1
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Xu T, Wang YC, Ma J, Cui Y, Wang L. In silico discovery and anti-tumor bioactivities validation of an algal lectin from Kappaphycus alvarezii genome. Int J Biol Macromol 2024; 275:133311. [PMID: 38909728 DOI: 10.1016/j.ijbiomac.2024.133311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/24/2024] [Accepted: 06/13/2024] [Indexed: 06/25/2024]
Abstract
Lectins are proteins that bind specifically and reversibly to carbohydrates, and some of them have significant anti-tumor activities. Compared to those of lectins from land plants, there are far fewer studies on algal lectins, despite of the high biodiversity of algae. However, canonical strategies based on chromatographic feature-oriented screening cannot satisfy the requirement for algal lectin discovery. In this study, prospecting for novel OAAH family lectins throughout 358 genomes of red algae and cyanobacteria was conducted. Then 35 candidate lectins and 1843 of their simulated mutated forms were virtually screened based on predicted binding specificities to characteristic carbohydrates on cancer cells inferred by a deep learning model. A new lectin, named Siye, was discovered in Kappaphycus alvarezii genome and further verified on different cancer cells. Without causing agglutination of erythrocytes, Siye showed significant cytotoxicity to four human cancer cell lines (IC50 values ranging from 0.11 to 3.95 μg/mL), including breast adenocarcinoma HCC1937, lung carcinoma A549, liver cancer HepG2 and romyelocytic leukemia HL60. And the cytotoxicity was induced through promoting apoptosis by regulating the caspase and the p53 pathway within 24 h. This study testifies the feasibility and efficiency of the genome mining guided by evolutionary theory and artificial intelligence in the discovery of algal lectins.
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Affiliation(s)
- Tongli Xu
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; Qingdao Academy of Chinese Medical Sciences, Shandong University of Traditional Chinese Medicine, Qingdao 266071, China
| | - Yin-Chu Wang
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; National Basic Science Data Center, Beijing 100190, China.
| | - Jiahao Ma
- Hong Kong University of Science and Technology, Clear Water Bay, 999077, Hong Kong
| | - Yulin Cui
- Binzhou Medical University, Yantai 264003, China.
| | - Lu Wang
- School of Pharmacy, Yantai University, Yantai 264005, China.
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2
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Imberty A, Bonnardel F, Lisacek F. UniLectin, A One-Stop-Shop to Explore and Study Carbohydrate-Binding Proteins. Curr Protoc 2021; 1:e305. [PMID: 34826352 DOI: 10.1002/cpz1.305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
All eukaryotic cells are covered with a dense layer of glycoconjugates, and the cell walls of bacteria are made of various polysaccharides, putting glycans in key locations for mediating protein-protein interactions at cell interfaces. Glycan function is therefore mainly defined as binding to other molecules, and lectins are proteins that specifically recognize and interact non-covalently with glycans. UniLectin was designed based on insight into the knowledge of lectins, their classification, and their biological role. This modular platform provides a curated and periodically updated classification of lectins along with a set of comparative and visualization tools, as well as structured results of screening comprehensive sequence datasets. UniLectin can be used to explore lectins, find precise information on glycan-protein interactions, and mine the results of predictive tools based on HMM profiles. This usage is illustrated here with two protocols. The first one highlights the fine-tuned role of the O blood group antigen in distinctive pathogen recognition, while the second compares the various bacterial lectin arsenals that clearly depend on living conditions of species even in the same genus. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Searching for the structural details of lectins binding the O blood group antigen Basic Protocol 2: Comparing the lectomes of related organisms in different environments.
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Affiliation(s)
- Anne Imberty
- Université Grenoble Alpes, CNRS, CERMAV, Grenoble, France
| | - François Bonnardel
- Université Grenoble Alpes, CNRS, CERMAV, Grenoble, France.,SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.,Computer Science Department, UniGe, Geneva, Switzerland
| | - Frédérique Lisacek
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.,Computer Science Department, UniGe, Geneva, Switzerland.,Section of Biology, UniGe, Geneva, Switzerland
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3
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Abstract
Lectins are widely distributed proteins having ability of binding selectively and reversibly with carbohydrates moieties and glycoconjugates. Although lectins have been reported from different biological sources, the legume lectins are the best-characterized family of plant lectins. Legume lectins are a large family of homologous proteins with considerable similarity in amino acid sequence and their tertiary structures. Despite having strong sequence conservation, these lectins show remarkable variability in carbohydrate specificity and quaternary structures. The ability of legume lectins in recognizing glycans and glycoconjugates on cells and other intracellular structures make them a valuable research tool in glycomic research. Due to variability in binding with glycans, glycoconjugates and multiple biological functions, legume lectins are the subject of intense research for their diverse application in different fields such as glycobiology, biomedical research and crop improvement. The present review specially focuses on structural and functional characteristics of legume lectins along with their potential areas of application.
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Affiliation(s)
- Rajan Katoch
- Biochemistry Laboratory, Department of Genetics and Plant Breeding, CSKHPKV, Palampur, 176 062 India
| | - Ankur Tripathi
- Biochemistry Laboratory, Department of Genetics and Plant Breeding, CSKHPKV, Palampur, 176 062 India
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4
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Protein Analysis: From Sequence to Structure. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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5
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Riley NM, Bertozzi CR, Pitteri SJ. A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-Based Glycoproteomics. Mol Cell Proteomics 2020; 20:100029. [PMID: 33583771 PMCID: PMC8724846 DOI: 10.1074/mcp.r120.002277] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/26/2022] Open
Abstract
Glycosylation is a prevalent, yet heterogeneous modification with a broad range of implications in molecular biology. This heterogeneity precludes enrichment strategies that can be universally beneficial for all glycan classes. Thus, choice of enrichment strategy has profound implications on experimental outcomes. Here we review common enrichment strategies used in modern mass spectrometry-based glycoproteomic experiments, including lectins and other affinity chromatographies, hydrophilic interaction chromatography and its derivatives, porous graphitic carbon, reversible and irreversible chemical coupling strategies, and chemical biology tools that often leverage bioorthogonal handles. Interest in glycoproteomics continues to surge as mass spectrometry instrumentation and software improve, so this review aims to help equip researchers with the necessary information to choose appropriate enrichment strategies that best complement these efforts.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, Stanford University, Stanford, California, USA.
