Identification of molecular processes needed for vascular formation through transcriptome analysis of different vascular systems

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Xu, Peng ^a   Kong, Yimeng ^a   Li, Xuan ^a   Li, Laigeng ^a  

^a INSTITUTE OF PLANT PHYSIOLOGY AND ECOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ARABIDOPSIS; ARTICLE; BIOGENESIS; CELL STRUCTURE; CELL WALL; CONTROLLED STUDY; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE LOCATION; GENETIC CONSERVATION; MOLECULAR DYNAMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT CELL; PLANT GENE; PLANT GENETICS; POPULUS; RICE; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION; TRANSCRIPTOMICS; VASCULARIZATION;

ARABIDOPSIS; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENES, PLANT; ORYZA SATIVA; PHLOEM; PLANT PROTEINS; SIGNAL TRANSDUCTION; XYLEM;

ARABIDOPSIS; DICOTYLEDONEAE;

EID: 84875506962     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-217     Document Type: Article

References (57)

1. Evert RF. Esau's Plant anatomy: meristems, cells, and tissues of the plant body: their structure, function, and development 2006, Hoboken, New Jersey: Jone Wiley & Sons, Inc, 3.
2. Ye ZH. Vascular tissue differentiation and pattern formation in plants. Annu Rev Plant Biol 2002, 53:183-202. 10.1146/annurev.arplant.53.100301.135245, 12221972.
3. Caño-Delgado A, Lee J-Y, Demura T. Regulatory mechanisms for specification and patterning of plant vascular tissues. Annu Rev Cell Dev Biol 2010, 26(1):605-637. 10.1146/annurev-cellbio-100109-104107, 20590454.
4. Hardtke CS, Berleth T. The arabidopsis gene MONOPTEROS encodes a transcription factor mediating embryo axis formation and vascular development. EMBO J 1998, 17(5):1405-1411. 10.1093/emboj/17.5.1405, 1170488, 9482737.
5. Bonke M, Thitamadee S, Mahonen AP, Hauser M-T, Helariutta Y. APL regulates vascular tissue identity in arabidopsis. Nature 2003, 426(6963):181-186. 10.1038/nature02100, 14614507.
6. Emery JF, Floyd SK, Alvarez J, Eshed Y, Hawker NP, Izhaki A, Baum SF, Bowman JL. Radial patterning of arabidopsis shoots by class III HD-ZIP and KANADI genes. Curr Biol 2003, 13(20):1768-1774. 10.1016/j.cub.2003.09.035, 14561401.
7. Kubo M. Transcription switches for protoxylem and metaxylem vessel formation. Genes Dev 2005, 19(16):1855-1860. 10.1101/gad.1331305, 1186185, 16103214.
8. Zhong R, Demura T, Ye ZH. SND1, A NAC domain transcription factor, is a Key regulator of secondary wall synthesis in fibers of arabidopsis. Plant Cell 2006, 18(11):3158-3170. 10.1105/tpc.106.047399, 1693950, 17114348.
9. Vanderauwera S. Genome-wide analysis of hydrogen peroxide-regulated gene expression in arabidopsis reveals a high light-induced transcriptional cluster involved in anthocyanin biosynthesis. Plant Physiol 2005, 139(2):806-821. 10.1104/pp.105.065896, 1255997, 16183842.
10. Hirai MY, Sugiyama K, Sawada Y, Tohge T, Obayashi T, Suzuki A, Araki R, Sakurai N, Suzuki H, Aoki K. Omics-based identification of arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proc Natl Acad Sci 2007, 104(15):6478-6483. 10.1073/pnas.0611629104, 1849962, 17420480.
11. Yonekura-Sakakibara K, Tohge T, Niida R, Saito K. Identification of a flavonol 7-O-rhamnosyltransferase gene determining flavonoid pattern in arabidopsis by transcriptome coexpression analysis and reverse genetics. J Biol Chem 2007, 282(20):14932-14941. 10.1074/jbc.M611498200, 17314094.
