Kashif Raza Siddique,
- Student, Department of Biotechnology, Goel Institute of Technology and Management, Uttar Pradesh, India
Abstract
ORI sites serve a critical function in DNA replication serving as the beginning point of the process. Identifying the spots appropriately means a lot and is important for the biologists working in the lab. Detecting the ORI is not only vital for the detection of replication sites but is also important in numerous biological processes. In this study, we offer a unique approach employing Python-based motif analysis to discover the ORI sites within the supplied genomic sequence. It also highlights the problems of finding the ORI site and what are the alternatives. The sequence of the nucleotides or the genome sequence of the organisms that are utilized in this study as a reference for the detection of ORI has been supplied in the reference section. In this study, we discuss the method will discovering the ORI of different organisms, we also share open-source Python programs and the genomic sequence that we utilized while completing this research. This research contributes to advance the field of bioinformatics by establishing a user-friendly framework for ORI site discovery, simplifying key exploration into DNA replication mechanisms and genome dynamics. In this paper, we have also spoken about the motif and the features. Also defined the circadian cycle and gene expressions and talked about the evening elements. Using skew arrays will increase the results and it will undoubtedly aid in detecting the ORI of complicated organisms like E. coli.
Keywords: ORI sites, DNA replication, Python-based motif analysis, Genomic sequence, Bioinformatics
[This article belongs to International Journal of Brain Sciences(ijbs)]
References
- Jacob, F., Brenner, S. & Cuzin, F. On the regulation of DNA replication in bacteria. Cold Spring Harbor Symposia on Quantitative Biology 28, 329–348, https://doi.org/10.1101/sqb.1963.028.01.048 (1963).
- Messer, W. The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. FEMS Microbiology Reviews 26, 355–374, https://doi.org/10.1111/j.1574-6976.2002.tb00620.x (2002).
- Harrison, P. W., Lower, R. P., Kim, N. K. & Young, J. P. W. Introducing the bacterial ‘chromid’: not a chromosome, not a plasmid. Trends in Microbiology 18, 141–148, https://doi.org/10.1016/j.tim.2009.12.010 (2010).
- Gao, F. Bacteria may have multiple replication origins. Front. Microbiol. 6, https://doi.org/10.3389/fmicb.2015.00324 (2015).
- Zakrzewska-Czerwińska, J., Jakimowicz, D., Zawilak-Pawlik, A. & Messer, W. Regulation of the initiation of chromosomal replication in bacteria. FEMS Microbiology Reviews 31, 378–387, https://doi.org/10.1111/j.1574-6976.2007.00070.x (2007).
- Leonard, A. C. & Grimwade, J. E. Te orisome: structure and function. Front. Microbiol. 6, https://doi.org/10.3389/fmicb.2015.00545 (2015).
- Krause, M., Rückert, B., Lurz, R. & Messer, W. Complexes at the replication origin of Bacillus subtilis with homologous and heterologous DnaA protein. Journal of Molecular Biology 274, 365–380, https://doi.org/10.1006/jmbi.1997.1404 (1997).
- Brilli, M. et al. Te diversity and evolution of cell cycle regulation in alpha-proteobacteria: a comparative genomic analysis. BMC Systems Biology 4, 52, https://doi.org/10.1186/1752-0509-4-52 (2010).
- Jaworski, P. et al. Unique and universal features of epsilon proteobacteria origins of chromosome replication and DnaA-DnaA box interactions. Frontiers in Microbiology 7, 1555, https://doi.org/10.3389/fmicb.2016.01555 (2016).
- Richardson, T. T., Harran, O. & Murray, H. Te bacterial DnaA-trio replication origin element specifes single-stranded dna initiator binding. Nature 534, 412–416, https://doi.org/10.1038/nature17962 (2016).
- Ryan, V. T., Grimwade, J. E., Camara, J. E., Crooke, E. & Leonard, A. C. Escherichia coli prereplication complex assembly is regulated by the dynamic interplay among fs, IHF, and DnaA. Molecular Microbiology 51, 1347–1359, https://doi.org/10.1046/j.1365-2958.2003. 03906.x (2004).
- Bramhill, D. & Kornberg, A. Duplex opening by dnaA protein at novel sequences in the initiation of replication at the origin of the E. coli chromosome. Cell 52, 743–755, https://doi.org/10.1016/0092-8674(88)90412-6 (1988).
- Kowalski, D. & Eddy, M. J. Te DNA unwinding element: a novel, cis-acting component that facilitates the opening of the Escherichia coli replication origin. EMBO J. 8, 4335–4344 (1989).
- Marczynski, G. T., Rolain, T. & Taylor, J. A. Redefining bacterial origins of replication as centralized information processors. Front. Microbiol. 6, https://doi.org/10.3389/fmicb.2015.00610 (2015).
- Song, C., Zhang, S. & Huang, H. Choosing a suitable method for the identification of replication origins in microbial genomes. Front. Microbiol. 6, https://doi.org/10.3389/fmicb.2015.01049 (2015).
- Song, J., Ware, A. & Liu, S.-L. Wavelet to predict bacterial ori and ter: a tendency towards a physical balance. BMC Genomics 4, 17, https://doi.org/10.1186/1471-2164-4-17 (2003).
- Gao, F. & Zhang, C.-T. Ori-finder: A web-based system for funding oriCs in unannotated bacterial genomes. BMC Bioinformatics 9, 79, https://doi.org/10.1186/1471-2105-9-79 (2008).
- Kundal, S., Lohiya, R. & Shah, K. iCorr: Complex correlation method to detect the origin of replication in prokaryotic and eukaryotic genomes. arXiv (2016).
- Maderankova, D., Sedlar, K., Vitek, M. & Skutkova, H. Te identification of replication origin in bacterial genomes by cumulated phase signal. In 2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), https:// doi.org/10.1109/cibcb.2017.8058561 (IEEE, 2017).
- Zhang, G. & Gao, F. Quantitative analysis of the correlation between AT and GC biases among bacterial genomes. PLOS ONE 12, e0171408, https://doi.org/10.1371/journal.pone.0171408 (2017).
- Lobry, J. A simple vectorial representation of DNA sequences for the detection of replication origins in bacteria. Biochimie 78, 323–326, https://doi.org/10.1016/0300-9084(96)84764-x (1996).
- Mackiewicz, P. Where does bacterial replication start? Rules for predicting the oriC region. Nucleic Acids Research 32, 3781–3791, https://doi.org/10.1093/nar/gkh699 (2004).
- Luo, H., Zhang, C.-T. & Gao, F. Ori-under 2, an integrated tool to predict replication origins in the archaeal genomes. Frontiers in Microbiology 5, https://doi.org/10.3389/fmicb.2014.00482 (2014).
- Gao, F. & Zhang, C.-T. DoriC: a database of oriC regions in bacterial genomes. Bioinformatics 23, 1866–1867, https://doi. org/10.1093/bioinformatics/btm255 (2007).
- Gao, F., Luo, H. & Zhang, C.-T. DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes. Nucleic Acids Research 41, D90–D93, https://doi.org/10.1093/nar/gks990 (2012).
Volume | 01 |
Issue | 02 |
Received | March 25, 2024 |
Accepted | April 25, 2024 |
Published | April 29, 2024 |