Structure and vascular tissue expression of duplicated TERMINAL EAR1-like paralogues in poplar

Planta

Volumn 231, Issue 3, 2010, Pages 525-535

  Charon, Céline ^a   Vivancos, Julien ^a   Mazubert, Christelle ^a   Paquet, Nicolas ^a   Pilate, Gilles ^b   Dron, Michel ^a  

^a INSTITUTE OF PLANT SCIENCES PARIS SACLAY IPS2   (France)

^b National Institute for Agricultural Research   (France)

Author keywords

Cell differentiation; Gene evolution; Populus; TEL RNA binding proteins; Vascular tissues

Indexed keywords

MESSENGER RNA; VEGETABLE PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; ASPEN; CELL DIFFERENTIATION; CHEMISTRY; GENE DUPLICATION; GENETIC TRANSCRIPTION; GENETICS; GROWTH, DEVELOPMENT AND AGING; IN SITU HYBRIDIZATION; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY; PLANT GENOME; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; CELL DIFFERENTIATION; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENOME, PLANT; IN SITU HYBRIDIZATION; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANT PROTEINS; POPULUS; RNA, MESSENGER; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; TRANSCRIPTION, GENETIC;

EMBRYOPHYTA; MAGNOLIOPHYTA; POACEAE; POPULUS; POPULUS ALBA; POPULUS TREMULA; POPULUS TRICHOCARPA;

EID: 76049122828     PISSN: 00320935     EISSN: 14322048     Source Type: Journal    
DOI: 10.1007/s00425-009-1066-4     Document Type: Article

References (45)

