An integrative approach to the identification of arabidopsis and rice genes involved in xylan and secondary wall development

PLoS ONE

Volumn 5, Issue 11, 2010, Pages

  Oikawa, Ai ^a,b   Joshi, Hiren J ^a,b   Rennie, Emilie A ^a,c   Ebert, Berit ^a,b   Manisseri, Chithra ^a,b   Heazlewood, Joshua L ^a,b   Scheller, Henrik Vibe ^a,b,c  

^a JOINT BIOENERGY INSTITUTE   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLUCURONIC ACID; GLUCURONOSYLTRANSFERASE; XYLAN; 1,4 BETA D XYLAN SYNTHASE; 1,4-BETA-D-XYLAN SYNTHASE; ARABIDOPSIS PROTEIN; GLUCURONOXYLAN; GLYCOSYLTRANSFERASE;

ANALYTIC METHOD; ARABIDOPSIS; ARTICLE; CARBOHYDRATE SYNTHESIS; CELL NUCLEUS; CELL WALL; CELLULAR DISTRIBUTION; CONTROLLED STUDY; ENZYME ACTIVITY; GENE EXPRESSION; GENE IDENTIFICATION; GOLGI COMPLEX; MULTIGENE FAMILY; MUTANT; NONHUMAN; ORTHOLOGY; PLANT GENE; PREDICTION; PROTEIN LOCALIZATION; RICE; SIGNAL TRANSDUCTION; BIOLOGY; BIOSYNTHESIS; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; METHODOLOGY; MUTATION;

ARABIDOPSIS;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CELL WALL; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GLUCURONOSYLTRANSFERASE; GLYCOSYLTRANSFERASES; GOLGI APPARATUS; MUTATION; ORYZA SATIVA; PENTOSYLTRANSFERASES; XYLANS;

EID: 78649527921     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0015481     Document Type: Article

References (82)

