EXPRESSED SEQUENCE TAGS ESTs

When the Arabidopsis Expressed Sequence Tag (EST) Database was searched with the tomato fmit Psubunit protein sequence two related cDNAs were identified (Figure 11). cDNA 2 is near full length and has been completely sequenced, cDNA 1 has also been sequenced but currently lacks approximately 100 amino acids of coding region. The two Arabidopsis cDNAs are 81% identical at the protein level and have lower identity to the protein encoded by tomato gene 1, 64 and 63% for cDNA 1 and cDNA 2, respectively. However, both cDNAs encode... 

TES-32 is the most abundant single protein product secreted by the parasite. It is also heavily labelled by surface iodination of live larvae (Maizels et al., 1984, 1987), and is known by monoclonal antibody reactivity to be expressed in the cuticular matrix of the larval parasite (Page et al, 1992a). TES-32 was cloned by matching peptide sequence derived from gel-purified protein to an expressed sequence tag (EST) dataset of randomly selected clones from a larval cDNA library (Loukas et al., 1999). Because of the high level of expression of TES-32 mRNA, clones encoding this protein were repeatedly sequenced and deposited in the dataset (Tetteh et al., 1999). Full sequence determination showed a major domain with similarity to mammalian C-type (calcium-dependent) lectins (C-TLs), together with shorter N-terminal tracts rich in cysteine and threonine residues. Native TES-32 was then shown to bind to immobilized monosaccharides in a calcium-dependent manner (Loukas et al., 1999). 

Expressed Sequence Tags (ESTs) and Computational Biology ... 

Expressed sequence tag (EST) analysis of cDNAs from specific plant tissues has proved to be a valuable tool for the identification of genes for secondary metabolite biosynthesis.36 We have used this approach to identify two distinct sequences predicted to encode OSCs from cDNA libraries from roots of diploid oat (Avena strigosa).35 One of these sequences is highly homologous to cycloartenol... 

PMF is generally used to identify proteins that have been previously separated by 2-D GE so that additional information including the molecular weights and isoelectric points can be used to supplement PMF identification. PMF is not well suited for searching expressed sequence tag (EST) databases that contain incomplete gene coding information for particular ESTs and it is not adequate for the analysis of complex protein mixtures in solution. 

Wolfsberg, T. G., and Landsman, D. (1997). A comparison of expressed sequence tags (ESTs) two human genomic sequences. Nucl. Adds Res. 25, 1626-1632. 

Expressed Sequence Tags and In Silico Methods Expressed sequence tags (ESTs) are short nucleotide sequences of complementary DNA with about 200-500 base pairs. They are parts of the DNA that code for the expression of particular proteins. EST sequencing provides a rapid method to scan for all the protein coding genes and to provide a tag for each gene on the genome. 

Potato type II (Potll) inhibitors are disulfide-rich peptides of approximately 50 amino acids in size. They were first discovered in leaves, seeds, and other organs of Solanaceae and are a source of much interest as plant defense proteins. Recently, Barta et analyzed expressed sequence tag (EST) and genomic data and discovered 11 genes that code for Potll inhibitors in various monocotyledonous and dicotyledonous plants. Potll inhibitors are expressed as large precursor proteins that contain up to eight sequence repeats of the inhibitor precursor. In one particularly fascinating case from the ornamental tobacco (N. data), the precursor adopts a circular permuted structure.Barta et al. observed that genes outside the Solanaceae family seem... 

In C. Clementina Hort. ex Tanaka x C reticulata, Blanco (fortune mandarin), two PAL genes (AJ238753 and AJ238754) were isolated from a flavedo cDNA library and subsequent Southern blot analysis confirmed that two or more copies of the gene were present in the genome [28]. In silico analysis of expressed sequence tags (ESTs) from C. sinensis (L) Osbeck identified three putative PAL isoforms in this species [29]. Most species analyzed to date (reviewed in 30, 31) have also shown that PAL is encoded by a multigene family. 

The second approach is the tandem mass spectrometric method (Wilm et ah, 1996 Link et ah, 1999 Yates, 2000). This method relies on fragmentation of individual peptides in the tryptic peptide mixture to gain sequence information. Its main advantage is that sequence information derived from several peptides is much more specific for the identification of a protein than a list of peptide masses. The sequence data can be used to search not only protein sequence databases but also nucleotide databases such as expressed sequence tag (EST) databases and, more recently, even... 

The advent of rapid DNA cloiung and sequencing techniques, and the pubhc availability of nucleotide sequence information from the tikes of ttie tiuman genome sequencing project, various expressed sequence tag (EST) databases, and various... 

The paper that introduced expressed sequence tags (ESTs). 

Mapping of eukaryotic chromosomes has involved additional methods which are discussed in Sections E and G,l. These incluse radiation hybrid mapping,104 use of meiotic recombination, identification of restriction fragment length polymorphisms (RFLPs described in Section E,7), and use of expressed sequence tags (ESTs), short DNA sequences deduced from mRNA molecules transcribed from the DNA.105 106... 

Efforts to elucidate the genetic basis of biosynthetic pathways tend to result in the identification of structural genes, i.e. genes encoding enzymes that catalyze the conversion of intermediates in a specific pathway. This is in part due to the relatively high expression of the structural genes, which results in abundant representation in expressed sequence tag (EST) libraries, or high probability of identification when cDNA subtraction methods or other methods that rely on differential expression are used. 

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