Evolution of non-specific lipid transfer protein (nsLTP) genes in the Poaceae family: Their duplication and diversity

Molecular Genetics and Genomics

Volumn 279, Issue 5, 2008, Pages 481-497

  Jang, Cheol Seong ^a   Yim, Won Cheol ^b   Moon, Jun Cheol ^b   Jung, Je Hyeong ^a   Lee, Tong Geon ^a   Lim, Sung Don ^b   Cho, Seon Hae ^a   Lee, Kwang Kook ^a   Kim, Wook ^a   Seo, Yong Weon ^a   Lee, Byung Moo ^b  

^a Korea University   (South Korea)

^b Dongguk University   (South Korea)

Author keywords

Duplication; Evolutionary fate; Functional diversity; Gene family; nsLTP; Poaceae

Indexed keywords

LIPID TRANSFER PROTEIN;

ARTICLE; GENE; GENE DUPLICATION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENETIC CONSERVATION; GENETIC SELECTION; GENETIC VARIABILITY; GENOME; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE REPEAT; POACEAE; PRIORITY JOURNAL; REGULATORY SEQUENCE; RICE; TALTP4 GENE; TRANSCRIPTION REGULATION; WHEAT;

CARRIER PROTEINS; CLUSTER ANALYSIS; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENETIC SPECIATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORYZA SATIVA; PHYLOGENY; POACEAE; TRITICUM; VARIATION (GENETICS);

POACEAE; TRITICUM AESTIVUM;

EID: 42549097967     PISSN: 16174615     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00438-008-0327-4     Document Type: Article

References (49)