1. Scheller HV, Ulvskov P (2010) Hemicelluloses. Annu Rev Plant Biol 61: 263-289.
2. Andersson SI, Samuelson O, Ishihara M, Shimizu K (1983) Structure of the reducing end-groups in spruce xylan. Carbohydr Res 111: 283-288.
3. Johansson MH, Samuelson O (1977) Reducing end groups in birch xylan and their alkaline degradation. Wood Sci Technol 11: 251-263.
4. Peña MJ, Zhong R, Zhou G-K, Richardson EA, O'Neill MA, et al. (2007) Arabidopsis irregular xylem8 and irregular xylem9: Implications for the complexity of glucuronoxylan biosynthesis. Plant Cell 19: 549-563.
5. Liepman AH, Wightman R, Geshi N, Turner SR, Scheller HV (2010) Arabidopsis - a powerful model system for plant cell wall research. Plant J 61: 1107-1121.
6. Harholt J, Suttangkakul A, Scheller HV (2010) Biosynthesis of pectin. Plant Physiol 153: 384-395.
7. Caffall KH, Mohnen D (2009) The structure, function, and biosynthesis of plant cell wall pectic polysaccharides. Carbohydr Res 344: 1879-1900.
8. Fincher GB (2009) Revolutionary times in our understanding of cell wall biosynthesis and remodeling in the grasses. Plant Physiol 149: 27-37.
9. Pauly M, Keegstra K (2008) Cell-wall carbohydrates and their modification as a resource for biofuels. Plant J 54: 559-568.
10. York WS, O'Neill MA (2008) Biochemical control of xylan biosynthesis - which end is up? Curr Opin Plant Biol 11: 258-265.
11. Brown DM, Zeef LA, Ellis J, Goodacre R, Turner SR (2005) Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. Plant Cell 17: 2281-2295.
12. Persson S, Wei H, Milne J, Pageand GP, Somerville CR (2005) Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proc Nat Acad Sci USA 102: 8633-8638.
13. Brown DM, Goubet F, Wong VW, Goodacre R, Stephens E, Dupree P, Turner SR (2007) Comparison of five xylan synthesis mutants reveals new insight into the mechanisms of xylan synthesis. Plant J 52: 1154-1168.
14. Brown DM, Zhang ZN, Stephens E, Dupree P, Turner SR (2009) Characterization of IRX10 and IRX10-like reveals an essential role in glucuronoxylan biosynthesis in Arabidopsis. Plant J 57: 732-746.
15. Lee C, O'Neill MA, Tsumuraya Y, Darvill AG, Ye ZH (2007) The irregular xylem9 mutant is deficient in xylan xylosyltransferase activity. Plant Cell Physiol 48: 1624-1634.
16. Balazsi G, Barabashi AL, Oltvai ZN (2005) Topological units of environmental signal processing in the transcriptional-regulatory network of Escherichia coli. Proc Nat Acad Sci USA 102: 7841-7846.
17. Ihmels J, Levy R, Barkai N (2004) Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae. Nat Biotechnol 22: 86-92.
18. Hirai MY, Sugiyama K, Sawada Y, Tohge T, Obayashi T, et al. (2007) Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proc Nat Acad Sci USA 104: 6478-6483.
19. Mitchell RAC, Dupree P, Shewry PR (2007) A novel bioinformatics approach identifies candidate genes for the synthesis and feruloylation of arabinoxylan. Plant Physiol 144: 43-53.
20. Jung KH, Lee J, Dardick C, Seo YS, Cao P, et al. (2008) Identification and functional analysis of light-responsive unique genes and gene family members in rice. PLoS Genet 4: e1000164.
21. Aoki K, Ogata Y, Shibata D (2007) Approaches for extracting practical information from gene co-expression networks in plant biology. Plant Cell Physiol 48: 381-390.
22. Mutwil M, Obro J, Willats WG, Persson S (2008) GeneCAT-novel webtools that combine BLAST and co-expression analyses. Nucleic Acids Res 36: W320-W326.
23. Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K (2009) ATTED-II provides coexpressed gene networks for Arabidopsis. Nucleic Acids Res 37: D987-D991.
24. Obayashi T, Kinoshita K (2009) Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression. DNA Res 16: 249-260.
25. Geisler-Lee J, O'Toole N, Ammar R, Provart NJ, Millar AH, Geisler M (2007) A predicted interactome for Arabidopsis. Plant Physiol 145: 317-329.
26. Rastogi S, Rost B (2010) Bioinformatics predictions of localization and targeting. In Protein Secretion. In: Economou A, ed. New York: Humana Press. Pp 285-305.
27. Wrzeszczynski KO, Rost B (2004) Annotating proteins from endoplasmic reticulum and Golgi apparatus in eukaryotic proteomes. Cell Mol Life Sci 61: 1341-1353.
28. Li X, Cordero I, Caplan J, Molhoj M, Reiter WD (2004) Molecular analysis of 10 coding regions from Arabidopsis that are homologous to the MUR3 xyloglucan galactosyltransferase. Plant Physiol 134: 940-950.
29. The International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463: 763-768.
30. Aspeborg H, Schrader J, Coutinho PM, Stam M, Kallas A, et al. (2005) Carbohydrate-active enzymes involved in the secondary cell wall biogenesis in hybrid aspen. Plant Physiol 137: 983-997.
