Evolution and function of the plant cell wall synthesis-related glycosyltransferase family 8

Plant Physiology

Volumn 153, Issue 4, 2010, Pages 1729-1746

  Yin, Yanbin ^a   Chen, Huiling ^a   Hahn, Michael G ^a   Mohnen, Debra ^a,b   Xu, Ying ^a,b  

^a UNIVERSITY OF GEORGIA   (United States)

^b NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCOSYLTRANSFERASE;

CELL WALL; ENZYMOLOGY; EUKARYOTE; GENETICS; METABOLISM; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT; PLANT GENE; PLANT GENOME; PROTEIN MOTIF; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS;

AMINO ACID MOTIFS; CELL WALL; CONSERVED SEQUENCE; EUKARYOTA; EVOLUTION, MOLECULAR; GENES, PLANT; GENOME, PLANT; GLYCOSYLTRANSFERASES; MULTIGENE FAMILY; PHYLOGENY; PLANTS; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ANALYSIS, PROTEIN;

EID: 77955708071     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.110.154229     Document Type: Article

References (83)

1. Ahola V, Aittokallio T, Vihinen M, Uusipaikka E (2006) A statistical score for assessing the quality of multiple sequence alignments. BMC Bio-informatics 7: 484
2. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2007) Genetic information in eucaryotes. In Molecular Biology of the Cell. Garland Science, New York, pp 26-30
3. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815
4. Bouton S, Leboeuf E, Mouille G, Leydecker MT, Talbotec J, Granier F, Lahaye M, Hofte H, Truong HN (2002) QUASIMODO1 encodes a putative membrane-bound glycosyltransferase required for normal pectin synthesis and cell adhesion in Arabidopsis. Plant Cell 14: 2577-2590
5. 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
6. 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
7. Brown DM, Zhang Z, 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
8. Burton RA, Wilson SM, Hrmova M, Harvey AJ, Shirley NJ, Medhurst A, Stone BA, Newbigin EJ, Bacic A, Fincher GB (2006) Cellulose synthase-like CslF genes mediate the synthesis of cell wall (1,3;1,4)-b-D-glucans. Science 311: 1940-1942
9. Caffall KH, Mohnen D (2009) The structure, function, and biosynthesis of plant cell wall pectic polysaccharides. Carbohydr Res 344: 1879-1900
10. Caffall KH, Pattathil S, Phillips SE, Hahn MG, Mohnen D (2009) Arabidopsis thaliana T-DNA mutants implicate GAUT genes in the biosynthesis of pectin and xylan in cell walls and seed testa. Mol Plant 2: 1000-1014
11. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B (2009) The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res 37: D233-D238
12. Cavalier-Smith T (2006) Cell evolution and Earth history: stasis and revolution. Philos Trans R Soc Lond B Biol Sci 361: 969-1006
13. Chatterjee M, Berbezy P, Vyas D, Coates S, Barsby T (2005) Reduced expression of a protein homologous to glycogenin leads to reduction of starch content in Arabidopsis leaves. Plant Sci 168: 501-509
14. Cocuron JC, Lerouxel O, Drakakaki G, Alonso AP, Liepman AH, Keegstra K, Raikhel N, Wilkerson CG (2007) A gene from the cellulose synthase-like C family encodes a b-1,4 glucan synthase. Proc Natl Acad Sci USA 104: 8550-8555
15. Cosgrove DJ (2005) Growth of the plant cell wall. Nat Rev Mol Cell Biol 6: 850-861
16. Coutinho PM, Deleury E, Davies GJ, Henrissat B (2003) An evolving hierarchical family classification for glycosyltransferases. J Mol Biol 328: 307-317
17. Cozzetto D, Kryshtafovych A, Fidelis K, Moult J, Rost B, Tramontano A (2009) Evaluation of template-based models in CASP8 with standard measures. Proteins (Suppl 9) 77: 18-28
18. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188-1190
19. de Duve C (2007) The origin of eukaryotes: a reappraisal. Nat Rev Genet 8: 395-403
20. Delano WL (2002) The PyMOL Molecular Graphics System. http://www.pymol.org (January 5, 2008)
21. Derelle E, Ferraz C, Rombauts S, Rouze P, Worden AZ, Robbens S, Partensky F, Degroeve S, Echeynie S, Cooke R, et al (2006) Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc Natl Acad Sci USA 103: 11647-11652
22. Dhugga KS, Barreiro R, Whitten B, Stecca K, Hazebroek J, Randhawa GS, Dolan M, Kinney AJ, Tomes D, Nichols S, et al (2004) Guar seed beta-mannan synthase is a member of the cellulose synthase super gene family. Science 303: 363-366
23. Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14: 755-763
24. Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, et al (2006) Pfam: clans, Web tools and services. Nucleic Acids Res 34: D247-D251