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, California, USA; Howard Hughes Medical Institute, Stanford, California, USA
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, California, USA.
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6
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Scherbinina SI, Toukach PV. Three-Dimensional Structures of Carbohydrates and Where to Find Them. Int J Mol Sci 2020; 21:E7702. [PMID: 33081008 PMCID: PMC7593929 DOI: 10.3390/ijms21207702] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023] Open
Abstract
Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.
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Affiliation(s)
- Sofya I. Scherbinina
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
- Higher Chemical College, D. Mendeleev University of Chemical Technology of Russia, Miusskaya Square 9, 125047 Moscow, Russia
| | - Philip V. Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
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7
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Francis F, Chen J, Yong L, Bosquee E. Aphid Feeding on Plant Lectins Falling Virus Transmission Rates: A Multicase Study. JOURNAL OF ECONOMIC ENTOMOLOGY 2020; 113:1635-1639. [PMID: 32515475 DOI: 10.1093/jee/toaa104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Indexed: 06/11/2023]
Abstract
Aphids are insect vectors that have piercing-sucking mouthparts supporting diversified patterns of virus-vector interactions. Aphids primarily retain circulative viruses in the midgut/hindgut, whereas noncirculative viruses tend to be retained in the stylet. Most viruses, and many proteins from animals, have carbohydrate or carbohydrate-binding sites. Lectins vary in their specificity, of which some are able to bind to viral glycoproteins. To assess the potential competition between lectins and viral particles in virus transmission by aphids, this study examined how feeding plant lectins to aphids affects the transmission efficiency of viruses. Sitobion avenae (F, 1794) (Homoptera: Aphididae) aphids fed with Pisum sativum lectin (PSL) transmitted Barley yellow dwarf virus with significantly lower efficiency (four-fold ratio). Pea enation mosaic virus was significantly reduced in Acyrthosiphon pisum Harris (Homoptera: Aphididae) aphids fed with the lectin Concanavalin A. In comparison, the transmission of Potato virus Y was significantly reduced when Myzus persicae Sultzer (Homoptera: Aphididae) aphids were fed with PSL. Thus, lectin could be used as a blocking agent of plant viruses, facilitating an alternative approach for crop protection.
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Affiliation(s)
- Frederic Francis
- Functional and Evolutionary Entomology, TERRA, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Passage des Deportes, Belgium
- College of Plant Protection, Shandong Agricultural University, Taian, PR China
| | - Julian Chen
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Liu Yong
- College of Plant Protection, Shandong Agricultural University, Taian, PR China
| | - Emilie Bosquee
- Functional and Evolutionary Entomology, TERRA, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Passage des Deportes, Belgium
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8
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Bonnardel F, Mariethoz J, Salentin S, Robin X, Schroeder M, Perez S, Lisacek F, Imberty A. UniLectin3D, a database of carbohydrate binding proteins with curated information on 3D structures and interacting ligands. Nucleic Acids Res 2020; 47:D1236-D1244. [PMID: 30239928 PMCID: PMC6323968 DOI: 10.1093/nar/gky832] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/07/2018] [Indexed: 01/02/2023] Open
Abstract
Lectins, and related receptors such as adhesins and toxins, are glycan-binding proteins from all origins that decipher the glycocode, i.e. the structural information encoded in the conformation of complex carbohydrates present on the surface of all cells. Lectins are still poorly classified and annotated, but since their functions are based on ligand recognition, their 3D-structures provide a solid foundation for characterization. UniLectin3D is a curated database that classifies lectins on origin and fold, with cross-links to literature, other databases in glycosciences and functional data such as known specificity. The database provides detailed information on lectins, their bound glycan ligands, and features their interactions using the Protein–Ligand Interaction Profiler (PLIP) server. Special care was devoted to the description of the bound glycan ligands with the use of simple graphical representation and numerical format for cross-linking to other databases in glycoscience. We conceived the design of the database architecture and the navigation tools to account for all organisms, as well as to search for oligosaccharide epitopes complexed within specified binding sites. UniLectin3D is accessible at https://www.unilectin.eu/unilectin3D.
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Affiliation(s)
- François Bonnardel
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France.,Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland.,Department of Computer Science, University of Geneva, Route de Drize 7, CH-1227 Geneva, Switzerland
| | - Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland.,Department of Computer Science, University of Geneva, Route de Drize 7, CH-1227 Geneva, Switzerland
| | - Sebastian Salentin
- Biotechnology Center (BIOTEC), TU Dresden, Tatzberg 47-49, 01307 Dresden, Germany
| | - Xavier Robin
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.,Computational Structural Biology Group, SIB Swiss Institute of Bioinformatics, CH-4056 Basel, Switzerland
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), TU Dresden, Tatzberg 47-49, 01307 Dresden, Germany
| | - Serge Perez
- Univ. Grenoble Alpes, CNRS, DPM, 38000 Grenoble, France
| | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland.,Department of Computer Science, University of Geneva, Route de Drize 7, CH-1227 Geneva, Switzerland.,Section of Biology, University of Geneva, CH-1205 Geneva, Switzerland
| | - Anne Imberty
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
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9
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Purification of GNA-Related Lectins from Natural Sources. Methods Mol Biol 2020. [PMID: 32306348 DOI: 10.1007/978-1-0716-0430-4_40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The Galanthus nivalis lectin, abbreviated as GNA, is the model protein for a large group of mannose-binding lectins. Here, we describe the purification of GNA starting from dry bulbs. Using a combination of ion exchange chromatography and affinity chromatography on mannose-Sepharose, a highly pure preparation of GNA can be obtained.
