Detecting molecular adaptation at individual codons in the pattern recognition protein, lipopolysaccharide- and β-1,3-glucan-binding protein of decapods

Fish and Shellfish Immunology

Volumn 24, Issue 5, 2008, Pages 638-648

  Padhi, Abinash ^a   Verghese, Bindhu ^a  

^a UNIVERSITY OF TULSA   (United States)

Author keywords

Decapods; Evolution; Innate immunity; Pattern recognition protein; Phylogeny; Positive selection

Indexed keywords

ARTHROPODA; INVERTEBRATA; NEGIBACTERIA;

EID: 41949092079     PISSN: 10504648     EISSN: 10959947     Source Type: Journal    
DOI: 10.1016/j.fsi.2008.02.002     Document Type: Article

References (49)

1. Hoffmann J.A., Kafatos F.C., Janeway C.A., and Ezekowitz R.A. Phylogenetic perspectives in innate immunity. Science 284 (1999) 1313-1318
2. Iwanaga S., and Lee B.L. Recent advances in the innate immunity of invertebrate animals. J Biochemistry and Mol Biol 38 2 (2005) 128-150
3. Lee S.Y., Wang R., and Soderhall K. A lipopolysaccharide- and β-1,3-glucan-binding protein from hemocytes of the freshwater crayfish Pacifastacus leniusculus. J Biol Chem 275 (2000) 1337-1343
4. Roux M.M., Pain A., Klimpel K.R., and Dhar A.K. The lipopolysaccharide and β-1,3-glucan binding protein gene is upregulated in white spot virus-infected shrimp (Penaeus stylirostris). J Virol 76 (2002) 7140-7149
5. Bulmer M.S., and Crozier R.H. Variation in positive selection in termite GNBPs and Relish. Mol Biol Evol 23 (2006) 317-326
6. Jiggins F.M., and Hurst G.D.D. The evolution of parasite recognition genes in the innate immune system: purifying selection on Drosophila melanogaster peptidoglycan recognition proteins. J Mol Evol 57 (2003) 598-605
7. Jiggins F.M., and Kim K.W. Contrasting evolutionary patterns in Drosophila immune receptors. J Mol Evol 63 (2006) 769-780
8. Jiggins F.M., and Kim K.W. A screen for immunity genes evolving under positive selection in Drosophila. J Evol Biol 20 (2007) 965-970
9. Little T.J., and Cobbe N. The evolution of immune-related genes from disease carrying mosquitoes: diversity in a peptidoglycan- and a thioester-recognizing protein. Insect Mol Biol 14 (2005) 599-605
10. Little T.J., Colbourne J.K., and Crease T.J. Molecular evolution of Daphnia immunity genes: polymorphism in a Gram-negative binding protein gene and an alpha-2-macroglobulin gene. J Mol Evol 59 (2004) 498-506
11. Sackton T.B., Lazzaro B.P., Schlenke T.A., Evans J.D., Hultmark D., and Clark A.G. Dynamic evolution of the innate immune system in Drosophila. Nat Genet 39 (2007) 1461-1468
12. Zhang S.-M., Zeng Y., and Loker E.S. Characterization of immune genes from the schistosome host snail Biomphalaria glabrata that encode peptidoglycan recognition proteins and Gram-negative bacteria binding protein. Immunogenetics 59 (2007) 883-898
13. Zou Z., Evans J.D., Lu Z., Zhao P., Williams M., Sumathipala N., et al. Comparative genomic analysis of the Tribolium immune system. Genome Biol 8 (2007) RI77
14. Cerenius L., Liang Z., Duvic B., Keyser P., Hellman U., Palva E.T., et al. Structure and biological activity of a 1,3-beta-d-glucan-binding protein in crustacean blood. J Biol Chem 269 (1994) 29462-29467
15. Du X.-J., Zha X.-F., and Wang J.-X. Molecular cloning and characterization of a lipopolysaccharide and β-1,3-glucan binding protein from fleshy prawn (Fenneropenaeus chinensis). Mol Immunol 44 (2007) 1085-1094
16. Cheng W., Liu C.-H., Tsai C.-H., and Chen J.-C. Molecular cloning and characterization of a pattern recognition molecule, lipopolysaccharide- and β-1,3-glucan binding protein (LGBP) from the white shrimp Litopenaeus vannamei. Fish Shellfish Immunol 18 (2005) 297-310
17. Hauton C., Hammond J.A., and Smith V.J. Real-time PCR quantification of the in vitro effects of crustacean immunostimulants on gene expression in lobster (Homarus gammarus) granular haemocytes. Dev Comp Immunol 29 (2005) 33-42
18. Sritunyalucksana K., Lee S.Y., and Söderhäll K. A β-1,3-glucan binding protein from the black tiger shrimp Penaeus monodon. Dev Comp Immunol 26 (2002) 237-245
19. Begun D.J., and Whitley P. Adaptive evolution of Relish, a Drosophila NF-κ B/IκB protein. Genetics 54 (2000) 1231-1238
20. Hughes A.L., and Nei M. Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection. Proc Natl Acad Sci USA 86 (1989) 958-962