1. Anderson GH, Alvarez ND, Gilman C, Jeffares DC, Trainor VC, Hanson MR, Veit B (2004) Diversification of genes encoding mei2-like RNA binding proteins in plants. Plant Mol Biol 54: 653-670.
2. Campalans A, Kondorosi A, Crespi M (2004) Enod40, a short open reading frame-containing mRNA, induces cytoplasmic localization of a nuclear RNA binding protein in Medicago truncatula. Plant Cell 16: 1047-1059.
3. Causier B, Castillo R, Zhou J, Ingram R, Xue Y, Schwarz-Sommer Z, Davies B (2005) Evolution in action: following function in duplicated floral homeotic genes. Curr Biol 15: 1508-1512.
4. Dayhoff MO, Eck RV (1968) Atlas of protein sequence and structure, 1967-1968. National Biomedical Research Foundation. Silver Spring, MD.
5. Déjardin A, Leplé J-C, Lesage-Descauses M-C, Costa G, Pilate G (2004) Expressed sequence tags from poplar wood tissues-a comparative analysis from multiple libraries. Plant Biol 6: 55-64.
6. Demura T, Fukuda H (2007) Transcriptional regulation in wood formation. Trends Plant Sci 12: 64-70.
7. Doyle J, Doyle J (1987) Isolation of plant DNA from fresh tissue. Focus 12: 13-15.
8. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368-376.
9. Felsenstein J (1989) PHYLIP-Phylogeny inference package (version 3. 2). Cladistics 5: 164-166.
10. Felsenstein J (2004) An ancestor's influence. Nat Genet 36: 1031.
11. Fukuda H (2004) Signals that control plant vascular cell differentiation. Nat Rev Mol Cell Biol 5: 379-391.
12. Guindon S, Gascuel O (2003) PHYML-a simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
13. Hertzberg M, Aspeborg H, Schrader J, Andersson A, Erlandsson R, Blomqvist K, Bhalerao R, Uhlén M, Teeri TT, Lundeberg J, Sundberg B, Nilsson P, Sandberg G (2001) A transcriptional roadmap to wood formation. Proc Natl Acad Sci USA 98: 14732-14737.
14. Huelsenbeck JP, Ronquist F (2001) MrBAYES: bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
15. Ito Y, Nakanomyo I, Motose H, Iwamoto K, Sawa S, Dohmae N, Fukuda H (2006) Dodeca-CLE peptides as suppressors of plant stem cell differentiation. Science 313: 842-845.
16. Jackson D (1991) In situ hybridisation in plants. In: Bowles DJ, Gurr SJ, McPherson M (eds) Molecular plant pathology: a practical approach. Oxford University Press, Oxford.
17. Jansson S, Douglas C (2007) Populus: a model system for plant biology. Annu Rev Plant Biol 58: 435-458.
18. Jeffares DC, Phillips MJ, Moore S, Veit B (2004) A description of the Mei2-like protein family: structure, phylogenetic distribution and biological context. Dev Genes Evol 214: 149-158.
19. Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8: 275-282.
20. Kalluri UC, DiFazio SP, Brunner AM, Tuskan GA (2007) Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa. BMC Plant Biol. doi: 10. 1186/1471-2229-7-59.
21. Kawakatsu T, Itoh J-I, Miyoshi K, Kurata N, Alvarez N, Veit B, Nagato Y (2006) PLASTOCHRON2 regulates leaf initiation and maturation in rice. Plant Cell 18: 612-625.
22. Ko J, Han K (2004) Arabidopsis whole-transcriptome profiling defines the features of coordinated regulations that occur during secondary growth. Plant Mol Biol 55: 433-453.
23. Koch MA, Haubold B, Mitchell-Olds T (2000) Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis and related genera (Brassicaceae). Mol Biol Evol 17: 1483-1498.
24. Laufs P, Dockx J, Kronenberger J, Traas J (1998) MGOUN1 and MGOUN2: two genes required for primordium initiation at the shoot apical and floral meristem in Arabidopsisthaliana. Development 125: 1253-1260.
25. Logemann J, Schell J, Willmitzer L (1987) Improved method for the isolation of RNA from plant tissues. Anal Biochem 163: 16-20.
26. Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
27. Matthews DL, Grogan CO, Manchester CE (1974) Terminal ear mutants of maize (Zea mays). J Agric Sci 82: 433-435.
28. McKhann HI, Hirsch AM (1993) In situ localisation of specific mRNAs in plant tissues. In: Glick BR, Thompson JE (eds) Methods in plant molecular biology and biotechnology. CRC Press, Boca Raton, pp 179-205.
29. Motose H, Sugiyama M, Fukuda H (2004) A proteoglycan mediates inductive interaction during plant vascular development. Nature 429: 873-878.
30. Page RDM (1996) TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12: 357-358.
31. Paquet N, Bernadet M, Morin H, Traas J, Dron M, Charon C (2005) Expression patterns of TEL genes in Poaceae suggest a conserved association with cell differentiation. J Exp Bot 56: 1605-1614.
32. Schrader J, Nilsson J, Mellerowicz E, Berglund A, Nilsson P, Hertzberg M, Sandberg G (2004) A high-resolution transcript profile across the wood-forming meristem of poplar identifies potential regulators of cambial stem cell identity. Plant Cell 16: 2278-2292.
33. Sterck L, Rombauts S, Jansson S, Sterky F, Rouzé P, van de Peer Y (2005) EST data suggest that poplar is an ancient polyploid. New Phytol 167: 165-170.
34. Sterky F, Bhalerao RR, Unneberg P, Segerman B, Nilsson P, Brunner AM, Campaa L, Jonsson Lindvall J, Tandre K, Strauss SH, Sundberg B, Gustafsson P, Uhlen M, Bhalerao RP, Nilsson O, Sandberg G, Karlsson J, Lundeberg J, Jansson S (2004) A Populus EST resource for plant functional genomics. Proc Natl Acad Sci USA 101: 13951-13956.
35. Thompson JF, Gibson F, Plewmiak F, Jenamougin F, Higgins DG (1997) The ClustalX window interface: flexible strategies for multiple sequence alignment aided by quality analysis tool. Nucleic Acids Res 25: 4876-4882.
36. Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Dejardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjarvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leple JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, de Peer YV, Rokhsar D (2006) The genome of black cottonwood, Populus trichocarpa (Torr & Gray). Science 313: 1596-1604.
37. van Raemdonck D, Pesquet E, Cloquet S, Beeckman H, Boerjan W, Goffner D, El Jaziri M, Baucher M (2005) Molecular changes associated with the setting up of secondary growth in aspen. J Exp Bot 56: 2211-2227.
38. Veerassamy S, Smith A, Tillier ERM (2003) A transition probability model for amino acid substitutions from Blocks. J Comput Biol 10: 997-1010.
39. Veit B, Briggs SP, Schmidt RJ, Yanofsky MF, Hake S (1998) Regulation of leaf initiation by the terminal ear1 gene of maize. Nature 393: 166-168.
40. Watanabe Y, Yamamoto M (1994) S. pombe mei2 + encodes an RNA-binding protein required for premeiotic DNA synthesis and meiosis I, which cooperates with a novel RNA species meiRNA. Cell 78: 487-498.
41. Xiong GS, Hu XM, Jiao YQ, Yu YC, Chu CC, Li JY, Qian Q, Wang YH (2006) LEAFY HEAD2, which encodes a putative RNA-binding protein, regulates shoot development of rice. Cell Res 16: 267-276.
42. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555-556.
43. Yang X, Tuskan GA, Cheng Z-M (2006) Divergence of the Dof gene families in poplar, Arabidopsis, and rice suggests multiple modes of gene evolution after duplication. Plant Physiol 142: 820-830.
44. Ye Z-H (2002) Vascular tissue differentiation and pattern formation in plants. Annu Rev Plant Biol 53: 183-202.
45. Zhao C, Craig J, Petzold H, Dickerman A, Beers E (2005) The xylem and phloem transcriptomes from secondary tissues of the Arabidopsis root-hypocotyl. Plant Physiol 138: 803-818.