Detail publikace

In Silico Prediction of Genes Coding Efflux Pumps in Clostridium Beijerinckii NRRL B-598

Originální název

In Silico Prediction of Genes Coding Efflux Pumps in Clostridium Beijerinckii NRRL B-598

Anglický název

In Silico Prediction of Genes Coding Efflux Pumps in Clostridium Beijerinckii NRRL B-598

Jazyk

en

Originální abstrakt

Predicting gene function can be very challenging. However, various in silico tools are available for this purpose. Here, we present a bioinformatics study focused on identifying potential genes that code efflux pumps in the strain Clostridium beijerinckii NRRL B-598. This rod-shaped, oxygen-tolerant, spore-forming bacterium is studied especially for its ability to produce acetone-butanol fermentation, with butanol being the main product. Current knowledge suggests that small uncharged molecules, including butanol, are transported out of the clostridial cell not only through a passive process of diffusion, but also due to the activity of efflux pumps. However, an ineffective excretion system together with low butanol tolerance currently present the most significant obstacles for industrial exploitation of butanol production in bacteria. Bioinformatics analysis of the strain C. beijerinckii NRRL B-598 can help us to understand these mechanisms in more detail not only for the studied strain, but also for Gram positive species in general. In this study, we used several online bioinformatics tools for the prediction of genes coding efflux pumps based on sequence information. Our results were verified by comparison with transcriptomic data using RNA-Seq technology. In silico identification of genes coding putative efflux pumps in C. beijerinckii NRRL B-598 will be further investigated in our future work, which will involve performing in vivo and in vitro lab experiments.

Anglický abstrakt

Predicting gene function can be very challenging. However, various in silico tools are available for this purpose. Here, we present a bioinformatics study focused on identifying potential genes that code efflux pumps in the strain Clostridium beijerinckii NRRL B-598. This rod-shaped, oxygen-tolerant, spore-forming bacterium is studied especially for its ability to produce acetone-butanol fermentation, with butanol being the main product. Current knowledge suggests that small uncharged molecules, including butanol, are transported out of the clostridial cell not only through a passive process of diffusion, but also due to the activity of efflux pumps. However, an ineffective excretion system together with low butanol tolerance currently present the most significant obstacles for industrial exploitation of butanol production in bacteria. Bioinformatics analysis of the strain C. beijerinckii NRRL B-598 can help us to understand these mechanisms in more detail not only for the studied strain, but also for Gram positive species in general. In this study, we used several online bioinformatics tools for the prediction of genes coding efflux pumps based on sequence information. Our results were verified by comparison with transcriptomic data using RNA-Seq technology. In silico identification of genes coding putative efflux pumps in C. beijerinckii NRRL B-598 will be further investigated in our future work, which will involve performing in vivo and in vitro lab experiments.

BibTex


@inproceedings{BUT148430,
  author="Kateřina {Jurečková} and Pavlína {Cicková} and Karel {Sedlář} and Jan {Kolek} and Petra {Patáková} and Ivo {Provazník}",
  title="In Silico Prediction of Genes Coding Efflux Pumps in Clostridium Beijerinckii NRRL B-598",
  annote="Predicting gene function can be very challenging. However, various in silico tools are available for this purpose. Here, we present a bioinformatics study focused on identifying potential genes that code efflux pumps in the strain Clostridium beijerinckii NRRL B-598. This rod-shaped, oxygen-tolerant, spore-forming bacterium is studied especially for its ability to produce acetone-butanol fermentation, with butanol being the main product. Current knowledge suggests that small uncharged molecules, including butanol, are transported out of the clostridial cell not only through a passive process of diffusion, but also due to the activity of efflux pumps. However, an ineffective excretion system together with low butanol tolerance currently present the most significant obstacles for industrial exploitation of butanol production in bacteria. Bioinformatics analysis of the strain C. beijerinckii NRRL B-598 can help us to understand these mechanisms in more detail not only for the studied strain, but also for Gram positive species in general. In this study, we used several online bioinformatics tools for the prediction of genes coding efflux pumps based on sequence information. Our results were verified by comparison with transcriptomic data using RNA-Seq technology. In silico identification of genes coding putative efflux pumps in C. beijerinckii NRRL B-598 will be further investigated in our future work, which will involve performing in vivo and in vitro lab experiments.",
  booktitle="BOOK OF ABSTRACTS, FULL PAPERS",
  chapter="148430",
  howpublished="online",
  year="2018",
  month="april",
  pages="1--5",
  type="conference paper"
}