Data bank based mining on the track of antimicrobial weapons in plant genomes

Current Protein and Peptide Science

Volumn 11, Issue 3, 2010, Pages 195-198

  Belarmino, Luis C ^a   Benko Iseppon, Ana M ^a  

^a DEPARTAMENTO DE MICOLOGIA   (Brazil)

Author keywords

Antimicrobial peptides; Bioinformatics; Computational modeling; Databases

Indexed keywords

ANTIBIOTIC AGENT; POLYPEPTIDE ANTIBIOTIC AGENT; ANTIINFECTIVE AGENT; ANTIMICROBIAL CATIONIC PEPTIDE;

ALGORITHM; ANTIBIOTIC RESISTANCE; ARTICLE; BIOINFORMATICS; DATA BASE; DATA MINING; INTERNET; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENOME; CHEMICAL STRUCTURE; GENETICS; NUCLEIC ACID DATABASE; REVIEW;

BACTERIA (MICROORGANISMS); EUKARYOTA;

ANTI-INFECTIVE AGENTS; ANTIMICROBIAL CATIONIC PEPTIDES; DATA MINING; DATABASES, NUCLEIC ACID; GENOME, PLANT; MODELS, MOLECULAR;

EID: 77952639612     PISSN: 13892037     EISSN: None     Source Type: Journal    
DOI: 10.2174/138920310791112084     Document Type: Article

References (24)

1. Asaduzzaman, S.M.; Sonomoto, K. Antibiotics: Diverse activities and unique modes of action. J. Biosci. Bioeng., 2009, 17, 475-487.
2. Bulet, P.; Stöcklin, R. Insect antimicrobial peptide: structures, properties end gene regulation. Protein Pept. Lett., 2005, 12, 3-11.
3. Marx, F. Small basic antifungal proteins secreted from filamentous ascomycetes: a comparative study regard expression, structure, function and potential application. Appl. Microbiol. Biotechnol., 2004, 65, 133-142.
4. Bulet, P.; Stoecklin, R.; Menin, L. Anti-microbial peptides: from invertebrates to vertebrates. Immunol. Rev., 2004, 198, 169-184.
5. Manners, J.M. Hidden weapons of microbial destruction in plant genomes. Genome Biol., 2007, 8, 225.
6. Silverstein, K.A.; Moskal, W.A. Jr; Wu, H.C.; Underwood, B.A.; Graham, M.A.; Town, C.D.; VandenBosch, KA. Small cysteinerich peptides resembling antimicrobial peptides have been underpredicted in plants. Plant J., 2007, 51, 262-280.
7. Fedorova, M.; Van de Mortel, J.; Matsuomoto, P.A.; Cho, J.; Town, C.D.; Vandenbosch, K.A.; Gantt, J.S.; Vance, C.P. Genomewide identification of nodule-specific transcripts in the model legume Medicago truncatula. Plant Physiol., 2002, 130, 519-537.
8. Mergaert, P.; Nikovics, K.; Kelemen, Z.; Maunoury, N.; Vaubert D.; Kondorosi, A.; Kondorosi, E. A Novel Family in Medicago truncatula Consisting of more than 300 nodule-specific genes coding for small, secreted polypeptides with conserved cysteine motifs. Plant Physiol., 2003, 132, 161-173.
9. Graham, MA; Silverstein, KA; Cannon, SB; VandenBosch, KA. Computational identification and characterization of novel genes from legumes. Plant Physiol., 2004, 135, 1179-1197.
10. Silverstein, K.A.; Graham, M.A.; Paape, T.D.; VandenBosch, K.A. Genome organization of more than 300 defensin-like genes in Arabidopsis. Plant Physiol., 2005, 138, 600-610.
11. Odintsova, T.I.; Egorov, T.A. In Peptidomics: Method and Application; Soloviev, M.; Shaw, C.; Andrén, P., Eds.; John Wiley & Sons, Inc: New Jersey, 2007, pp. 99-117.
12. Antcheva, N.; Zelezetsky, I.; Tossi, A. Cationic Antimicrobial Peptides - The Defensins, Kastin, A.J., Ed. The Handbook of Biologically Active Peptides, Elsevier, Burlington, MA, 2006, 55-66.
13. Brahmachary, M.; Krishnan, S.P.T.; Koh, J.L.Y.; Khan, A.M.; Seah, S.H.; Tan, T.W.; Brusic, V.; Bajic, V.B. ANTIMIC: a database of antimicrobial sequences. Nucleic Acids Res., 2004, 32, 586-589.
14. Seebah, S.; Suresh, A.; Zhuo, S.; Choong, Y.H.; Chua, H.; Chuon, D.; Beuerman, R.; Verma, C. Defensins knowledgebase: a manually curated database and information source focused on the defensins family of antimicrobial peptides. Nucleic Acids Res., 2007, 35, D265-8.
15. Wang, C.K.; Kaas, Q.; Chiche, L.; Craik D.J. CyBase: a database of cyclic protein sequences and structures, with applications in protein discovery and engineering. Nucleic Acids Res., 2008, 36, D206-10.
16. Fjell, C.D.; Hancock, R.E.W.; Cherkasov, A. AMPer: a database and an automated discovery tool for antimicrobial peptides. Bioinformatics, 2007, 23, 1148-1155.
17. Wang, Z.; Wang, G. A.P.D: the antimicrobial peptide database. Nucleic Acids Res., 2004, 32, D590-D592.
18. Wang, G.; Li, X.; Wang, Z. APD2: the updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Res., 2008, 37, D933-D937.
19. Hammami, R.; Hamida, J.B.; Vergoten, G.; Fliss, I. PhytAMP: a database dedicated to antimicrobial plant peptides. Nucleic Acids Res., 2009, 37, D963-D968.
20. Nagarajan, V.; kaushik, N.; Murali, B.; Zhang, C.; Lakhera, S.; Elasri, M.O.; Deng, Y. A Fourier transformation based method to mine peptide space for antimicrobial activity. BMC Bioinformatics, 2006, 7, S2.
21. Loose, C.; Jensen, K.; Rigoutsos, I.; Stephanopoulos G. A linguistic model for the rational design of antimicrobial peptides. Nature, 2006, 443, 867-869.
22. Lata, S.; Sharma, B.K.; Raghava, G.P.S. Analysis and prediction of antibacterial peptides. BMC Bioinformatics, 2007, 8, 263.
23. Padovan, L.; Segat, L.; Tossi, A.; Antcheva, N.; Benko-Iseppon, A.M.; Ederson, A.K.; Brandao, L.; Calsa, T. Jr.; Crovella, S. A plant-defensin from sugarcane (Saccharum spp.). Protein Pept. Lett., 2009, 16, 430-436.
24. Padovan, L.; Segat, L.; Tossi A.; Calsa, Jr, T.; Ederson, A.K.; Brandao, L.; Guimarães, R.L.; Pandolfi, V.; Pestana-Calsa, M.C.; Belarmino, L.C.; Benko-Iseppon, A.M.; Crovella, S. Characterization of a new defensin from cowpea (Vigna unguiculata (L.) Walp.) Protein Pept. Lett., 2010, 17, 297-304.