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10
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Siva Shanmugam NR, Jino Blessy J, Veluraja K, Michael Gromiha M. ProCaff: protein–carbohydrate complex binding affinity database. Bioinformatics 2020; 36:3615-3617. [DOI: 10.1093/bioinformatics/btaa141] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 01/29/2020] [Accepted: 02/26/2020] [Indexed: 12/28/2022] Open
Abstract
Abstract
Motivation
Protein–carbohydrate interactions perform several cellular and biological functions and their structure and function are mainly dictated by their binding affinity. Although plenty of experimental data on binding affinity are available, there is no reliable and comprehensive database in the literature.
Results
We have developed a database on binding affinity of protein–carbohydrate complexes, ProCaff, which contains 3122 entries on dissociation constant (Kd), Gibbs free energy change (ΔG), experimental conditions, sequence, structure and literature information. Additional features include the options to search, display, visualization, download and upload the data.
Availability and implementation
The database is freely available at http://web.iitm.ac.in/bioinfo2/procaff/. The website is implemented using HTML and PHP and supports recent versions of major browsers such as Chrome, Firefox, IE10 and Opera.
Contact
gromiha@iitm.ac.in
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- N R Siva Shanmugam
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - J Jino Blessy
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - K Veluraja
- School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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11
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Bonnardel F, Perez S, Lisacek F, Imberty A. Structural Database for Lectins and the UniLectin Web Platform. Methods Mol Biol 2020; 2132:1-14. [PMID: 32306309 DOI: 10.1007/978-1-0716-0430-4_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The search for new biomolecules requires a clear understanding of biosynthesis and degradation pathways. This view applies to most metabolites as well as other molecule types such as glycans whose repertoire is still poorly characterized. Lectins are proteins that recognize specifically and interact noncovalently with glycans. This particular class of proteins is considered as playing a major role in biology. Glycan-binding is based on multivalence, which gives lectins a unique capacity to interact with surface glycans and significantly contribute to cell-cell recognition and interactions. Lectins have been studied for many years using multiple technologies and part of the resulting information is available online in databases. Unfortunately, the connectivity of these databases with the most popular omics databases (genomics, proteomics, and glycomics) remains limited. Moreover, lectin diversity is extended and requires setting out a flexible classification that remains compatible with new sequences and 3D structures that are continuously released. We have designed UniLectin as a new insight into the knowledge of lectins, their classification, and their biological role. This platform encompasses UniLectin3D, a curated database of lectin 3D structures that follows a periodically updated classification, a set of comparative and visualizing tools and gradually released modules dedicated to specific lectins predicted in sequence databases. The second module is PropLec, focused on β-propeller lectin prediction in all species based on five distinct family profiles. This chapter describes how UniLectin can be used to explore the diversity of lectins, their 3D structures, and associated functional information as well as to perform reliable predictions of β-propeller lectins.
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Affiliation(s)
- François Bonnardel
- Univ. Grenoble Alpes, CNRS, CERMAV, Grenoble, France.,Swiss Institute of Bioinformatics, Geneva, Switzerland.,Computer Science Department, UniGe, Geneva, Switzerland
| | - Serge Perez
- Univ. Grenoble Alpes, CNRS, CERMAV, Grenoble, France
| | - Frédérique Lisacek
- Swiss Institute of Bioinformatics, Geneva, Switzerland. .,Computer Science Department, UniGe, Geneva, Switzerland. .,Section of Biology, UniGe, Geneva, Switzerland.
| | - Anne Imberty
- Univ. Grenoble Alpes, CNRS, CERMAV, Grenoble, France.
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12
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Sivaji N, Abhinav KV, Vijayan M. Crystallization and biochemical characterization of an archaeal lectin from Methanococcus voltae A3. Acta Crystallogr F Struct Biol Commun 2017; 73:300-304. [PMID: 28471363 PMCID: PMC5417321 DOI: 10.1107/s2053230x17006173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 04/24/2017] [Indexed: 12/13/2022] Open
Abstract
A lectin from Methanococcus voltae A3 has been cloned, expressed, purified and characterized. The lectin appears to be specific for complex sugars. The protein crystallized in a tetragonal space group, with around 16 subunits in the asymmetric unit. Sequence comparisons indicate the lectin to have a β-prism I fold, with poor homology to lectins of known three-dimensional structure.
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Affiliation(s)
- N. Sivaji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - K. V. Abhinav
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - M. Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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13
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Docking polysaccharide to proteins that have a Tryptophan box in the binding pocket. Carbohydr Res 2015; 414:78-84. [DOI: 10.1016/j.carres.2015.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 07/09/2015] [Accepted: 07/12/2015] [Indexed: 11/20/2022]
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14
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Pinedo M, Orts F, Carvalho ADO, Regente M, Soares JR, Gomes VM, de la Canal L. Molecular characterization of Helja, an extracellular jacalin-related protein from Helianthus annuus: Insights into the relationship of this protein with unconventionally secreted lectins. JOURNAL OF PLANT PHYSIOLOGY 2015; 183:144-53. [PMID: 26140981 DOI: 10.1016/j.jplph.2015.06.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 05/21/2015] [Accepted: 06/11/2015] [Indexed: 05/25/2023]
Abstract
Jacalin-related lectins (JRLs) encompass cytosolic, nuclear and vacuolar members displaying the jacalin domain in one or more copies or in combination with unrelated domains. Helianthus annuus jacalin (Helja) is a mannose-specific JRL previously identified in the apoplast of Helianthus annuus seedlings, and this protein has been proposed to follow unconventional secretion. Here, we describe the full-length Helja cDNA sequence, which presents a unique jacalin domain (merolectin) and the absence of a signal peptide, confirming that the protein cannot follow the classical ER-dependent secretory pathway. Helja mRNA is present in seeds, cotyledons, roots and hypocotyls, but no transcripts were detected in the leaves. Searches for sequence similarity showed that Helja is barely similar to other JRLs present in H. annuus databases and less than 45% identical to other monocot or dicot JRLs. Strikingly, most of the merolectins recovered through data mining using Helja as a query were predicted as apoplastic, although most of these proteins lack the signal peptide required for classical secretion. Thus, Helja is the first bait identified to recover putative unconventionally secreted lectins. Because the recovered JRLs are widely distributed among the plant kingdom, an as yet unknown role for jacalin lectins in the apoplast is emerging.