12. Brown DM. Identification of novel genes in arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. Plant Cell 2005, 17(8):2281-2295. 10.1105/tpc.105.031542, 1182489, 15980264.
13. Persson S. Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proc Natl Acad Sci 2005, 102(24):8633-8638. 10.1073/pnas.0503392102, 1142401, 15932943.
14. Mutwil M, Klie S, Tohge T, Giorgi FM, Wilkins O, Campbell MM, Fernie AR, Usadel B, Nikoloski Z, Persson S. PlaNet: combined sequence and expression comparisons across plant networks derived from seven species. Plant Cell 2011, 23(3):895-910. 10.1105/tpc.111.083667, 3082271, 21441431.
15. Persson S, Nikoloski Z, Eder M, Saxe F, Mutwil M, Ruprecht C. Large-scale Co-expression approach to dissect secondary cell wall formation across plant species 2011, 2. Plant Science: Frontiers in Plant Science.
16. Oikawa A, Joshi HJ, Rennie EA, Ebert B, Manisseri C, Heazlewood JL, Scheller HV. An integrative approach to the identification of arabidopsis and rice genes involved in xylan and secondary wall development. PLoS One 2010, 5(11):e15481. 10.1371/journal.pone.0015481, 2990762, 21124849.
17. Zhao C. The xylem and phloem transcriptomes from secondary tissues of the arabidopsis root-hypocotyl. Plant Physiol 2005, 138(2):803-818. 10.1104/pp.105.060202, 1150398, 15923329.
18. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 2011, 27(3):431-432. 10.1093/bioinformatics/btq675, 3031041, 21149340.
19. Zhong R, Richardson EA, Ye ZH. The MYB46 transcription factor is a direct target of SND1 and regulates secondary wall biosynthesis in arabidopsis. Plant Cell 2007, 19(9):2776-2792. 10.1105/tpc.107.053678, 2048704, 17890373.
20. Zhong R, Lee C, Zhou J, McCarthy RL, Ye ZH. A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in arabidopsis. Plant Cell 2008, 20(10):2763-2782. 10.1105/tpc.108.061325, 2590737, 18952777.
21. Abel S, Savchenko T, Levy M. Genome-wide comparative analysis of the IQD gene families in arabidopsis thaliana and oryza sativa. BMC Evol Biol 2005, 5:72. 10.1186/1471-2148-5-72, 1368998, 16368012.
22. Atanassov II, Pittman JK, Turner SR. Elucidating the mechanisms of assembly and subunit interaction of the cellulose synthase complex of arabidopsis secondary cell walls. J Biol Chem 2008, 284(6):3833-3841. 10.1074/jbc.M807456200, 19056734.
23. Persson S, Caffall KH, Freshour G, Hilley MT, Bauer S, Poindexter P, Hahn MG, Mohnen D, Somerville C. The arabidopsis irregular xylem8 mutant is deficient in glucuronoxylan and homogalacturonan, which Are essential for secondary cell wall integrity. Plant Cell 2007, 19(1):237-255. 10.1105/tpc.106.047720, 1820957, 17237350.
24. Wu A-M, Rihouey C, Seveno M, Hörnblad E, Singh SK, Matsunaga T, Ishii T, Lerouge P, Marchant A. The arabidopsis IRX10 and IRX10-LIKE glycosyltransferases are critical for glucuronoxylan biosynthesis during secondary cell wall formation. Plant J 2009, 57(4):718-731. 10.1111/j.1365-313X.2008.03724.x, 18980649.
25. Berthet S, Demont-Caulet N, Pollet B, Bidzinski P, Cezard L, Le Bris P, Borrega N, Herve J, Blondet E, Balzergue S. Disruption of LACCASE4 and 17 results in tissue-specific alterations to lignification of arabidopsis thaliana stems. Plant Cell 2011, 23(3):1124-1137. 10.1105/tpc.110.082792, 3082258, 21447792.
