Classification and identification of Arabidopsis cell wall mutants using Fourier-Transform InfraRed (FT-IR) microspectroscopy.

We have developed a novel procedure for the rapid classification and identification of Arabidopsis mutants with altered cell wall architecture based on Fourier-Transform Infrared (FT-IR) microspectroscopy. FT-IR transmission spectra were sampled from native 4-day-old dark-grown hypocotyls of 46 mutants and the wild type treated with various drugs. The Mahalanobis distance between mutants, calculated from the spectral information after compression with the Discriminant Variables Selection procedure, was used for alpha hierarchical cluster analysis. Despite the completely unsupervised nature of the classification procedure, we show that all mutants with cellulose defects appeared in the same cluster. In addition, mutant alleles of similar strength for several unrelated loci were also clustered, which demonstrates the sensitivity of the method to detect a wide array of cell wall defects. Comparing the cellulose-deficient cluster with the cluster that contained wild-type controls led to the identification of wave numbers that were diagnostic for altered cellulose content in the context of an intact cell wall. The results show that FT-IR spectra can be used to identify different classes of mutants and to characterize cell wall changes at a microscopic level in unknown mutants. This procedure significantly accelerates the identification and classification of cell wall mutants, which makes cell wall polysaccharides more accessible to functional genomics approaches.

[1]  M. Caboche,et al.  Cellular Basis of Hypocotyl Growth in Arabidopsis thaliana , 1997, Plant physiology.

[2]  G. Mouille,et al.  A procedure for the clustering of cell wall mutants in the model plant Arabidopsis based on Fourier-transform infrared (FT-IR) spectroscopy , 2003 .

[3]  Chris Somerville,et al.  Auxin-resistant mutants of Arabidopsis thaliana with an altered morphology , 1987, Molecular and General Genetics MGG.

[4]  D. Delmer,et al.  Modifications of cellulose synthase confer resistance to isoxaben and thiazolidinone herbicides in Arabidopsis Ixr1 mutants , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[5]  M. Caboche,et al.  Procuste1 mutants identify two distinct genetic pathways controlling hypocotyl cell elongation, respectively in dark- and light-grown Arabidopsis seedlings. , 1996, Development.

[6]  Christopher P. Bonin,et al.  The MUR1 gene of Arabidopsis thaliana encodes an isoform of GDP-D-mannose-4,6-dehydratase, catalyzing the first step in the de novo synthesis of GDP-L-fucose. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[7]  C. Hocart,et al.  Cellulose synthesis: mutational analysis and genomic perspectives using Arabidopsis thaliana , 2001, Cellular and Molecular Life Sciences CMLS.

[8]  P. Albersheim,et al.  Requirement of Borate Cross-Linking of Cell Wall Rhamnogalacturonan II for Arabidopsis Growth , 2001, Science.

[9]  P. Quail,et al.  cop1: a regulatory locus involved in light-controlled development and gene expression in Arabidopsis. , 1991, Genes & development.

[10]  N. Chua,et al.  KORRIGAN, an Arabidopsis Endo-1,4-β-Glucanase, Localizes to the Cell Plate by Polarized Targeting and Is Essential for Cytokinesis , 2000, Plant Cell.

[11]  Sophie Bouton,et al.  QUASIMODO1 Encodes a Putative Membrane-Bound Glycosyltransferase Required for Normal Pectin Synthesis and Cell Adhesion in Arabidopsis Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.004259. , 2002, The Plant Cell Online.

[12]  R. Zhong,et al.  A Katanin-like Protein Regulates Normal Cell Wall gBiosynthesis and Cell Elongation , 2001, Plant Cell.

[13]  J. Chory,et al.  A Role for Brassinosteroids in Light-Dependent Development of Arabidopsis , 1996, Science.

[14]  P. Benfey,et al.  Root development in Arabidopsis: four mutants with dramatically altered root morphogenesis. , 1993, Development.

[15]  P. Quail,et al.  Phytochrome photosensory signalling networks , 2002, Nature Reviews Molecular Cell Biology.

[16]  K. Waldron,et al.  The mechanical properties and molecular dynamics of plant cell wall polysaccharides studied by Fourier-transform infrared spectroscopy. , 2000, Plant physiology.

[17]  J. Huvenne,et al.  Investigation of the glycosidic linkages in several oligosaccharides using FT-IR and FT Raman spectroscopies , 1995 .

[18]  C. Chapple,et al.  Substitution of l-Fucose by l-Galactose in Cell Walls of Arabidopsis mur1 , 1996, Science.

[19]  D. Naumann,et al.  Classification and identification of bacteria by Fourier-transform infrared spectroscopy. , 1991, Journal of general microbiology.

[20]  Michael R. Anderberg,et al.  Cluster Analysis for Applications , 1973 .

[21]  S. R. Searle,et al.  The theory of linear models and multivariate analysis , 1981 .

[22]  P. Benfey,et al.  The SABRE gene is required for normal cell expansion in Arabidopsis. , 1995, Genes & development.

[23]  Michael Seibold,et al.  Evaluation of Phenotypic Markers for Selection and Identification of Candida dubliniensis , 2000, Journal of Clinical Microbiology.

[24]  C R Somerville,et al.  The cellulose synthase superfamily. , 2000, Plant physiology.

[25]  Zheng-Hua Ye,et al.  Mutation of a Chitinase-Like Gene Causes Ectopic Deposition of Lignin, Aberrant Cell Shapes, and Overproduction of Ethylene Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.010278. , 2002, The Plant Cell Online.