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Affiliation(s)
- Marcela Pinedo
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata-CONICET, Funes 3250, 7600 Mar del Plata, Argentina.
| | - Facundo Orts
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata-CONICET, Funes 3250, 7600 Mar del Plata, Argentina.
| | - André de Oliveira Carvalho
- Laboratório de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes 28013-602, RJ, Brazil.
| | - Mariana Regente
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata-CONICET, Funes 3250, 7600 Mar del Plata, Argentina.
| | - Julia Ribeiro Soares
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata-CONICET, Funes 3250, 7600 Mar del Plata, Argentina.
| | - Valdirene Moreira Gomes
- Laboratório de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes 28013-602, RJ, Brazil.
| | - Laura de la Canal
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata-CONICET, Funes 3250, 7600 Mar del Plata, Argentina.
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15
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Parasuraman P, Murugan V, Selvin JFA, Gromiha MM, Fukui K, Veluraja K. Theoretical investigation on the glycan-binding specificity ofAgrocybe cylindraceagalectin using molecular modeling and molecular dynamics simulation studies. J Mol Recognit 2015; 28:528-38. [DOI: 10.1002/jmr.2468] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 01/23/2015] [Accepted: 01/23/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Ponnusamy Parasuraman
- Department of Physics; Manonmaniam Sundaranar University; Tirunelveli Tamil Nadu 627012 India
| | - Veeramani Murugan
- Department of Physics; Manonmaniam Sundaranar University; Tirunelveli Tamil Nadu 627012 India
| | | | - M Michael Gromiha
- Department of Biotechnology; Indian Institute of Technology Madras; Chennai Tamil Nadu 600036 India
| | - Kazuhiko Fukui
- Molecular Profiling Research Center for Drug Discovery (molprof); National Institute of Advanced Industrial Science and Technology (AIST); 2-4-7 Aomi Koto-ku Tokyo 135-0064 Japan
| | - Kasinadar Veluraja
- School of Advanced Sciences; VIT University; Vellore Tamil Nadu 632014 India
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16
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Parasuraman P, Murugan V, Selvin JFA, Gromiha MM, Fukui K, Veluraja K. Insights into the binding specificity of wild type and mutated wheat germ agglutinin towards Neu5Acα(2-3)Gal: a study by in silico mutations and molecular dynamics simulations. J Mol Recognit 2015; 27:482-92. [PMID: 24984865 DOI: 10.1002/jmr.2369] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 02/02/2014] [Accepted: 02/02/2014] [Indexed: 02/06/2023]
Abstract
Wheat germ agglutinin (WGA) is a plant lectin, which specifically recognizes the sugars NeuNAc and GlcNAc. Mutated WGA with enhanced binding specificity can be used as biomarkers for cancer. In silico mutations are performed at the active site of WGA to enhance the binding specificity towards sialylglycans, and molecular dynamics simulations of 20 ns are carried out for wild type and mutated WGAs (WGA1, WGA2, and WGA3) in complex with sialylgalactose to examine the change in binding specificity. MD simulations reveal the change in binding specificity of wild type and mutated WGAs towards sialylgalactose and bound conformational flexibility of sialylgalactose. The mutated polar amino acid residues Asn114 (S114N), Lys118 (G118K), and Arg118 (G118R) make direct and water mediated hydrogen bonds and hydrophobic interactions with sialylgalactose. An analysis of possible hydrogen bonds, hydrophobic interactions, total pair wise interaction energy between active site residues and sialylgalactose and MM-PBSA free energy calculation reveals the plausible binding modes and the role of water in stabilizing different binding modes. An interesting observation is that the binding specificity of mutated WGAs (cyborg lectin) towards sialylgalactose is found to be higher in double point mutation (WGA3). One of the substituted residues Arg118 plays a crucial role in sugar binding. Based on the interactions and energy calculations, it is concluded that the order of binding specificity of WGAs towards sialylgalactose is WGA3 > WGA1 > WGA2 > WGA. On comparing with the wild type, double point mutated WGA (WGA3) exhibits increased specificity towards sialylgalactose, and thus, it can be effectively used in targeted drug delivery and as biological cell marker in cancer therapeutics.
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Affiliation(s)
- Ponnusamy Parasuraman
- Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, 627 012, India
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Abhinav KV, Sharma K, Swaminathan CP, Surolia A, Vijayan M. Jacalin-carbohydrate interactions: distortion of the ligand molecule as a determinant of affinity. ACTA ACUST UNITED AC 2015; 71:324-31. [PMID: 25664742 DOI: 10.1107/s139900471402553x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 11/21/2014] [Indexed: 11/10/2022]
Abstract
Jacalin is among the most thoroughly studied lectins. Its carbohydrate-binding site has also been well characterized. It has been postulated that the lower affinity of β-galactosides for jacalin compared with α-galactosides is caused by steric interactions of the substituents in the former with the protein. This issue has been explored energetically and structurally using different appropriate carbohydrate complexes of jacalin. It turns out that the earlier postulation is not correct. The interactions of the substituent with the binding site remain essentially the same irrespective of the anomeric nature of the substitution. This is achieved through a distortion of the sugar ring in β-galactosides. The difference in energy, and therefore in affinity, is caused by a distortion of the sugar ring in β-galactosides. The elucidation of this unprecedented distortion of the ligand as a strategy for modulating affinity is of general interest. The crystal structures also provide a rationale for the relative affinities of the different carbohydrate ligands for jacalin.
