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Abstract
Some newly synthesized proteins require the assistance of molecular chaperones for their correct folding. Chaperones are also involved in the dissolution of protein aggregates making their study significant for both biotechnology and medicine and the identification of chaperones and stress-related protein sequences in different organisms is an important task. We used bioinformatic tools to investigate the information generated by the Sugarcane Expressed Sequence Tag (SUCEST) genome project in order to identify and annotate molecular chaperones. We considered that the SUCEST sequences belonged to this category of proteins when their E-values were lower than 1.0e-05. Our annotation shows that 4,164 of the 5’ expressed sequence tag (EST) sequences were homologous to molecular chaperones, nearly 1.8% of all the 5’ ESTs sequenced during the SUCEST project. About 43% of the chaperones which we found were Hsp70 chaperones and its co-chaperones, 10% were Hsp90 chaperones and 13% were peptidyl-prolyl cis, trans isomerase. Based on the annotation results we predicted 156 different chaperone gene subclasses in the sugarcane genome. Taken together, our results indicate that genes which encode chaperones were diverse and abundantly expressed in sugarcane cells, which emphasizes their biological importance.
Highlights
Large-scale cDNA sequencing has become a fast and satisfactory alternative to the complete sequencing of the entire genome of an organism
The information available at sugarcane expressed sequence tag (SUCEST) was searched for the annotation of molecular chaperone genes by homology comparison with public databases using bioinformatic tools
The results were used to predict gene expression profiles based on the gross number of annotated 5’ expressed sequence tag (EST) sequences
Summary
Large-scale cDNA sequencing has become a fast and satisfactory alternative to the complete sequencing of the entire genome of an organism. By generating and sequencing cDNAs researchers can obtain the coded information of the genes responsible for different mRNAs, and these partial cDNA sequences (known as expressed sequence tags or ESTs) can quickly provide information on the genetic profile of an organism by using bioinformatics to mine sequences in public databases and annotation the original ESTs by homology. This approach was used by us to identify chaperones in the Brazilian sugarcane expressed sequence tag (SUCEST) database More than twenty chaperone families have been described according to their molecular weight and biochemical function (Cowan and Lewis, 1999), the most important families of chaperones and stress-related proteins being summarized in the few paragraphs
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