[26]  P. Benfey,et al.  Conditional root expansion mutants of Arabidopsis. , 1995, Development.

[27]  Michael J Gidley,et al.  Molecular interactions in bacterial cellulose composites studied by 1D FT-IR and dynamic 2D FT-IR spectroscopy. , 2002, Carbohydrate research.

[28]  W Herth,et al.  Molecular analysis of cellulose biosynthesis in Arabidopsis. , 1998, Science.

[29]  M. McCann,et al.  Pectin engineering: modification of potato pectin by in vivo expression of an endo-1,4-beta-D-galactanase. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[30]  B. Usadel,et al.  Rapid Structural Phenotyping of Plant Cell Wall Mutants by Enzymatic Oligosaccharide Fingerprinting1 , 2002, Plant Physiology.

[31]  Nikolaus Wellner,et al.  FT-IR study of plant cell wall model compounds: pectic polysaccharides and hemicelluloses , 2000 .

[32]  D. Bouchez,et al.  Normal differentiation patterns in plants lacking microtubular preprophase bands , 1995, Nature.

[33]  C. Somerville,et al.  Genetic dissection of plant cell-wall biosynthesis. , 2001, Biochemical Society transactions.

[34]  Samantha Vernhettes,et al.  A plasma membrane‐bound putative endo‐1,4‐β‐D‐glucanase is required for normal wall assembly and cell elongation in Arabidopsis , 1998, The EMBO journal.

[35]  Maureen C. McCann,et al.  Infrared microspectroscopy: Sampling heterogeneity in plant cell wall composition and architecture , 1997 .

[36]  S. Turner,et al.  BOTERO1 is required for normal orientation of cortical microtubules and anisotropic cell expansion in Arabidopsis. , 2001, The Plant journal : for cell and molecular biology.

[37]  A. Jauneau,et al.  Altered pectin composition in primary cell walls of korrigan, a dwarf mutant of Arabidopsis deficient in a membrane-bound endo-1,4-β-glucanase , 2001, Planta.

[38]  C. Wilkerson,et al.  Characterization of a Family of Arabidopsis Genes Related to Xyloglucan Fucosyltransferase1 , 2001 .

[39]  Guislaine Refregier,et al.  PROCUSTE1 Encodes a Cellulose Synthase Required for Normal Cell Elongation Specifically in Roots and Dark-Grown Hypocotyls of Arabidopsis , 2000, Plant Cell.

[40]  N. Raikhel,et al.  The mur2 mutant of Arabidopsis thaliana lacks fucosylated xyloglucan because of a lesion in fucosyltransferase AtFUT1 , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[41]  Liangcai Peng,et al.  Fractionation of carbohydrates in Arabidopsis root cell walls shows that three radial swelling loci are specifically involved in cellulose production , 2000, Planta.

[42]  Sandra Pelletier,et al.  Resistance against Herbicide Isoxaben and Cellulose Deficiency Caused by Distinct Mutations in Same Cellulose Synthase Isoform CESA61 , 2002, Plant Physiology.

[43]  P. Benfey,et al.  COBRA encodes a putative GPI-anchored protein, which is polarly localized and necessary for oriented cell expansion in Arabidopsis. , 2001, Genes & development.

[44]  M. McCann,et al.  Fourier-Transform Raman and Fourier-Transform Infrared Spectroscopy (An Investigation of Five Higher Plant Cell Walls and Their Components) , 1994, Plant physiology.

[45]  W. Willats,et al.  Pectin: cell biology and prospects for functional analysis , 2001 .

[46]  W. Lukowitz,et al.  Arabidopsis cyt1 mutants are deficient in a mannose-1-phosphate guanylyltransferase and point to a requirement of N-linked glycosylation for cellulose biosynthesis , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[47]  C. Gillmor,et al.  α-Glucosidase I is required for cellulose biosynthesis and morphogenesis in Arabidopsis , 2002, The Journal of cell biology.

[48]  W. Reiter,et al.  The mur4 mutant of arabidopsis is partially defective in the de novo synthesis of uridine diphospho L-arabinose. , 1999, Plant physiology.

[49]  T. Baskin,et al.  Temperature-sensitive alleles of RSW2 link the KORRIGAN endo-1,4-beta-glucanase to cellulose synthesis and cytokinesis in Arabidopsis. , 2001, Plant physiology.

[50]  P. Lerouge,et al.  KOBITO1 Encodes a Novel Plasma Membrane Protein Necessary for Normal Synthesis of Cellulose during Cell Expansion in Arabidopsis Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.002873. , 2002, The Plant Cell Online.

[51]  David J. Hand,et al.  Discrimination and Classification , 1982 .

[52]  C. Chapple,et al.  Mutants of Arabidopsis thaliana with altered cell wall polysaccharide composition. , 1997, The Plant journal : for cell and molecular biology.

[53]  G. Pelletier,et al.  In planta Agrobacterium-mediated transformation of adult Arabidopsis thaliana plants by vacuum infiltration. , 1998, Methods in molecular biology.

[54]  N. Carpita,et al.  A rapid method to screen for cell-wall mutants using discriminant analysis of Fourier transform infrared spectra. , 1998, The Plant journal : for cell and molecular biology.

[55]  T. Kurata,et al.  petit1, a conditional growth mutant of Arabidopsis defective in sucrose-dependent elongation growth. , 1998, Plant physiology.