Using the IMG/M and CollecTC Databases to Analyze Bacterial Genomic and Transcription Factor Binding Sites

     The databases I will be utilizing in my research this week are the Integrated Microbial Genomes and Microbiomes (IMG/M) database and the CollecTF database. IMG/M is a microbial genomics database created by the United States’ Department of Energy for the purpose of cataloguing microbial genomic datasets (Chen, Chu, Palaniappan, et al., 2021) (Mukherjee, Stamatis, Bertsch, et al., 2021), while CollecTF indexes transcription factor binding sites in bacteria (Kiliç, White, Sagitova, et al.,2014). A transcription factor is a protein that binds to a specific domain of DNA, thus enabling RNA polymerase to catalyze the transcription of that portion of DNA into RNA. 

The IMG/M website contains an absolutely baffling amount of information; the breadth and thoroughness of the project is admirable and impressive, if not difficult for someone inexperienced with the website, such as myself, to navigate. After a little trial and error I managed to navigate to a list of human host-associated; here are three of the bacteria I found on the IMG/M database, as well as the ecosystem details provided by the database. 

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Next I will be utilizing the CollecTC database to gather information on the transcription factors of Deinococcus-Thermus, an extremophile species of bacterium (Gupta, 2011). CollecTC returned only one known transcription factor in Deinococcus-Thermus, CsoR, a copper-binding protein thought to repress DNA transcription in Deinococcus-Thermus when deficient in copper ions. In the presence of copper ions, copper binds CsoR, resulting in CsoR ceasing to bind to DNA, thereby halting the CsoR induced transcriptional repression of downstream genes that, to the best of my understanding, encode CopZ, a copper chaperon that transports copper ions to the enzyme ATPase CopA (ATPase CopA is also encoded by the genes repressed during CsoR activation). ATPase CopA then hydrolyzes ATP to ADP, thereby producing enough chemical energy to pump copper atoms outside of the cell’s cytoplasm and into its outer plasma membrane (Sakamoto, Agari Y., Agari K., et al., 2010). CsoR essentially enables Deinococcus-Thermus to regulate the amount of copper it intakes by halting its DNA regulatory processes when copper concentration becomes too great, which results in the encoding of proteins that are capable of removing the excess copper from the cell’s interior. 

Furthermore, CollecTF describes the CsoR transcription factor in Deinococcus-Thermus as having an inverted repeat motif and a GC-content of 69.23%. In addition, there is a regulatory mode of 100%, a tetramer conformation of 100%, and 1 motif-associated binding site. CollecTF also provided the following detailed view of the information provided: 

References

Gupta RS. Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure
rather than endosymbiosis likely led to the evolution of bacterial cells with two
membranes. Antonie Van Leeuwenhoek. 2011;100(2):171-182.
doi:10.1007/s10482-011-9616-8

I-Min A Chen, Ken Chu, Krishnaveni Palaniappan, Anna Ratner, Jinghua Huang, Marcel
Huntemann, Patrick Hajek, Stephan Ritter, Neha Varghese, Rekha Seshadri,
Simon Roux, Tanja Woyke, Emiley A Eloe-Fadrosh, Natalia N Ivanova, Nikos C
Kyrpides, The IMG/M data management and analysis system v.6.0: new tools
and advanced capabilities, Nucleic Acids Research, Volume 49, Issue D1, 8
January 2021, Pages D751–D763, https://doi.org/10.1093/nar/gkaa939

Kiliç S, White ER, Sagitova DM, Cornish JP, Erill I. CollecTF: a database of
experimentally validated transcription factor-binding sites in Bacteria. Nucleic
Acids Res. 2014 Jan;42(Database issue):D156-60. doi: 10.1093/nar/gkt1123.
Epub 2013 Nov 14. PMID: 24234444; PMCID: PMC3965012.

Sakamoto K, Agari Y, Agari K, Kuramitsu S, Shinkai A. Structural and functional
characterization of the transcriptional repressor CsoR from Thermus
thermophilus HB8. Microbiology (Reading). 2010 Jul;156(Pt 7):1993-2005. doi:
10.1099/mic.0.037382-0. Epub 2010 Apr 15. Erratum in: Microbiology. 2014
Dec;160(Pt 12):2820. PMID: 20395270.

Supratim Mukherjee, Dimitri Stamatis, Jon Bertsch, Galina Ovchinnikova, Jagadish
Chandrabose Sundaramurthi, Janey Lee, Mahathi Kandimalla, I-Min A Chen,
Nikos C Kyrpides, T B K Reddy, Genomes OnLine Database (GOLD) v.8:
overview and updates, Nucleic Acids Research, Volume 49, Issue D1, 8 January
2021, Pages D723–D733, https://doi.org/10.1093/nar/gkaa983