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Affiliation(s)
- K V Abhinav
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Kaushal Sharma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - C P Swaminathan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - A Surolia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - M Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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Mundi S, Aluko RE. Effects of NaCl and pH on the structural conformations of kidney bean vicilin. Food Chem 2013; 139:624-30. [DOI: 10.1016/j.foodchem.2012.12.051] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 11/06/2012] [Accepted: 12/21/2012] [Indexed: 11/30/2022]
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Carbohydrate Binding and Unfolding of Spatholobus parviflorus Lectin: Fluorescence and Circular Dichroism Spectroscopic Study. Appl Biochem Biotechnol 2013; 171:80-92. [DOI: 10.1007/s12010-013-0340-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 06/17/2013] [Indexed: 02/02/2023]
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Structural investigation of a novel N-acetyl glucosamine binding chi-lectin which reveals evolutionary relationship with class III chitinases. PLoS One 2013; 8:e63779. [PMID: 23717482 PMCID: PMC3662789 DOI: 10.1371/journal.pone.0063779] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Accepted: 04/06/2013] [Indexed: 01/03/2023] Open
Abstract
The glycosyl hydrolase 18 (GH18) family consists of active chitinases as well as chitinase like lectins/proteins (CLPs). The CLPs share significant sequence and structural similarities with active chitinases, however, do not display chitinase activity. Some of these proteins are reported to have specific functions and carbohydrate binding property. In the present study, we report a novel chitinase like lectin (TCLL) from Tamarindus indica. The crystal structures of native TCLL and its complex with N-acetyl glucosamine were determined. Similar to the other CLPs of the GH18 members, TCLL lacks chitinase activity due to mutations of key active site residues. Comparison of TCLL with chitinases and other chitin binding CLPs shows that TCLL has substitution of some chitin binding site residues and more open binding cleft due to major differences in the loop region. Interestingly, the biochemical studies suggest that TCLL is an N-acetyl glucosamine specific chi-lectin, which is further confirmed by the complex structure of TCLL with N-acetyl glucosamine complex. TCLL has two distinct N-acetyl glucosamine binding sites S1 and S2 that contain similar polar residues, although interaction pattern with N-acetyl glucosamine varies extensively among them. Moreover, TCLL structure depicts that how plants utilize existing structural scaffolds ingenuously to attain new functions. To date, this is the first structural investigation of a chi-lectin from plants that explore novel carbohydrate binding sites other than chitin binding groove observed in GH18 family members. Consequently, TCLL structure confers evidence for evolutionary link of lectins with chitinases.
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Abhilash J, Dileep KV, Palanimuthu M, Geethanandan K, Sadasivan C, Haridas M. Metal ions in sugar binding, sugar specificity and structural stability of Spatholobus parviflorus seed lectin. J Mol Model 2013; 19:3271-8. [DOI: 10.1007/s00894-013-1854-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 04/16/2013] [Indexed: 12/12/2022]
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Abstract
BACKGROUND The glycomics field has made great advancements in the last decade due to technologies for their synthesis and analysis including carbohydrate microarrays. Accordingly, databases for glycomics research have also emerged and been made publicly available by many major institutions worldwide. OBJECTIVE This review introduces these and other useful databases on which new methods for drug discovery can be developed. METHODS The scope of this review covers current documented and accessible databases and resources pertaining to glycomics. These were selected with the expectation that they may be useful for drug discovery research. RESULTS/CONCLUSION There is a plethora of glycomics databases that have much potential for drug discovery. This may seem daunting at first but this review helps to put some of these resources into perspective. Additionally, some thoughts on how to integrate these resources to allow more efficient research are presented.
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Affiliation(s)
- Kiyoko F Aoki-Kinoshita
- Associate Professor, Department of Bioinformatics, Faculty of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo, 192-8577, Japan +81 42 691 4116 ; +81 42 691 4116 ;
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Chandran T, Sharma A, Vijayan M. Generation of Ligand Specificity and Modes of Oligomerization in β-Prism I Fold Lectins. DYNAMICS OF PROTEINS AND NUCLEIC ACIDS 2013; 92:135-78. [DOI: 10.1016/b978-0-12-411636-8.00004-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Abhinav KV, Sharma A, Vijayan M. Identification of mycobacterial lectins from genomic data. Proteins 2012. [DOI: 10.1002/prot.24219] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Lopez-Jaramillo FJ, Ortega-Muñoz M, Megia-Fernandez A, Hernandez-Mateo F, Santoyo-Gonzalez F. Vinyl Sulfone Functionalization: A Feasible Approach for the Study of the Lectin–Carbohydrate Interactions. Bioconjug Chem 2012; 23:846-55. [DOI: 10.1021/bc200681c] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Francisco Javier Lopez-Jaramillo
- Departamento de Química
Orgánica, Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Mariano Ortega-Muñoz
- Departamento de Química
Orgánica, Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | | | - Fernando Hernandez-Mateo
- Departamento de Química
Orgánica, Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Francisco Santoyo-Gonzalez
- Departamento de Química
Orgánica, Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
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Geethanandan K, Abhilash J, Bharath SR, Sadasivan C, Haridas M. Crystallization and preliminary X-ray studies of a galactose-specific lectin from the seeds of Spatholobus parviflorus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:700-2. [PMID: 21636916 PMCID: PMC3107147 DOI: 10.1107/s174430911101387x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Accepted: 04/12/2011] [Indexed: 11/11/2022]
Abstract
A galactose-specific seed lectin was purified from the legume Spatholobus parviflorus and crystallized using the hanging-drop vapour-diffusion technique. The crystals belonged to space group P1, with unit-cell parameters a = 60.998, b = 60.792, c = 78.179 Å, α = 101.32, β = 91.38, γ = 104.32°. X-ray diffraction data were collected under cryoconditions (100 K) to a resolution of 2.04 Å using a MAR image-plate detector system mounted on a rotating-anode X-ray (Cu Kα) generator. Molecular replacement using legume-lectin coordinates as a search model gave a tetrameric structure.
