Identification and in silico expression pattern analysis of Eucalyptus expressed sequencing tags (ESTs) encoding molecular chaperones

Expressed Sequence Tags (ESTs) sequencing provides reliable and useful information concerning gene expression patterns in the genomic context. Our group used bioinformatics to identify and annotate 5'EST-contigs belonging to the molecular chaperones within the Eucalyptus Genome Sequencing Project Consortium (FORESTs) database. We found that 1,959 5'EST-contigs, or approximately 1.6% of the total 5'EST-contigs, encoded chaperones, emphasizing their biological importance. About 55% of the chaperones that we found were Hsp70 chaperones and its co-chaperones, 18% were Hsp90 chaperones, 15% were Hsp60 and its co-chaperone, 8% were Hsp100 chaperones, and 4% were Small Hsps. We also investigated the digital expression profile of the chaperone genes to gain information on gene expression levels in the different libraries and we found that molecular chaperones may have differential expression. The results discussed here give important hints about the role of chaperones in Eucalyptus cells

In silico identification of potential chaperone genes that belong to type III and type IV secretion systems in Xanthomonas axonopodis pv citri

The secretion of bacterial virulence factors and flagellar components requires the assistance of specific type III and flagellar chaperones. Standard computational annotation of the genome of Xanthomonas axonopodis pv citri, a plant pathogen that causes citrus canker, initially did not identify any genes belonging to these chaperone categories since the primary sequence homology between them was very low. However, in a search for hypothetical proteins with characteristics similar to these chaperones, we have now identified 30 chromosomal and 10 plasmidial potential genes encoding chaperones belonging to types III/IV, and flagellar secretion systems in this organism. The significance of these findings is discussed.

Molecular chaperone genes in the sugarcane expressed sequence database (SUCEST)

Algumas proteínas ao serem sintetizadas necessitam do auxílio de chaperones moleculares para seu correto enovelamento. Chaperones também estäo envolvidas na dissoluçäo de agregados protéicos, fazendo com que seu estudo seja de relevância biotecnológica e médica. Portanto, a identificaçäo de seqüências de chaperones moleculares é uma tarefa importante. Nós usamos ferramentas de bioinformática para procurar informações geradas pelo sugarcane EST Genome Project (SUCEST) a fim de identificar e anotar chaperones e proteínas relacionadas ao estresse. As seqüências do SUCEST eram anotadas como pertencentes a uma categoria de proteínas se o E-value encontrado fosse menor que 1,0e-05. Nossas anotações mostram que 4.164 seqüências 5' EST säo homólogas a chaperones moleculares, aproximadamente 1,8 por cento de todos os 5' EST que foram seqüenciados pelo SUCEST. Deste total, cerca de 44 por cento pertence à família Hsp70 e suas co-chaperones, 10 por cento à família Hsp90 e 13 por cento à peptidil cis, trans isomerase. Do resultado da anotaçäo, nós predizemos a existência de 156 diferentes subclasses de genes relacionados a chaperones no genoma da cana-de-açúcar. Juntos, nossos resultados apontam que os genes que codificam para estas proteínas säo diversos e abundantemente expressos, o que enfatiza sua importância biológica.