DNA structural and physical properties reveal peculiarities in promoter sequences of the bacterium Escherichia coli K-12
Abstract The gene transcription of bacteria starts with a promoter sequence being recognized by a transcription factor found in the RNAP enzyme, this process is assisted through the conservation of nucleotides as well as other factors governing these intergenic regions. Faced with this, the coding o...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Springer
2021-07-01
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| Series: | SN Applied Sciences |
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| Online Access: | https://doi.org/10.1007/s42452-021-04713-2 |
| _version_ | 1818576603676934144 |
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| author | Gustavo Sganzerla Martinez Scheila de Ávila e Silva Aditya Kumar Ernesto Pérez-Rueda |
| author_facet | Gustavo Sganzerla Martinez Scheila de Ávila e Silva Aditya Kumar Ernesto Pérez-Rueda |
| author_sort | Gustavo Sganzerla Martinez |
| collection | DOAJ |
| description | Abstract The gene transcription of bacteria starts with a promoter sequence being recognized by a transcription factor found in the RNAP enzyme, this process is assisted through the conservation of nucleotides as well as other factors governing these intergenic regions. Faced with this, the coding of genetic information into physical aspects of the DNA such as enthalpy, stability, and base-pair stacking could suggest promoter activity as well as protrude differentiation of promoter and non-promoter data. In this work, a total of 3131 promoter sequences associated to six different sigma factors in the bacterium E. coli were converted into numeric attributes, a strong set of control sequences referring to a shuffled version of the original sequences as well as coding regions is provided. Then, the parameterized genetic information was normalized, exhaustively analyzed through statistical tests. The results suggest that strong signals in the promoter sequences match the binding site of transcription factor proteins, indicating that promoter activity is well represented by its conversion into physical attributes. Moreover, the features tested in this report conveyed significant variances between promoter and control data, enabling these features to be employed in bacterial promoter classification. The results produced here may aid in bacterial promoter recognition by providing a robust set of biological inferences. |
| first_indexed | 2024-12-16T06:16:39Z |
| format | Article |
| id | doaj.art-052889a1abde4986bcdeb12f3053865f |
| institution | Directory Open Access Journal |
| issn | 2523-3963 2523-3971 |
| language | English |
| last_indexed | 2024-12-16T06:16:39Z |
| publishDate | 2021-07-01 |
| publisher | Springer |
| record_format | Article |
| series | SN Applied Sciences |
| spelling | doaj.art-052889a1abde4986bcdeb12f3053865f2022-12-21T22:41:15ZengSpringerSN Applied Sciences2523-39632523-39712021-07-013811010.1007/s42452-021-04713-2DNA structural and physical properties reveal peculiarities in promoter sequences of the bacterium Escherichia coli K-12Gustavo Sganzerla Martinez0Scheila de Ávila e Silva1Aditya Kumar2Ernesto Pérez-Rueda3Programa de Pós-Graduação Em Biotecnologia, Universidade de Caxias Do SulPrograma de Pós-Graduação Em Biotecnologia, Universidade de Caxias Do SulDepartment of Molecular Biology and Biotechnology, Tezpur UniversityInstituto de Investigaciones en Matemáticas Aplicadas Y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica de Yucatán. MéridaAbstract The gene transcription of bacteria starts with a promoter sequence being recognized by a transcription factor found in the RNAP enzyme, this process is assisted through the conservation of nucleotides as well as other factors governing these intergenic regions. Faced with this, the coding of genetic information into physical aspects of the DNA such as enthalpy, stability, and base-pair stacking could suggest promoter activity as well as protrude differentiation of promoter and non-promoter data. In this work, a total of 3131 promoter sequences associated to six different sigma factors in the bacterium E. coli were converted into numeric attributes, a strong set of control sequences referring to a shuffled version of the original sequences as well as coding regions is provided. Then, the parameterized genetic information was normalized, exhaustively analyzed through statistical tests. The results suggest that strong signals in the promoter sequences match the binding site of transcription factor proteins, indicating that promoter activity is well represented by its conversion into physical attributes. Moreover, the features tested in this report conveyed significant variances between promoter and control data, enabling these features to be employed in bacterial promoter classification. The results produced here may aid in bacterial promoter recognition by providing a robust set of biological inferences.https://doi.org/10.1007/s42452-021-04713-2Gene transcriptionTranscription factorsBacteriaEnthalpyFree-stabilityBase-pair stacking |
| spellingShingle | Gustavo Sganzerla Martinez Scheila de Ávila e Silva Aditya Kumar Ernesto Pérez-Rueda DNA structural and physical properties reveal peculiarities in promoter sequences of the bacterium Escherichia coli K-12 SN Applied Sciences Gene transcription Transcription factors Bacteria Enthalpy Free-stability Base-pair stacking |
| title | DNA structural and physical properties reveal peculiarities in promoter sequences of the bacterium Escherichia coli K-12 |
| title_full | DNA structural and physical properties reveal peculiarities in promoter sequences of the bacterium Escherichia coli K-12 |
| title_fullStr | DNA structural and physical properties reveal peculiarities in promoter sequences of the bacterium Escherichia coli K-12 |
| title_full_unstemmed | DNA structural and physical properties reveal peculiarities in promoter sequences of the bacterium Escherichia coli K-12 |
| title_short | DNA structural and physical properties reveal peculiarities in promoter sequences of the bacterium Escherichia coli K-12 |
| title_sort | dna structural and physical properties reveal peculiarities in promoter sequences of the bacterium escherichia coli k 12 |
| topic | Gene transcription Transcription factors Bacteria Enthalpy Free-stability Base-pair stacking |
| url | https://doi.org/10.1007/s42452-021-04713-2 |
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