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Affiliation(s)
- K. Geethanandan
- Department of Biotechnology and Microbiology, Kannur University, Kerala 670 661, India
| | - Joseph Abhilash
- Department of Biotechnology and Microbiology, Kannur University, Kerala 670 661, India
| | - S. R. Bharath
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - C. Sadasivan
- Department of Biotechnology and Microbiology, Kannur University, Kerala 670 661, India
- Inter University Centre for Bioscience, Kannur University, Kerala 670 661, India
| | - M. Haridas
- Department of Biotechnology and Microbiology, Kannur University, Kerala 670 661, India
- Inter University Centre for Bioscience, Kannur University, Kerala 670 661, India
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Abstract
AbstractPromise of cell therapy has advanced the use of adult stem cells towards the development of novel approaches to promote regeneration of injured endothelium. The aim of this study was to stimulate endothelial progenitor cells (EPCs) with lectin isolated from Solanum tuberosum (potato) shoot and Calendula officinalis (marigold) extracts, in order to increase EPCs proliferation and gene expression of molecules with roles in chemotaxis and adhesion for a better attachment to injured vascular tissue. EPCs were differentiated from umbilical cord blood-derived mononuclear cells and characterized by light microscopy, flow cytometry, and vascular tube-like structures formation on Matrigel. Cell proliferation was determined by MTS assay, and gene expression of molecules involved in EPCs adhesion (VCAM-1, VE-cadherin, ICAM-1, PECAM-1, P-selectin) and chemotaxis was determined (CXCR4, Tie-2) by RT-PCR. For the assessment of cell motility, wound-healing assay was employed. Both potato shoot lectin and marigold extracts stimulated EPCs proliferation in a concentration dependent manner and were able to increase expression of adhesion and chemotactic molecules. Marigold flower extract proved to be more efficient. This study demonstrates the usefulness of potato lectin and marigold extracts to increase EPCs proliferation and modulate gene expression of chemotactic and adhesion molecules, which may facilitate EPCs attachment to injured endothelium.
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Structural bioinformatics: deriving biological insights from protein structures. Interdiscip Sci 2010; 2:347-66. [PMID: 21153779 DOI: 10.1007/s12539-010-0045-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 06/18/2010] [Accepted: 06/21/2010] [Indexed: 12/27/2022]
Abstract
Structural bioinformatics can be described as an approach that will help decipher biological insights from protein structures. As an important component of structural biology, this area promises to provide a high resolution understanding of biology by assisting comprehension and interpretation of a large amount of structural data. Biological function of protein molecules can be inferred from their three-dimensional structures by comparing structures, classifying them and transferring function from a related protein or family. It is well known now that the structure space of protein molecules is more conserved than the sequence space, making it important to seek functional associations at the structural level. An added advantage of structural bioinformatics over simpler sequence-based methods is that the former also provides ultimate insights into the mechanisms by which various biological events take place. A bird's eye-view of the different aspects of structural bioinformatics is given here along with various recent advances in the area including how knowledge obtained from structural bioinformatics can be applied in drug discovery.
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Granell A, Fernández del-Carmen A, Orzáez D. In planta production of plant-derived and non-plant-derived adjuvants. Expert Rev Vaccines 2010; 9:843-58. [PMID: 20673009 DOI: 10.1586/erv.10.80] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recombinant antigen production in plants is a safe and economically sound strategy for vaccine development, particularly for oral/mucosal vaccination, but subunit vaccines usually suffer from weak immunogenicity and require adjuvants that escort the antigens, target them to relevant sites and/or activate antigen-presenting cells for elicitation of protective immunity. Genetic fusions of antigens with bacterial adjuvants as the B subunit of the cholera toxin have been successful in inducing protective immunity of plant-made vaccines. In addition, several plant compounds, mainly plant defensive molecules as lectins and saponins, have shown strong adjuvant activities. The molecular diversity of the plant kingdom offers a vast source of non-bacterial compounds with adjuvant activity, which can be assayed in emerging plant manufacturing systems for the design of new plant vaccine formulations.
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Affiliation(s)
- Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de Valencia, Spain
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Chandran T, Sharma A, Vijayan M. Crystallization and preliminary X-ray studies of a galactose-specific lectin from the seeds of bitter gourd (Momordica charantia). Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1037-40. [PMID: 20823520 PMCID: PMC2935221 DOI: 10.1107/s174430911002659x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 07/05/2010] [Indexed: 11/10/2022]
Abstract
A galactose-specific lectin from the seeds of bitter gourd (Momordica charantia) is a four-chain type II ribosome-inactivating protein (RIP) resulting from covalent association through a disulfide bridge between two identical copies of a two-chain unit. The available structural information on such four-chain RIPs is meagre. The bitter gourd lectin was therefore crystallized for structural investigation and the crystals have been characterized. It is anticipated that the structure of the orthorhombic crystals will be analysed using molecular replacement by taking advantage of its sequence, and presumably structural, homology to normal two-chain type II RIPs.