1. Adams KL, Cronn R, Percifield R, Wendel JF (2003) Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc Natl Acad Sci USA 100:4649-4654
2. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815
3. Arondel VV, Vergnolle C, Cantrel C, Kader J (2000) Lipid transfer proteins are encoded by a small multigene family in Arabidopsis thaliana. Plant Sci 157:1-12
4. Blanc G, Wolfe KH (2004a) Wide spread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16:1667-1678
5. Blanc G, Wolfe KH (2004b) Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16:1679-1691
6. Blanchette M, Tompa M (2003) FootPrinter: a program designed for phylogenetic footprinting. Nucleic Acids Res 31:3840-3842
7. Boutrot F, Guirao A, Alary R, Joudrier P, Gautier MF (2005) Wheat non-specific lipid transfer protein genes display a complex pattern of expression in developing seeds. Biochim Biophys Acta 1730:114-125
8. Boutrot F, Meynard D, Guiderdoni E, Joudrier P, Gautier MF (2007) The Triticum aestivum non-specific lipid transfer protein (TaLtp) gene family: comparative promoter activity of six TaLtp genes in transgenic rice. Planta 225:843-862
9. Carvalho Ade O, Gomes VM (2007) Role of plant lipid transfer proteins in plant cell physiology-a concise review. Peptides 28:1144-1153
10. de Hoon MJ, Imoto S, Nolan J, Miyano S (2004) Open source clustering software. Bioinformatics 20:1453-1454
11. Ezcurra I, Ellerstrom M, Wycliffe P, Stalberg K, Rask L (1999) Interaction between composite elements in the napA promoter: both the B-box ABA-responsive complex and the RY/G complex are necessary for seed-specific expression. Plant Mol Biol 40:699-709
12. Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-1545
13. Gausing K (1994) Lipid transfer protein genes specifically expressed in barley leaves and coleoptiles. Planta 192:574-580
14. Green PJ, Yong MH, Cuozzo M, Kano-Murakami Y, Silverstein P, Chua NH (1988) Binding site requirements for pea nuclear protein factor GT-1 correlate with sequences required for light-dependent transcriptional activation of the rbcS-3A gene. EMBO J 7:4035-4044
15. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95-98
16. Herrero J, Valencia A, Dopazo J (2001) A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics 17:126-136
17. Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 27:297-300
18. Huang X, Madan A (1999) CAP3: A DNA sequence assembly program. Genome Res 9:868-877
19. Jang CS, Kim DS, Bu SY, Kim JB, Lee SS, Kim JY, Johnson JW, Seo YW (2002) Isolation and characterization of lipid transfer protein (LTP) genes from a wheat-rye translocation line. Plant Cell Rep 20:961-966
20. Jang CS, Lee HJ, Chang SJ, Seo YW (2004) Expression and promoter analysis of the TaLTP1 gene induced by drought and salt stress in wheat (Triticum aestivum L.). Plant Sci 167:995-1001
21. Jang CS, Johnson JW, Seo YW (2005) Differential expression of TaLTP3 and TaCOMT1 induced by Hessian fly larval infestation in a wheat line possessing H21 resistance gene. Plant Sci 168:1319-1326
22. Jang CS, Jung JH, Yim WC, Lee B-M, Seo YW, Kim W (2007) Divergence of genes encoding non-specific lipid transfer proteins in the Poaceae family. Mol Cells 24:215-223
23. Kader JC (1996) Lipid-transfer proteins in plants. Annu Rev Plant Physiol Plant Mol Biol 47:627-654
24. Kaplinsky NJ, Braun DM, Penterman J, Goff SA, Freeling M (2002) Utility and distribution of conserved noncoding sequences in the grasses. Proc Natl Acad Sci USA 99:6147-6151
25. Kramer EM, Jaramillo MA, Di Stilio VS (2004) Patterns of gene duplication and functional evolution during the diversification of the AGAMOUS subfamily of MADS box genes in angiosperms. Genetics 166:1011-1023
26. Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150-163
27. Lee TG, Jang CS, Kim JY, Kim DS, Park JH, Kim DY, Seo YW (2007) A Myb transcription factor (TaMyb1) from wheat roots is expressed during hypoxia: roles in response to the oxygen concentration in root environment and abiotic stresses. Physiol Plantarum 129:375-385
28. Lockton S, Gaut BS (2005) Plant conserved non-coding sequences and paralogue evolution. Trends Genet 21:60-65
29. Maldonado AM, Doerner P, Dixon RA, Lamb CJ, Cameron RK (2002) A putative lipid transfer protein involved in systemic resistance signalling in Arabidopsis. Nature 419:399-403
30. Moore RC, Purugganan MD (2005) The evolutionary dynamics of plant duplicate genes. Curr Opin Plant Biol 8:122-128
31. Nagao RT, Goekjian VH, Hong JC, Key JL (1993) Identification of protein-binding DNA sequences in an auxin-regulated gene of soybean. Plant Mol Biol 21:1147-1162
32. Nei M, Kumar S (2000) Molecular evolution and phylogentics. Oxford University Press, New York, p 52
33. Papp B, Pal C, Hurst LD (2003) Evolution of cis-regulatory elements in duplicated genes of yeast. Trends Genet 19:417-422
34. Park HC, Kim ML, Kang YH, Jeon JM, Yoo JH, Kim MC, Park CY, Jeong JC, Moon BC, Lee JH (2004) Pathogen-and NaCl-induced expression of the SCaM-4 promoter is mediated in part by a GT-1 box that interacts with a GT-1-like transcription factor 1. Plant Physiol 135:2150-2161
35. Paterson AH, Bowers JE, Chapman BA (2004) Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci USA 101:9903-9908
36. Qi LL, Echalier B, Chao S, Lazo GR, Butler GE, Anderson OD, Akhunov ED, Dvorak J, Linkiewicz AM, Ratnasiri A, Dubcovsky J, Bermudez-Kandianis CE, Greene RA, Kantety R, La Rota CM, Munkvold JD, Sorrells SF, Sorrells ME, Dilbirligi M, Sidhu D, Erayman M, Randhawa HS, Sandhu D, Bondareva SN, Gill KS, Mahmoud AA, Ma XF, Miftahudin, Gustafson JP, Conley EJ, Nduati V, Gonzalez-Hernandez JL, Anderson JA, Peng JH, Lapitan NL, Hossain KG, Kalavacharla V, Kianian SF, Pathan MS, Zhang DS, Nguyen HT, Choi DW, Fenton RD, Close TJ, McGuire PE, Qualset CO, Gill BS (2004) A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics 168:701-712
37. Rice chromosomes 11, 12 sequencing consortia (2005) The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. BMC Biol 3:20. doi: 10.1186/1741-7007-3-20
38. Rubio V, Linhares F, Solano R, Martin AC, Iglesias J, Leyva A, Paz-Ares J (2001) A conserved MYB transcription factor involved in phosphate starvation signaling both in vascular plants and in unicellular algae. Gene Dev 15:2122-2133
39. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
40. Seo YW, Johnson JW, Jarret RL (1997) A molecular marker associated with the H21 Hessian fly resistance gene in wheat. Mol Breed 3:177-181
41. Shirsat A, Wilford N, Croy R, Boulter D (1989) Sequences responsible for the tissue specific promoter activity of a pea legumin gene in tobacco. Mol Gen Genet 215:326-331
42. Stuart JM, Segal E, Koller D, Kim SK (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302:249-255
43. Swigonova Z, Lai J, Ma J, Ramakrishna W, Llaca V, Bennetzen JL, Messing J (2004) Close split of sorghum and maize genome progenitors. Genome Res 14:1916-1923
44. Vignols F, Lund G, Pammi S, Tremousaygue D, Grellet F, Kader JC, Puigdomenech P, Delseny M (1994) Characterization of a rice gene coding for a lipid transfer protein. Gene 142:265-270
45. Vignols F, Wigger M, Garcia-Garrido JM, Grellet F, Kader JC, Delseny M (1997) Rice lipid transfer protein (LTP) genes belong to a complex multigene family and are differentially regulated. Gene 195:177-186
46. Villain P, Mache R, Zhou DX (1996) The mechanism of GT element-mediated cell type-specific transcriptional control. J Biol Chem 271:32593-32598
47. Wang X, Tang H, Bowers JE, Feltus FA, Paterson AH (2007) Extensive concerted evolution of rice paralogs and the road to regaining independence. Genetics 177:1753-1763
48. Zahn LM, Leebens-Mack JH, Arrington JM, Hu Y, Landherr LL, dePamphilis CW, Becker A, Theissen G, Ma H (2006) Conservation and divergence in the AGAMOUS subfamily of MADS-box genes: evidence of independent sub- and neofunctionalization events. Evol Dev 8:30-45
49. Zhu Q, Ordiz MI, Dabi T, Beachy RN, Lamb C (2002) Rice TATA binding protein interacts functionally with transcription factor IIB and the RF2a bZIP transcriptional activator in an enhanced plant in vitro transcription system. Plant Cell 14:795-803