31. Kinoshita K, Obayashi T (2009) Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis. Bioinformatics 20: 2677-2684.
32. Wu AM, Hornblad E, Voxeur A, Gerber L, Rihouey C, et al. (2010) Analysis of the Arabidopsis IRX9/IRX9-L and IRX14/IRX14-L pairs of glycosyltransferase genes reveals critical contributions to biosynthesis of the hemicellulose glucuronoxylan. Plant Physiol 153: 542-554.
33. Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, et al. (2007) F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol 143: 1467-1483.
34. Li Y, Qian Q, Zhou Y, Yan M, Sun L, et al. (2003) BRITTLE CULM1, which encodes a COBRA-like Protein, affects the mechanical properties of rice plants. Plant Cell 15: 2020-2031.
35. Tanaka K, Murata K, Yamazaki M, Onosato K, Miyao A, et al. (2003) Three distinct rice cellulose synthase catalytic subunit genes required for cellulose synthesis in the secondary wall. Plant Physiol 133: 73-83.
36. Guda C, Subramaniam S (2005) pTARGET: A new method for predicting protein sub-cellular localization in eukaryotes. Bioinformatics 21: 3963-3969.
37. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, et al. (2004) The Pfam protein families database. Nucleic Acids Res 32: D138-D141.
38. Heazlewood JL, Verboom RE, Tonti-Filippini J, Small I, Millar AH (2007) SUBA: the Arabidopsis Subcellular Database. Nucleic Acids Res 35: D213-D218.
39. Brembu T, Winge P, Bones AM (2005) The small GTPase AtRAC2/ROP7 is specifically expressed during late stages of xylem differentiation in Arabidopsis. J Exp Bot 419: 2465-2476.
40. Gu Y, Fu Y, Dowd P, Li S, Vernoud V, et al. (2005) A Rho family GTPase controls actin dynamics and tip growth via two counteracting downstream pathways in pollen tubes. J Cell Biol 169: 127-138.
41. Chatterjeea M, Berbezya P, Vyasa D, Coatesb S, Barsbya T (2005) Reduced expression of a protein homologous to glycogenin leads to reduction of starch content in Arabidopsis leaves. Plant Sci 168: 501-509.
42. Bischoff V, Nita S, Neumetzler L, Schindelasch D, Urbain A, et al. (2010) TRICHOME BIREFRINGENCE and its homolog At5g01360 encode plant specific DUF231 proteins required for cellulose biosynthesis in Arabidopsis. Plant Physiol 153: 590-602.
43. Prag S, Parsons M, Keppler MD, Ameer-Beg SM, Barber P, et al. (2007) Activated ezrin promotes cell migration through recruitment of the GEF Dbl to lipid rafts and preferential downstream activation of Cdc42. Mol Biol Cell 18: 2935-2948.
44. Yang T, Chaudhuri S, Yang L, Chen Y, Poovaiah BW (2004) Calcium/calmodulin up-regulates a cytoplasmic receptor-like kinase in plants. J Biol Chem 279: 42552-42559.
45. Konishi T, Takeda T, Miyazaki Y, Ohnishi-Kameyama M, Hayashi T, et al. (2007) A plant mutase that interconverts UDP-arabinofuranose and UDParabinopyranose. Glycobiology 17: 345-354.
46. Toole GA, Le Gall G, Colquhoun IJ, Nemeth C, Saulnier L, et al. (2010) Temporal and spatial changes in cell wall composition in developing grains of wheat cv. Hereward. Planta 232: 677-689.
47. Yin Y, Chen H, Hahn MG, Mohnen D, Xu Y (2010) Evolution and function of the plant cell wall synthesis-related glycosyltransferase family 8. Plant Physiol 153: 1729-1746.
48. Ko JH, Beers EP, Han KH (2006) Global comparative transcriptome analysis identifies gene network regulating secondary xylem development in Arabidopsis thaliana. Mol Gen Genomics 276: 517-531.
49. Mutwil M, Ruprecht C, Giorgi FM, Bringmann M, Usadel B, et al. (2009) Transcriptional wiring of cell wall-related genes in Arabidopsis. Mol Plant 2: 1015-1024.
50. van Dijk AD, Bosch D, ter Braak CJ, van der Krol AR, van Ham RC (2008) Predicting sub-Golgi localization of type II membrane proteins. Bioinformatics 24: 1779-1786.
51. Kaundal R, Saini R, Zhao PX (2010) Combining machine learning and homology-based approaches to accurately predict subcellular localization in Arabidopsis. Plant Physiol 154: 36-54.
52. Anantharaman V, Aravind L (2010) Novel eukaryotic enzymes modifying cellsurface biopolymers. Biol Direct 5: 1.
53. Piston F, Uauy C, Fu L, Langston J, Labavitch J, et al. (2010) Down-regulation of four putative arabinoxylan feruloyltransferase genes from family PF02458 reduces ester-linked ferulate content in rice cell walls. Planta 231: 677-691.
54. Buanafina MMO (2009) Feruloylation in grasses: current and future perspectives. Mol Plant 2: 861-872.
55. Ruse M, Knaus UG (2006) New players in TLR-mediated innate immunity: PI3K and small Rho GTPases. Immunol Res 34: 33-48.
56. Da Silva CA, Hartl D, Liu W, Lee CG, Elias JA (2008) TLR-2 and IL-17A in chitin-induced macrophage activation and acute inflammation. J Immunol 181: 4279-4286.