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Affiliation(s)
- Thyageshwar Chandran
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Alok Sharma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - M. Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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Sharma A, Vijayan M. Influence of glycosidic linkage on the nature of carbohydrate binding in β-prism I fold lectins: An X-ray and molecular dynamics investigation on banana lectin–carbohydrate complexes. Glycobiology 2010; 21:23-33. [DOI: 10.1093/glycob/cwq128] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Antifungal and Antiproliferative Activities of Lectin from the Rhizomes of Curcuma amarissima Roscoe. Appl Biochem Biotechnol 2009; 162:912-25. [DOI: 10.1007/s12010-009-8804-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Accepted: 09/28/2009] [Indexed: 10/20/2022]
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Oliveira C, Costa S, Teixeira JA, Domingues L. cDNA Cloning and Functional Expression of the α-d-Galactose-Binding Lectin Frutalin in Escherichia coli. Mol Biotechnol 2009; 43:212-20. [DOI: 10.1007/s12033-009-9191-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Accepted: 05/26/2009] [Indexed: 11/25/2022]
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Shridhar S, Chattopadhyay D, Yadav G. PLecDom: a program for identification and analysis of plant lectin domains. Nucleic Acids Res 2009; 37:W452-8. [PMID: 19474338 PMCID: PMC2703983 DOI: 10.1093/nar/gkp409] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
PLecDom is a program for detection of Plant Lectin Domains in a polypeptide or EST sequence, followed by a classification of the identified domains into known families. The web server is a collection of plant lectin domain families represented by alignments and profile Hidden Markov Models. PLecDom was developed after a rigorous analysis of evolutionary relationships between available sequences of lectin domains with known specificities. Users can test their sequences for potential lectin domains, catalog the identified domains into broad substrate classes, estimate the extent of divergence of new domains with existing homologs, extract domain boundaries and examine flanking sequences for further analysis. The high prediction accuracy of PLecDom combined with the ease with which it handles large scale input, enabled us to apply the program to protein and EST data from 48 plant genome-sequencing projects in various stages of completion. Our results represent a significant enrichment of the currently annotated plant lectins, and highlight potential targets for biochemical characterization. The search algorithm requires input in fasta format and is designed to process simultaneous connection requests from multiple users, such that huge sets of input sequences can be scanned in a matter of seconds. PLecDom is available at http://www.nipgr.res.in/plecdom.html.
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Affiliation(s)
- Smriti Shridhar
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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Lyou SH, Park HJ, Jung C, Sohn HB, Lee G, Kim CH, Kim M, Choi YD, Cheong JJ. The Arabidopsis AtLEC gene encoding a lectin-like protein is up-regulated by multiple stimuli including developmental signal, wounding, jasmonate, ethylene, and chitin elicitor. Mol Cells 2009; 27:75-81. [PMID: 19214436 DOI: 10.1007/s10059-009-0007-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Revised: 10/13/2008] [Accepted: 10/13/2008] [Indexed: 11/24/2022] Open
Abstract
The Arabidopsis gene AtLEC (At3g15356) gene encodes a putative 30-kDa protein with a legume lectin-like domain. Likely to classic legume lectin family of genes, AtLEC is expressed in rosette leaves, primary inflorescences, and roots, as observed in Northern blot analysis. The accumulation of AtLEC transcript is induced very rapidly, within 30 min, by chitin, a fungal wall-derived oligosaccharide elictor of the plant defense response. Transgenic Arabidopsis carrying an AtLEC promoter-driven beta-glucuronidase (GUS) construct exhibited GUS activity in the leaf veins, secondary inflorescences, carpel heads, and silique receptacles, in which no expression could be seen in Northern blot analysis. This observation suggests that AtLEC expression is induced transiently and locally during developmental processes in the absence of an external signal such as chitin. In addition, mechanically wounded sites showed strong GUS activity, indicating that the AtLEC promoter responds to jasmonate. Indeed, methyl jasmonate and ethylene exposure induced AtLEC expression within 3-6 h. Thus, the gene appears to play a role in the jasmonate-/ethylene-responsive, in addition to the chitin-elicited, defense responses. However, chitin-induced AtLEC expression was also observed in jasmonate-insensitive (coi1) and ethylene-insensitive (etr1-1) Arabidopsis mutants. Thus, it appears that chitin promotes AtLEC expression via a jasmonate- and/or ethylene-independent pathway.
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Affiliation(s)
- Seoung Hyun Lyou
- Department of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Seoul, 151-921, Korea
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Lin J, Zhou X, Gao S, Liu X, Wu W, Sun X, Tang K. cDNA cloning and expression analysis of a mannose-binding lectin from Pinellia pedatisecta. J Biosci 2008; 32:241-9. [PMID: 17435316 DOI: 10.1007/s12038-007-0024-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Pinellia pedatisecta agglutinin (PPA)is a very basic protein that accumulates in the tuber of P.pedatisecta .PPA is a hetero-tetramer protein of 40 kDa,composed of two polypeptide chains A (about 12 kDa)and two polypeptides chains B (about 12 kDa).The full-length cDNA of PPA was cloned from P.pedatisecta using SMART RACE-PCR technology; it was 1146 bp and contained a 771 bp open reading frame (ORF)encoding a lectin precursor of 256 amino acid residues with a 24 amino acid signal peptide.The PPA precursor contained 3 mannose-binding sites (QXDXNXVXY) and two conserved domains of 43% identity,PPA-DOM 1 (polypeptides A)and PPA-DOM 2 (polypeptides B).PPA shared varying identities,ranging from 40% to 85%,with mannose-binding lectins from other species of plant families such as Araceae, Alliaceae, Iridaceae, Liliaceae, Amaryllidaceae and Bromeliaceae. Southern blot analysis indicated that ppa belonged to a multi-copy gene family. Expression pattern analysis revealed that ppa expressed in most tested tissues, with high expression being found in spadix,spathe and tuber.Cloning of the ppa gene not only provides a basis for further investigation of its structure,expression and regulatory mechanism,but also enables us to test its potential role in controlling pests and fungal diseases by transferring the gene into plants in the future.