26. Mizrachi E, Mansfield SD, Myburg AA. Cellulose factories: advancing bioenergy production from forest trees. New Phytol 2012, 194(1):54-62. 10.1111/j.1469-8137.2011.03971.x, 22474687.
27. Yang Z. Cell polarity signaling inArabidopsis. Annu Rev Cell Dev Biol 2008, 24(1):551-575. 10.1146/annurev.cellbio.23.090506.123233, 2739732, 18837672.
28. Oda Y, Fukuda H. Initiation of cell wall pattern by a Rho- and microtubule-driven symmetry breaking. Science 2012, 337(6100):1333-1336. 10.1126/science.1222597, 22984069.
29. Brembu T. The small GTPase AtRAC2/ROP7 is specifically expressed during late stages of xylem differentiation in arabidopsis. J Exp Bot 2005, 56(419):2465-2476. 10.1093/jxb/eri239, 16061508.
30. De Smet I, Voß U, Jürgens G, Beeckman T. Receptor-like kinases shape the plant. Nat Cell Biol 2009, 11(10):1166-1173. 10.1038/ncb1009-1166, 19794500.
31. Boerjan W, Ralph J, Baucher M. LIGNIN BIOSYNTHESIS. Annu Rev Plant Biol 2003, 54(1):519-546. 10.1146/annurev.arplant.54.031902.134938, 14503002.
32. Prigge MJ, Otsuga D, Alonso JM, Ecker JR, Drews GN, Clark SE. Class III homeodomain-leucine zipper gene family members have overlapping, antagonistic, and distinct roles in arabidopsis development. Plant Cell 2005, 17(1):61-76. 10.1105/tpc.104.026161, 544490, 15598805.
33. Baima S, Possenti M, Matteucci A, Wisman E, Altamura MM, Ruberti I, Morelli G. The arabidopsis ATHB-8 HD-Zip protein acts as a differentiation-promoting transcription factor of the vascular meristems. Plant Physiol 2001, 126(2):643-655. 10.1104/pp.126.2.643, 111156, 11402194.
34. Green KA. CORONA, a member of the class III homeodomain leucine zipper gene family in arabidopsis, regulates stem cell specification and organogenesis. Plant Cell 2005, 17(3):691-704. 10.1105/tpc.104.026179, 1069692, 15705957.
35. Robischon M, Du J, Miura E, Groover A. The populus class III HD ZIP, popREVOLUTA, influences cambium initiation and patterning of woody stems. Plant Physiol 2010, 155(3):1214-1225. 3046580, 21205615.
36. Rahman A, Du J, Miura E, Robischon M, Martinez C, Groover A. The populus class III HD ZIP transcription factor POPCORONA affects cell differentiation during secondary growth of woody stems. PLoS One 2011, 6(2):e17458. 10.1371/journal.pone.0017458, 3046250, 21386988.
37. Zhu Y, Song D, Sun J, Wang X, Li L. PtrHB7, A class III HD-Zip gene, plays a critical role in regulation of vascular cambium differentiation in populus. Mol Plant 2013,
38. Mele G. The knotted1-like homeobox gene BREVIPEDICELLUS regulates cell differentiation by modulating metabolic pathways. Genes Dev 2003, 17(17):2088-2093. 10.1101/gad.1120003, 196451, 12923061.
39. Du J, Mansfield SD, Groover AT. The populus homeobox gene ARBORKNOX2 regulates cell differentiation during secondary growth. Plant J 2009, 60(6):1000-1014. 10.1111/j.1365-313X.2009.04017.x, 19737362.
40. Zhong R, Lee C, Ye Z-H. Evolutionary conservation of the transcriptional network regulating secondary cell wall biosynthesis. Trends Plant Sci 2010, 15(11):625-632. 10.1016/j.tplants.2010.08.007, 20833576.
41. Zhong R, Lee C, McCarthy RL, Reeves CK, Jones EG, Ye ZH. Transcriptional activation of secondary wall biosynthesis by rice and maize NAC and MYB transcription factors. Plant Cell Physiol 2011, 52(10):1856-1871. 10.1093/pcp/pcr123, 21908441.