21. Kimura M. The neutral theory of molecular evolution (1983), Cambridge University Press, New York
22. Ford M.J. Applications of selective neutrality tests to molecular ecology. Mol Ecol 11 (2002) 1245-1262
23. Padhi A., Verghese B., Otta S.K., Varghese B., and Ramu K. Adaptive evolution after duplication of penaeidin antimicrobial peptides. Fish Shellfish Immunol 23 (2007) 553-566
24. Tennessen J.A. Molecular evolution of animal antimicrobial peptides: widespread moderate positive selection. J Evol Biol 18 (2005) 1387-1394
25. Xia X. Data analysis in molecular biology and evolution (2000), Kluwer Academic Publishers, Boston
26. Xia X., and Xie Z. DAMBE: Data analysis in molecular biology and evolution. J Hered 92 (2001) 371-373
27. Hall T. BioEdit: a user friendly biological sequence alignment editor and analysis program for windows 95/98/N.T. Nucleic Acids Symp Ser 41 (1999) 95-98
28. Maddison Y., and Maddison D. Mesquite: A modular system for evolutionary analysis. Version 1.12 (2006). http://mesquiteproject.org
29. Guindon S., and Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52 (2003) 696-704
30. Huelsenbeck J.P., and Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
31. Abascal F., Zardoya R., and Posada D. ProtTest: Selection of best-fit models of protein evolution. Bioinformatics 21 9 (2005) 2104-2105
32. Page R.D. TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12 4 (1996) 357-358
33. Rambout A., and Drummond A.J. Tracer. Version 1.4. Available from (2005). http://evolve.zoo.ox.ac.uk/
34. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
35. Swofford D.L. PAUP*: Phylogenetic Analyses Using Parsimony (* and Other methods) 4.0β (2002), Sinauer Associates, Sunderland, MA, USA
36. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13 (1997) 555-556
37. Yang Z., Nielsen R., Goldman N., and Pederson A.M. Codon-substitution models for heterogeneous selection pressures at amino acid sites. Genetics 155 (2000) 431-449
38. Swanson W., Nielsen R., and Yang Q. Pervasive adaptive evolution in mammalian fertilization proteins. Mol Biol Evol 20 (2003) 18-20
39. Yang Z., Wong W.S.W., and Nielsen R. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol 22 (2005) 1107-1118
40. Maddison W. Gene trees in species trees. Syst Biol 46 (1997) 523-536
41. Padhi A., Verghese B., Vaid A., and Otta S.K. Pattern of nucleotide substitution and divergence of prophenoloxidase in decapods. Fish Shellfish Immunol 22 (2007) 628-640
42. Nene V., Wortman J.R., Lawson D., Haas B., Kodira C., Tu Z.J., et al. Genome sequence of Aedes aegypti, a major arbovirus vector. Science 316 (2007) 1718-1723
43. Slotman M.A., Parmakelis A., Marshall J.C., Awono-Ambene P.H., Antonio-Nkondjo C., Simard F., et al. Patterns of selection in anti-malarial immune genes in malaria vectors: evidence for adaptive evolution in LRIM1 in Anopheles arabiensis. PLoS ONE 2 8 (2007) E793
44. Bachman E.S., and McClay D.R. Molecular cloning of the first metazoan beta-1,3 glucanase from eggs of the sea urchin Strongylocentrotus purpuratus. Proc Natl Acad Sci USA 93 (1996) 6808-6813
45. Beschin A., Bilej M., Hanssens F., Raymakers J., Van Dyck E., Revets H., et al. Identification and cloning of a glucan- and lipopolysaccharide-binding protein from Eisenia foetida earthworm involved in the activation of prophenoloxidase cascade. J Biol Chem 273 (1998) 24948-24954
46. Bilej M., De Baetselier P., Van Dijck E., Stijlemans B., Colige A., and Beschin A. Distinct carbohydrate recognition domains of an invertebrate defense molecule recognize Gram-negative and Gram-positive bacteria. J Biol Chem 276 (2001) 45840-45847
47. Silerova M., Prochazkova P., Joskova R., Josens G., Beschin A., DeBaetselier P., et al. Comparative study of the CCF-like pattern recognition protein in different Lumbricid species. Dev Comp Immunol 30 (2006) 765-771
48. Richards S., Liu Y., Bettencourt B.R., Hradecky P., Letovsky S., Nielsen R., et al. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res 15 (2005) 1-18
49. Kozhemyako V.B., Rebrikov D.V., Lukyanov S.A., Bogdanova E.A., Marin A., Mazur A.K., et al. Molecular cloning and characterization of an endo-1,3-beta-D-glucanase from the mollusk Spisula sachalinensis. Comp Biochem Physiol B, Biochem Mol Biol 137 (2004) 169-178