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Affiliation(s)
- Juan Lin
- State Key Laboratory of Genetic Engineering, Fudan-SJTU-Nottingham Plant Biotechnology R and D Center, School of Life Sciences, Morgan-Tan International Center for Life Sciences, Fudan University, Shanghai 200433, People's Republic of China
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Liquid Chromatography/Mass Spectrometry (LC/MS)-Based Glycoproteomics Technologies for Cancer Biomarker Discovery. Clin Proteomics 2008. [DOI: 10.1007/s12014-008-9004-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Abstract
Introduction
Biomarker discovery is a major objective of clinical proteomics; molecular biomarkers allow for detection of early-stage human diseases, especially cancer, and for monitoring their progression and/or regression after treatment. Biomarkers also help to elucidate the pathology of disease and its diagnosis, drug discovery, and toxicology. Glycans are ideal candidates for biomarkers because (1) glycoconjugates are localized on the cell surface and in the secretions such as plasma, (2) their structures are frequently and drastically changed during normal and aberrant cell differentiation, and (3) different cell types express different glycan signatures. Certain serodiagnostic glycoconjugate markers, such as carcinoembryonic antigen (CEA), are currently available; however, comprehensive glycome analysis has yet to be performed, mainly because of the difficulties of isolating and structurally analyzing complex glycans. Large-scale glycoprotein analysis, termed glycoproteomics, has the potential to effectively trace cellular glycoproteins and therefore to search for new serodiagnostic biomarkers.
Conclusions
In this review, we describe current mass spectrometry-based glycoproteomics technologies. Quantitative “shotgun” proteomics analyses of glycopeptides captured from complex biological mixtures such as plasma, coupled with advanced glycome technologies, enhance our knowledge of protein glycosylation and facilitate discovery of new biomarkers for human diseases.
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Damodaran D, Jeyakani J, Chauhan A, Kumar N, Chandra NR, Surolia A. CancerLectinDB: a database of lectins relevant to cancer. Glycoconj J 2007; 25:191-8. [DOI: 10.1007/s10719-007-9085-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Revised: 10/31/2007] [Accepted: 11/01/2007] [Indexed: 10/22/2022]
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Tissue-specific mRNA expression profiling in grape berry tissues. BMC Genomics 2007; 8:187. [PMID: 17584945 PMCID: PMC1925093 DOI: 10.1186/1471-2164-8-187] [Citation(s) in RCA: 179] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Accepted: 06/21/2007] [Indexed: 01/09/2023] Open
Abstract
Background Berries of grape (Vitis vinifera) contain three major tissue types (skin, pulp and seed) all of which contribute to the aroma, color, and flavor characters of wine. The pericarp, which is composed of the exocarp (skin) and mesocarp (pulp), not only functions to protect and feed the developing seed, but also to assist in the dispersal of the mature seed by avian and mammalian vectors. The skin provides volatile and nonvolatile aroma and color compounds, the pulp contributes organic acids and sugars, and the seeds provide condensed tannins, all of which are important to the formation of organoleptic characteristics of wine. In order to understand the transcriptional network responsible for controlling tissue-specific mRNA expression patterns, mRNA expression profiling was conducted on each tissue of mature berries of V. vinifera Cabernet Sauvignon using the Affymetrix GeneChip® Vitis oligonucleotide microarray ver. 1.0. In order to monitor the influence of water-deficit stress on tissue-specific expression patterns, mRNA expression profiles were also compared from mature berries harvested from vines subjected to well-watered or water-deficit conditions. Results Overall, berry tissues were found to express approximately 76% of genes represented on the Vitis microarray. Approximately 60% of these genes exhibited significant differential expression in one or more of the three major tissue types with more than 28% of genes showing pronounced (2-fold or greater) differences in mRNA expression. The largest difference in tissue-specific expression was observed between the seed and pulp/skin. Exocarp tissue, which is involved in pathogen defense and pigment production, showed higher mRNA abundance relative to other berry tissues for genes involved with flavonoid biosynthesis, pathogen resistance, and cell wall modification. Mesocarp tissue, which is considered a nutritive tissue, exhibited a higher mRNA abundance of genes involved in cell wall function and transport processes. Seeds, which supply essential resources for embryo development, showed higher mRNA abundance of genes encoding phenylpropanoid biosynthetic enzymes, seed storage proteins, and late embryogenesis abundant proteins. Water-deficit stress affected the mRNA abundance of 13% of the genes with differential expression patterns occurring mainly in the pulp and skin. In pulp and seed tissues transcript abundance in most functional categories declined in water-deficit stressed vines relative to well-watered vines with transcripts for storage proteins and novel (no-hit) functional assignments being over represented. In the skin of berries from water-deficit stressed vines, however, transcripts from several functional categories including general phenypropanoid and ethylene metabolism, pathogenesis-related responses, energy, and interaction with the environment were significantly over-represented. Conclusion These results revealed novel insights into the tissue-specific expression mRNA expression patterns of an extensive repertoire of genes expressed in berry tissues. This work also establishes an extensive catalogue of gene expression patterns for future investigations aimed at the dissection of the transcriptional regulatory hierarchies that govern tissue-specific expression patterns associated with tissue differentiation within berries. These results also confirmed that water-deficit stress has a profound effect on mRNA expression patterns particularly associated with the biosynthesis of aroma and color metabolites within skin and pulp tissues that ultimately impact wine quality.
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Sharon N. Lectins: carbohydrate-specific reagents and biological recognition molecules. J Biol Chem 2007; 282:2753-64. [PMID: 17145746 DOI: 10.1074/jbc.x600004200] [Citation(s) in RCA: 297] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Nathan Sharon
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel.
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