Oligonucleotide Probe Design for the Study of Cellulolytic and Solventogenic Genes in Colombian Clostridiumsp. strains (Clostridiaceae)
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...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Universidad Nacional de Colombia
2007-08-01
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| Series: | Acta Biológica Colombiana |
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| Online Access: | https://revistas.unal.edu.co/index.php/actabiol/article/view/27241 |
| _version_ | 1818513168218980352 |
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| author | José David Montoya Solano Zulma Rocío Suárez Moreno Diego Mauricio Riaño Pachón Dolly Montoya Castaño Fabio Ancízar Aristizábal Gutiérrez |
| author_facet | José David Montoya Solano Zulma Rocío Suárez Moreno Diego Mauricio Riaño Pachón Dolly Montoya Castaño Fabio Ancízar Aristizábal Gutiérrez |
| author_sort | José David Montoya Solano |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-10T23:57:26Z |
| format | Article |
| id | doaj.art-bef987ae1f174e0386f9ab1ca64c83d8 |
| institution | Directory Open Access Journal |
| issn | 0120-548X 1900-1649 |
| language | English |
| last_indexed | 2024-12-10T23:57:26Z |
| publishDate | 2007-08-01 |
| publisher | Universidad Nacional de Colombia |
| record_format | Article |
| series | Acta Biológica Colombiana |
| spelling | doaj.art-bef987ae1f174e0386f9ab1ca64c83d82022-12-22T01:28:33ZengUniversidad Nacional de ColombiaActa Biológica Colombiana0120-548X1900-16492007-08-01120557424248Oligonucleotide Probe Design for the Study of Cellulolytic and Solventogenic Genes in Colombian Clostridiumsp. strains (Clostridiaceae)José David Montoya Solano0Zulma Rocío Suárez Moreno1Diego Mauricio Riaño Pachón2Dolly Montoya Castaño3Fabio Ancízar Aristizábal Gutiérrez4Universidad Nacional de ColombiaLaboratorios ICGEBUniversidad de PotsdamUniversidad Nacional de ColombiaUniversidad Nacional de ColombiaThe 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.https://revistas.unal.edu.co/index.php/actabiol/article/view/27241Sondas de OligonucleótidosClostridium SPMicroarreglosBioinformática |
| spellingShingle | José David Montoya Solano Zulma Rocío Suárez Moreno Diego Mauricio Riaño Pachón Dolly Montoya Castaño Fabio Ancízar Aristizábal Gutiérrez Oligonucleotide Probe Design for the Study of Cellulolytic and Solventogenic Genes in Colombian Clostridiumsp. strains (Clostridiaceae) Acta Biológica Colombiana Sondas de Oligonucleótidos Clostridium SP Microarreglos Bioinformática |
| title | Oligonucleotide Probe Design for the Study of Cellulolytic and Solventogenic Genes in Colombian Clostridiumsp. strains (Clostridiaceae) |
| title_full | Oligonucleotide Probe Design for the Study of Cellulolytic and Solventogenic Genes in Colombian Clostridiumsp. strains (Clostridiaceae) |
| title_fullStr | Oligonucleotide Probe Design for the Study of Cellulolytic and Solventogenic Genes in Colombian Clostridiumsp. strains (Clostridiaceae) |
| title_full_unstemmed | Oligonucleotide Probe Design for the Study of Cellulolytic and Solventogenic Genes in Colombian Clostridiumsp. strains (Clostridiaceae) |
| title_short | Oligonucleotide Probe Design for the Study of Cellulolytic and Solventogenic Genes in Colombian Clostridiumsp. strains (Clostridiaceae) |
| title_sort | oligonucleotide probe design for the study of cellulolytic and solventogenic genes in colombian clostridiumsp strains clostridiaceae |
| topic | Sondas de Oligonucleótidos Clostridium SP Microarreglos Bioinformática |
| url | https://revistas.unal.edu.co/index.php/actabiol/article/view/27241 |
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