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Oligonucleotide Probe Design for the Study of Cellulolytic and Solventogenic Genes in Colombian Clostridiumsp. strains (Clostridiaceae)

Authors :
José David Montoya Solano
Zulma Rocío Suárez Moreno
Diego Mauricio Riaño Pachón
Dolly Montoya Castaño
Fabio Ancízar Aristizábal Gutiérrez
Source :
Acta Biológica Colombiana, Vol 12, Iss 0, Pp 55-74 (2007)
Publication Year :
2007
Publisher :
Universidad Nacional de Colombia, 2007.

Abstract

The goal of the present study was to analyze the metabolic pathways involved in solvent production and cellulose consumption by promising Colombian native strains of the genus Clostridium. Therefore a set of oligonucleotide probes was designed, with the aim of analyzing potential targets for genetic improvement of the Colombian strains. The database named MULTICLOST was created in Microsoft Access® using the sequences from 485 genes involved in solventogenesis, 1,3propanodiol production and cellulolysis from 45 bacterial and 10 fungal species. The genes were grouped according to their respective enzyme function and to the catalytic domain or the substrate binding domain in the case of cellulases. ClustalW 1.83 was used for multiple alignment of every group. Subgroups of sequences with more than 50% identity among themselves were created. Conserved sequences longer than 19 nucleotides were identified using GeneDoc 2.6.002 and their thermodynamic values were calculated with GeneRunner v3.05, while their sensitivity and specificity were verified by searching in GenBank with BLASTN 2.2.8. Ninetyfour conserved sequences were obtained with an average 24nucleotide length, 65.8ºC average Tm and a (G+C) content between 14.3% and 60.0%. None of these probes forms stable secondary structures at temperatures higher than 36.1ºC. According to the former results, all of the probes could be used in an oligonucleotide microarray or in PCR reactions for the identification of metabolic targets for improvement of the industrial process.

Details

Language :
English, Spanish; Castilian
ISSN :
0120548X and 19001649
Volume :
12
Issue :
0
Database :
Directory of Open Access Journals
Journal :
Acta Biológica Colombiana
Publication Type :
Academic Journal
Accession number :
edsdoj.bef987ae1f174e0386f9ab1ca64c83d8
Document Type :
article