrolase family (GH) 11 and Aspergillus oryzae GH 10 xylanases were selected for coating ELISA plate wells to capture TAXI and XIP, respectively, prior to probing with antibodies. The detection threshold of the developed ELISA was much lower than that of the currently used xylanase inhibitor assay and the recently described Western blot approach. Because of its broad dynamic range (TAXI, 30-600 ng/mL, and XIP, 3-60 ng/mL), one proper standard extract dilution can be used for analyzing different wheat varieties, whereas for the currently used colorimetric assay, often different dilutions need to be analyzed. The TAXI ELISA for wheat was successfully adapted for barley ( Hordeum vulgare) and could also be used for other cereals.
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Affiliation(s)
- Johnny Beaugrand
- Laboratory of Food Chemistry and Biochemistry, Katholieke Universiteit Leuven, Kasteelpark Arenberg 30, B-3001 Leuven, Belgium
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Fierens E, Rombouts S, Gebruers K, Goesaert H, Brijs K, Beaugrand J, Volckaert G, Van Campenhout S, Proost P, Courtin C, Delcour J. TLXI, a novel type of xylanase inhibitor from wheat (Triticum aestivum) belonging to the thaumatin family. Biochem J 2007; 403:583-91. [PMID: 17269932 PMCID: PMC1876379 DOI: 10.1042/bj20061291] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Wheat (Triticum aestivum) contains a previously unknown type of xylanase (EC 3.2.1.8) inhibitor, which is described in the present paper for the first time. Based on its >60% similarity to TLPs (thaumatin-like proteins) and the fact that it contains the Prosite PS00316 thaumatin family signature, it is referred to as TLXI (thaumatin-like xylanase inhibitor). TLXI is a basic (pI> or =9.3 in isoelectric focusing) protein with a molecular mass of approx. 18-kDa (determined by SDS/PAGE) and it occurs in wheat with varying extents of glycosylation. The TLXI gene sequence encodes a 26-amino-acid signal sequence followed by a 151-amino-acid mature protein with a calculated molecular mass of 15.6-kDa and pI of 8.38. The mature TLXI protein was expressed successfully in Pichia pastoris, resulting in a 21-kDa (determined by SDS/PAGE) recombinant protein (rTLXI). Polyclonal antibodies raised against TLXI purified from wheat react with epitopes of rTLXI as well as with those of thaumatin, demonstrating high structural similarity between these three proteins. TLXI has a unique inhibition specificity. It is a non-competitive inhibitor of a number of glycoside hydrolase family 11 xylanases, but it is inactive towards glycoside hydrolase family 10 xylanases. Progress curves show that TLXI is a slow tight-binding inhibitor, with a K(i) of approx. 60-nM. Except for zeamatin, an alpha-amylase/trypsin inhibitor from maize (Zea mays), no other enzyme inhibitor is currently known among the TLPs. TLXI thus represents a novel type of inhibitor within this group of proteins.
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Affiliation(s)
- Ellen Fierens
- *Laboratory of Food Chemistry and Biochemistry, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Sigrid Rombouts
- †Laboratory of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, B-3001 Leuven, Belgium
| | - Kurt Gebruers
- *Laboratory of Food Chemistry and Biochemistry, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
- To whom correspondence should be addressed (email )
| | - Hans Goesaert
- *Laboratory of Food Chemistry and Biochemistry, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Kristof Brijs
- *Laboratory of Food Chemistry and Biochemistry, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Johnny Beaugrand
- *Laboratory of Food Chemistry and Biochemistry, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Guido Volckaert
- †Laboratory of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, B-3001 Leuven, Belgium
| | - Steven Van Campenhout
- *Laboratory of Food Chemistry and Biochemistry, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Paul Proost
- ‡Laboratory of Molecular Immunology, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Christophe M. Courtin
- *Laboratory of Food Chemistry and Biochemistry, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Jan A. Delcour
- *Laboratory of Food Chemistry and Biochemistry, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
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Abstract
We identified 1113 articles (103 reviews, 1010 primary research articles) published in 2005 that describe experiments performed using commercially available optical biosensors. While this number of publications is impressive, we find that the quality of the biosensor work in these articles is often pretty poor. It is a little disappointing that there appears to be only a small set of researchers who know how to properly perform, analyze, and present biosensor data. To help focus the field, we spotlight work published by 10 research groups that exemplify the quality of data one should expect to see from a biosensor experiment. Also, in an effort to raise awareness of the common problems in the biosensor field, we provide side-by-side examples of good and bad data sets from the 2005 literature.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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