25. Geisler-Lee J, Geisler M, Coutinho PM, Segerman B, Nishikubo N, Takahashi J, Aspeborg H, Djerbi S, Master E, Andersson-Gunneras S, et al (2006) Poplar carbohydrate-active enzymes: gene identification and expression analyses. Plant Physiol 140: 946-962
26. Gibbons BJ, Roach PJ, Hurley TD (2002) Crystal structure of the autocatalytic initiator of glycogen biosynthesis, glycogenin. J Mol Biol 319: 463-477
27. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100
28. Gouet P, Robert X, Courcelle E (2003) ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res 31: 3320-3323
29. Gray MW, Burger G, Lang BF (1999) Mitochondrial evolution. Science 283: 1476-1481
30. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704
31. Hall BG (2005) Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences. Mol Biol Evol 22: 792-802
32. Henrissat B, Coutinho PM, Davies GJ (2001) A census of carbohydrate-active enzymes in the genome of Arabidopsis thaliana. Plant Mol Biol 47: 55-72
33. Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449: 463-467
34. Katoh K, Kuma K, Toh H, Miyata T (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33: 511-518
35. King N, Westbrook MJ, Young SL, Kuo A, Abedin M, Chapman J, Fairclough S, Hellsten U, Isogai Y, Letunic I, et al (2008) The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature 451: 783-788
36. Kopp J, Bordoli L, Battey JN, Kiefer F, Schwede T (2007) Assessment of CASP7 predictions for template-based modeling targets. Proteins (Suppl 8) 69: 38-56
37. Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, Pupko T, Ben-Tal N (2005) ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res 33: W299-W302
38. Lee C, O'Neill MA, Tsumuraya Y, Darvill AG, Ye ZH (2007a) The irregular xylem9 mutant is deficient in xylan xylosyltransferase activity. Plant Cell Physiol 48: 1624-1634
39. Lee CH, Zhong RQ, Richardson EA, Himmelsbach DS, McPhail BT, Ye ZH (2007b) The PARVUS gene is expressed in cells undergoing secondary wall thickening and is essential for glucuronoxylan biosynthesis. Plant Cell Physiol 48: 1659-1672
40. Lerouxel O, Cavalier DM, Liepman AH, Keegstra K (2006) Biosynthesis of plant cell wall polysaccharides-a complex process. Curr Opin Plant Biol 9: 621-630
41. Letunic I, Bork P (2007) Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23: 127-128
42. Li WZ, Godzik A (2006) CD-HIT: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659
43. Liepman AH, Wilkerson CG, Keegstra K (2005) Expression of cellulose synthase-like (Csl) genes in insect cells reveals that CslA family members encode mannan synthases. Proc Natl Acad Sci USA 102: 2221-2226
44. McFadden GI (2001) Primary and secondary endosymbiosis and the origin of plastids. J Phycol 37: 951-959
45. Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Marechal-Drouard L, et al (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318: 245-250
46. Mohnen D (2008) Pectin structure and biosynthesis. Curr Opin Plant Biol 11: 266-277
47. Mohnen D, Bar-Peled M, Somerville CR (2008) Cell wall polysaccharide synthesis. In ME Himmel, ed, Biomass Recalcitrance: Deconstructing the Plant Cell Wall for Bioenergy. Blackwell Publishing, Singapore, pp 94-159
48. Nobles DR, Brown RM (2004) The pivotal role of cyanobacteria in the evolution of cellulose synthases and cellulose synthase-like proteins. Cellulose 11: 437-448
49. Nobles DR, Romanovicz DK, Brown RM Jr (2001) Cellulose in cyanobacteria: origin of vascular plant cellulose synthase? Plant Physiol 127: 529-542
50. Nuin PA, Wang Z, Tillier ER (2006) The accuracy of several multiple sequence alignment programs for proteins. BMC Bioinformatics 7: 471
51. Ogden TH, Rosenberg MS (2006) Multiple sequence alignment accuracy and phylogenetic inference. Syst Biol 55: 314-328
52. Orfila C, Sørensen SO, Harholt J, Geshi N, Crombie H, Truong HN, Reid JS, Knox JP, Scheller HV (2005) QUASIMODO1 is expressed in vascular tissue of Arabidopsis thaliana inflorescence stems, and affects homogalacturonan and xylan biosynthesis. Planta 222: 613-622
53. Palenik B, Grimwood J, Aerts A, Rouze P, Salamov A, Putnam N, Dupont C, Jorgensen R, Derelle E, Rombauts S, et al (2007) The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci USA 104: 7705-7710
54. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551-556
55. Pauly M, Keegstra K (2008) Cell-wall carbohydrates and their modification as a resource for biofuels. Plant J 54: 559-568
56. Peña MJ, Zhong R, Zhou GK, Richardson EA, O'Neill MA, Darvill AG, York WS, Ye ZH (2007) Arabidopsis irregular xylem8 and irregular xylem9: implications for the complexity of glucuronoxylan biosynthesis. Plant Cell 19: 549-563