57. Shibolet O, Giallourakis C, Rosenberg I, Mueller T, Xavier RJ, et al. (2007) AKAP13, a RhoA GTPase-specific guanine exchange factor, is a novel regulator of tlr2 signaling. J Biol Chem 282: 35308-35317.
58. Rolls A, Shechter R, London A, Ziv Y, Ronen A, et al. (2007) Toll-like receptors modulate adult hippocampal neurogenesis. Nature Cell Biol 9: 1081-1088.
59. Wu G, Gu Y, Li S, Yang Z (2001) A genome-wide analysis of Arabidopsis Ropinteractive CRIB motif-containing proteins that act as Rop GTPase targets. Plant Cell 13: 2841-2856.
60. Nibau C, Wu HM, Cheung AY (2006) RAC/ROP GTPases: 'Hubs' for signal integration and diversification in plants. Trends Plant Sci 11: 309-315.
61. Brill S, Li S, Lyman CW, Church DM, Wasmuth JJ, et al. (1996) The Ras GTPase-activating-protein-related human protein IQGAP2 harbors a potential actin binding domain and interacts with calmodulin and Rho family GTPases. Mol Cell Biol 16: 4869-4878.
62. Lafarguette F, Leplé JC, De ́jardin A, Laurans F, Costa C, et al. (2004) Poplar genes encoding fasciclin-like arabinogalactan proteins are highly expressed in tension wood. New Phytologist 164: 107-121.
63. Geisler-Lee J, Geisler M, Coutinho PM, Segerman B, Nishikubo N, et al. (2006) Poplar carbohydrate-active enzymes. Gene identification and expression analyses. Plant Physiol 140: 946-962.
64. Liu D, Tu L, Li Y, Wang L, Zhu L, et al. (2008) Genes encoding fasciclin-like arabinogalactan proteins are specifically expressed during cotton fiber development. Plant Mol Biol Rep 26: 98-113.
65. Zhang D, Hrmova M, Wan CH, Wu C, Balzen J, et al. (2004) Members of a new group of chitinase-like genes are expressed preferentially in cotton cells with secondary walls. Plant Mol Biol 54: 353-372.
66. Lin B, Madan A, Yoon JG, Fang X, Yan X, et al. (2010) Massively parallel signature sequencing and bioinformatics analysis identifies up-regulation of TGFBI and SOX4 in human glioblastoma. PLoS ONE 5: e10210.
67. Kzhyshkowska J, Mamidi S, Gratchev A, Kremmer E, Schmuttermaier C, et al. (2006) Novel stabilin-1 interacting chitinase-like protein (SI-CLP) is up-regulatedin alternatively activated macrophages and secreted via lysosomal pathway. Blood 107: 3221-3228.
68. Hermans C, Porco S, Verbruggen N, Bush DR (2010) Chitinase-like protein CTL1 plays a role in altering root system architecture in response to multiple environmental conditions. Plant Physiol 152: 904-917.
69. Mitsuda N, Iwase A, Yamamoto H, Yoshida M, Seki M, et al. (2007) NAC transcription factors, NST1 and NST3, are key regulators of the formation of secondary walls in woody tissues of Arabidopsis. Plant Cell 19: 270-280.
70. Wightman R, Turner SR (2008) The roles of the cytoskeleton during cellulose deposition at the secondary cell wall. Plant J 54: 794-805.
71. Zhong R, Ye ZH (2007) Regulation of cell wall biosynthesis. Curr Opin Plant Biol 10: 564-572.
72. Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, et al. (2007) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res 35: D883-D887.
73. Earley KW, Haag JR, Pontes O, Opper K, Juehne T, et al. (2006) Gatewaycompatible vectors for plant functional genomics and proteomics. Plant J 45: 616-629.
74. Boevink P, Santa Cruz S, Hawes C, Harris N, Oparka KJ (1996) Virus-mediated delivery of the green fluorescent protein to the endoplasmic reticulum of plant cells. Plant J 10: 935-941.
75. Nelson BK, Cai X, Nebenführ A (2007) A multicolored set of in vivo organelle markers for co-localization studies in Arabidopsis and other plants. Plant J 51: 1126-1136.
76. Harholt J, Jensen JK, Sorensen SO, Orfila C, Pauly M, et al. (2006) ARABINAN DEFICIENT 1 is a putative arabinosyltransferase involved in biosynthesis of pectic arabinan in Arabidopsis. Plant Physiol 140: 49-58.
77. Bannai H, Tamada Y, Maruyama O, Nakai K, Miyano S (2002) Extensive feature detection of N-terminal protein sorting signals. Bioinformatics 18: 298-305.
78. Claros MG, Vicens P (1996) Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur J Biochem 241: 779-786.
79. Small I, Peeters N, Legeai F, Lurin C (2004) Predotar: a tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics 4: 1581-1590.
80. Emanuelsson O, Nielsen H, Brunak S, von Heijne G (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 300: 1005-1016.
81. Horton P, Park KJ, Obayashi T, Fujita N, Harad H, et al. (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res 35: W585-W587.
82. Dunkley TP, Watson R, Griffin JL, Dupree P, Lilley KS (2004) Localization of organelle proteins by isotope tagging (LOPIT). Mol Cell Proteomics 3: 1128-1134.