42. Hirakawa Y, Shinohara H, Kondo Y, Inoue A, Nakanomyo I, Ogawa M, Sawa S, Ohashi-Ito K, Matsubayashi Y, Fukuda H. Non-cell-autonomous control of vascular stem cell fate by a CLE peptide/receptor system. Proc Natl Acad Sci 2008, 105(39):15208-15213. 10.1073/pnas.0808444105, 2567516, 18812507.
43. Fisher K, Turner S. PXY, a receptor-like kinase essential for maintaining polarity during plant vascular-tissue development. Curr Biol 2007, 17(12):1061-1066. 10.1016/j.cub.2007.05.049, 17570668.
44. Etchells JP, Turner SR. The PXY-CLE41 receptor ligand pair defines a multifunctional pathway that controls the rate and orientation of vascular cell division. Development 2010, 137(5):767-774. 10.1242/dev.044941, 20147378.
45. Levy M, Wang Q, Kaspi R, Parrella MP, Abel S. Arabidopsis IQD1, a novel calmodulin-binding nuclear protein, stimulates glucosinolate accumulation and plant defense. Plant J 2005, 43(1):79-96. 10.1111/j.1365-313X.2005.02435.x, 15960618.
46. Lee C, Zhong R, Richardson EA, Himmelsbach DS, McPhail BT, Ye ZH. The PARVUS gene is expressed in cells undergoing secondary wall thickening and is essential for glucuronoxylan biosynthesis. Plant Cell Physiol 2007, 48(12):1659-1672. 10.1093/pcp/pcm155, 17991630.
47. Lee C, Teng Q, Huang W, Zhong R, Ye ZH. The poplar GT8E and GT8F glycosyltransferases are functional orthologs of arabidopsis PARVUS involved in glucuronoxylan biosynthesis. Plant Cell Physiol 2009, 50(11):1982-1987. 10.1093/pcp/pcp131, 19789274.
48. Abel S, Oeller PW, Theologis A. Early auxin-induced genes encode short-lived nuclear proteins. Proc Natl Acad Sci 1994, 91(1):326-330. 10.1073/pnas.91.1.326, 42940, 8278386.
49. Ouellet F, Overvoorde PJ, Theologis A. IAA17/AXR3: biochemical insight into an auxin mutant phenotype. Plant Cell 2001, 13(4):829-841. 135541, 11283339.
50. Sachs T. Integrating cellular and organismic aspects of vascular differentiation. Plant Cell Physiol 2000, 41(6):649-656. 10.1093/pcp/41.6.649, 10945333.
51. Mao G. The role of MAP65-1 in microtubule bundling during zinnia tracheary element formation. J Cell Sci 2006, 119(4):753-758. 10.1242/jcs.02813, 16449317.
52. Brown D, Wightman R, Zhang Z, Gomez LD, Atanassov I, Bukowski J-P, Tryfona T, McQueen-Mason SJ, Dupree P, Turner S. Arabidopsis genes IRREGULAR XYLEM (IRX15) and IRX15L encode DUF579-containing proteins that are essential for normal xylan deposition in the secondary cell wall. Plant J 2011, 66(3):401-413. 10.1111/j.1365-313X.2011.04501.x, 21251108.
53. Urbanowicz BR, Pena MJ, Ratnaparkhe S, Avci U, Backe J, Steet HF, Foston M, Li H, O'Neill MA, Ragauskas AJ. 4-O-methylation of glucuronic acid in Arabidopsis glucuronoxylan is catalyzed by a domain of unknown function family 579 protein. Proc Natl Acad Sci 2012, 109(35):14253-14258. 10.1073/pnas.1208097109, 3435161, 22893684.
54. Zhang Y, Szustakowski J, Schinke M. Bioinformatics analysis of microarray data. Methods Mol Biol 2009, 573:259-284. 10.1007/978-1-60761-247-6_15, 19763933.
55. Du Z, Zhou X, Ling Y, Zhang Z, Su Z. AgriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 2010, 38(Web Server issue):W64-70. 2896167, 20435677.
56. Arvidsson S, Kwasniewski M, Riano-Pachon DM, Mueller-Roeber B. QuantPrime - a flexible tool for reliable high-throughput primer design for quantitative PCR. BMC Bioinforma 2008, 9(1):465.
57. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-delta delta C(T)) method. Methods 2001, 25(4):402-408. 10.1006/meth.2001.1262, 11846609.