Further progress towards a catalogue of all <i>Arabidopsis</i> genes: analysis of a set of 5000 non‐redundant ESTs

Cooke, Richard; Raynal, Monique; Laudié, Michèle; Grellet, Françoise; Delseny, Michel; Morris, P. I.; Guerrier, D.; Giraudat, Jérôme; Quigley, Françoise; Clabault, Gerard; Li, Youfang; Mache, Régis; Krivitzky, Micheline; Gy, Isabelle; Kreis, Martin E.; Lecharny, Alain; Parmentier, Yves; Marbach, J.; Fleck, Jacqueline; Clément, Bernadette; Philipps, Gabriel; Hervé, Christine; Bardet, Claude; Trémousaygue, Dominique; Lescure, Bernard; Lacomme, Christophe; Roby, Dominique; Jourjon, Marie‐Françoise; Chabrier, Patrick; Charpenteau, Jean-Louis; Desprez, Thierry; Amselem, Joëlle; Chiapello, H; Höfte, Monica

doi:10.1046/j.1365-313x.1996.09010101.x

Cited by 193 publications

(100 citation statements)

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“…It is envisaged that, within the foreseeable future, most if not all of the genes in several plants will be available in public access data bases. However, it has also been estimated that the function of at least 70% of the Arabidopsis genes alone, at present, cannot be identified by sequence homology to genes or proteins that have already been designated a function (7,8). Therefore, having prior knowledge relating to a gene, such as its expression pattern or the eventual location of the expressed protein, may help in elucidating function.…”

Section: Discussionmentioning

confidence: 99%

“…The reasons for choosing these species relates to their academic and commercial interest. Arabidopsis has not been as extensively used in tissue culture but is currently the target of an extensive EST 1 sequencing exercise, and an international program aimed at the sequencing of its entire genome is under way (7,8). Carrot, a member of the Umbelliferae, has been an important species in modeling embryogenesis and elongation growth (9).…”

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Differential Extraction and Protein Sequencing Reveals Major Differences in Patterns of Primary Cell Wall Proteins from Plants

Robertson¹,

Mitchell²,

Gilroy³

et al. 1997

Journal of Biological Chemistry

123

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The proteins of the primary cell walls of suspension cultured cells of five plant species, Arabidopsis, carrot, French bean, tomato, and tobacco, have been compared. The approach that has been adopted is differential extraction followed by SDS-polyacrylamide gel electrophoresis (PAGE), rather than two-dimensional gel analysis, to facilitate protein sequencing. Whole cells were washed sequentially with the following aqueous solutions, CaCl 2 , CDTA (cyclohexane diaminotetraacetic acid, DTT (dithiothreitol), NaCl, and borate. SDS-PAGE analysis showed consistent differences between species. From the 233 proteins that were selected for sequencing, 63% gave N-terminal data. This analysis shows that (i) patterns of proteins revealed by SDS-PAGE are strikingly different for all five species, (ii) a large number of these proteins cannot be identified by data base searches indicating that a significant proportion of wall proteins have not been previously described, (iii) the major proteins that can be identified belong to very different classes of proteins, (iv) the majority of proteins found in the extracellular growth media are absent from their respective cell wall extracts, and (v) the results of the extraction process are indicative of higher order structure. It appears that aspects of speciation reside in the complement of extracellular wall proteins. The data represent a protein resource for cell wall studies complementary to EST (expressed sequence tag) and DNA sequencing strategies.The plant cell wall is a dynamic system generally considered to be composed of more than 90% carbohydrate polymers. Proteins, phenolics and possibly lipids make up the remainder of the wall (1-3). To date, most research interest has been in the carbohydrate components because of considerations of their structural role and commercial interest. This has led to a number of models for the integration, interpolymeric association, and assembly of the wall (3, 4). By comparison, our knowledge of the complexity of protein in the plant cell wall is in a less advanced state. Much of the understanding of the range of structural wall proteins has come from cDNA and genomic cloning exercises and has led to the identification of glycine-, cysteine-, proline-, and hydroxyproline-rich subsets of wall proteins. In addition, many extracellular enzymes have been identified that are required for the restructuring and modification of this dynamic extracellular matrix which underpin its role in defense, detoxification, signaling, cell-cell recognition, cell expansion, cell adhesion, cell separation, translocation, differentiation, and morphogenesis (2, 5, 6). However, there is a lack of direct studies on the proteins themselves and the true range of extracellular proteins and their species differences remains to be elucidated. The present work describes the systematic extraction and sequencing of the major primary wall proteins from five species representing four families of plants.Since whole plant tissue is complicated by the presence of different tissue...

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

Differential Extraction and Protein Sequencing Reveals Major Differences in Patterns of Primary Cell Wall Proteins from Plants

Robertson¹,

Mitchell²,

Gilroy³

et al. 1997

Journal of Biological Chemistry

123

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“…These represent 62 nonredundant sequences. No conclusions can be drawn about the relative levels of expression of the various genes based on the number of ESTs identified for each gene because EST clones are not sequenced at random from the source libraries (Cooke et al, 1996;Newman et al, 1994). However, most genes were represented by a single R-EST, suggesting that the genes analyzed are not highly expressed.…”

Section: Identification Of R-ests and Pto-like Sequencesmentioning

confidence: 99%

Map positions of 47 Arabidopsis sequences with sequence similarity to disease resistance genes

et al. 1997

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“…Remaining sequences were inspected and those which contained ambiguous base calls were further trimmed to a maximum length of 330 bases. This length was chosen as it is the average length of sequences submitted to EMBL by the European sequencing consortium (Cooke et aL, 1996;H6fte et aL, 1993) and thus corresponds to the average length of high-quality sequence data which can be obtained from a singlepass sequencing run. These trimming criteria were applied to all sequences from the American project (Newman et aL, 1994).…”

Section: Assembly Of Contigsmentioning

confidence: 99%

Identification of members of gene families in Arabidopsis thaliana by contig construction from partial cDNA sequences: 106 genes encoding 50 cytoplasmic ribosomal proteins

et al. 1997

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SummaryPartial cDNA sequencing to obtain expressed sequence tags (ESTs) has led to the identification of tags to about 8000 of the estimated 20 000 genes in Arabidopsis thaliana. This figure represents four to five times the number of complete coding sequences from this organism available in international databases. In contrast to mammals, many proteins are encoded by multigene families in A. thaliana. Using ribosomal protein gene families as an example, it is possible to construct relatively long sequences from overlapping ESTs which are of sufficiently high quality to be able to unambiguously identify tags to individual members of multigene families, even when the sequences are highly conserved. A total of 106 genes encoding 50 different cytoplasmic ribosomal protein types have been identified, most proteins being encoded by at least two and up to four genes. Coding sequences of members of individual gene families are almost always very highly conserved and derived amino acid sequences are almost, if not completely, identical in the vast majority of cases. Sequence divergence is observed in untranslated regions which allows the definition of gene-specific probes. The method can be used to construct high-quality tags to any protein.

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Further progress towards a catalogue of all Arabidopsis genes: analysis of a set of 5000 non‐redundant ESTs

Cited by 193 publications

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Differential Extraction and Protein Sequencing Reveals Major Differences in Patterns of Primary Cell Wall Proteins from Plants

Differential Extraction and Protein Sequencing Reveals Major Differences in Patterns of Primary Cell Wall Proteins from Plants

Map positions of 47 Arabidopsis sequences with sequence similarity to disease resistance genes

Identification of members of gene families in Arabidopsis thaliana by contig construction from partial cDNA sequences: 106 genes encoding 50 cytoplasmic ribosomal proteins

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