57. Penning BW, Hunter CT III, Tayengwa R, Eveland AL, Dugard CK, Olek AT, Vermerris W, Koch KE, McCarty DR, Davis MF, et al (2009) Genetic resources for maize cell wall biology. Plant Physiol 151: 1703-1728
58. Persson K, Ly HD, Dieckelmann M, Wakarchuk WW, Withers SG, Strynadka NCJ (2001) Crystal structure of the retaining galactosyl-transferase LgtC from Neisseria meningitidis in complex with donor and acceptor sugar analogs. Nat Struct Biol 8: 166-175
59. Persson S, Caffall KH, Freshour G, Hilley MT, Bauer S, Poindexter P, Hahn MG, Mohnen D, Somerville C (2007) The Arabidopsis irregular xylem8 mutant is deficient in glucuronoxylan and homogalacturonan, which are essential for secondary cell wall integrity. Plant Cell 19: 237-255
60. Popper ZA (2008) Evolution and diversity of green plant cell walls. Curr Opin Plant Biol 11: 286-292
61. Popper ZA, Fry SC (2003) Primary cell wall composition of bryophytes and charophytes. Ann Bot (Lond) 91: 1-12
62. Price MN, Dehal PS, Arkin AP (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26: 1641-1650
63. Ragauskas AJ, Williams CK, Davison BH, Britovsek G, Cairney J, Eckert CA, Frederick WJ Jr, Hallett JP, Leak DJ, Liotta CL, et al (2006) The path forward for biofuels and biomaterials. Science 311: 484-489
64. Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, et al (2008) The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319: 64-69
65. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574
66. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463: 178-183
67. Sterling JD, Atmodjo MA, Inwood SE, Kumar Kolli VS, Quigley HF, Hahn MG, Mohnen D (2006) Functional identification of an Arabidopsis pectin biosynthetic homogalacturonan galacturonosyltransferase. Proc Natl Acad Sci USA 103: 5236-5241
68. Taji T, Ohsumi C, Iuchi S, Seki M, Kasuga M, Kobayashi M, Yamaguchi-Shinozaki K, Shinozaki K (2002) Important roles of drought- and cold-inducible genes for galactinol synthase in stress tolerance in Arabidopsis thaliana. Plant J 29: 417-426
69. Talavera G, Castresana J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56: 564-577
70. Timmis JN, Ayliffe MA, Huang CY, Martin W (2004) Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet 5: 123-135
71. Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596-1604
72. Vogel JP, Garvin DF, Mockler TC, Schmutz J, Rokhsar D, Bevan MW, Barry K, Lucas S, Harmon-Smith M, Lail K, et al (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463: 763-768
73. Wiggins CA, Munro S (1998) Activity of the yeast MNN1 a-1,3-mannosyltransferase requires a motif conserved in many other families of glycosyltransferases. Proc Natl Acad Sci USA 95: 7945-7950
74. Worden AZ, Lee JH, Mock T, Rouze P, Simmons MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E, Everett MV, et al (2009) Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science 324: 268-272
75. Wu AM, Rihouey C, Seveno M, Hornblad E, Singh SK, Matsunaga T, Ishii T, Lerouge P, Marchant A (2009) The Arabidopsis IRX10 and IRX10-LIKE glycosyltransferases are critical for glucuronoxylan biosynthesis during secondary cell wall formation. Plant J 57: 718-731
76. Wu S, Zhang Y (2007) LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res 35: 3375-3382
77. Yin Y, Mohnen D, Gelineo-Albersheim I, Xu Y, Hahn MG (2010) Glyco-syltransferases of family 8 (GT8). In P Ulvskov, ed, Plant Cell Wall Polysaccharides: Biosynthesis and Bioengineering. Annual Plant Reviews. Blackwell Publishing, Singapore (in press)
78. Yokoyama R, Nishitani K (2004) Genomic basis for cell-wall diversity in plants: a comparative approach to gene families in rice and Arabidopsis. Plant Cell Physiol 45: 1111-1121
79. Yong W, Link B, O'Malley R, Tewari J, Hunter CT, Lu CA, Li X, Bleecker AB, Koch KE, McCann MC, et al (2005) Genomics of plant cell wall biogenesis. Planta 221: 747-751
80. York WS, O'Neill MA (2008) Biochemical control of xylan biosynthesis: which end is up? Curr Opin Plant Biol 11: 258-265
81. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79-92
82. Zhang Y (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9: 40
83. Zhong RQ, Peña MJ, Zhou GK, Nairn CJ, Wood-Jones A, Richardson EA, Morrison WH, Darvill AG, York WS, Ye ZH (2005) Arabidopsis fragile fiber8, which encodes a putative glucuronyltransferase, is essential for normal secondary wall synthesis. Plant Cell 17: 3390-3408