ABSTRACT
Databases are valuable resources that are capable of collecting and disseminating sizeable quantities of data with the purpose of furthering research done in that particular field. Currently, there are databases for organismal genomes and classes of proteins, but currently there is no database for bacterial autolysins in particular. Autolysins such as LytA in Streptococcus pneumoniae are of vital importance as it allows the bacterium to evade antimicrobial peptides (Kietzman et. al, 2015). Additionally autolysins have been found to promote horizontal gene transfer in S. pneumoniae, as well as promoting sporulation in Bacillus subtilis (Allocati et. al, 2015). While some methods currently exist to manipulate autolysin expression, such as a broth with 2% choline, a large scale computational analysis of these proteins may provide more insight to these mechanisms (Balachandran et al, 2001). 11,458 proteomes encompassing all available Streptococcus (n=9,341), Bacillus (n=1,003), and Listeria (n=1,114) were obtained from GenBank, and 5 autolytic domains including amidase 3 and glucosaminidase were detected using hmmer with an E-value threshold of 10^-5. Resulting 68,748 output files were analyzed indicating 35,319 positive results containing at least one detected domain. This revealed that certain domains such as Glucosaminidase and LysM are highly conserved having been detected in 98.6%, 93.6%, and 99.9% of Streptococcus, Bacillus, and Listeria proteomes respectively, whereas others were noticeably more prevalent in a particular genus such as amidase 2 (75.5% Streptococcus, 92.1% Bacillus, 76.5% Listeria). Additionally, the proteomic locus of each detected domain has been recorded. Currently we aim to organize and compile data into a useful database using SQLite. Additionally, more genera are expected to be added to eventually encompass all bacterial proteomes. Moreover we aim to determine associated domains using hmm scan.
- Allocati, N., Masulli, M., Ilio, C. D., & Laurenzi, V. D. (2015). Die for the community: an overview of programmed cell death in bacteria. Cell Death and Disease,6(1).Google Scholar
- Balachandran, P., Hollingshead, S. K., Paton, J. C., & Briles, D. E. (2001). The Autolytic Enzyme LytA of Streptococcus pneumoniae Is Not Responsible for Releasing Pneumolysin. Journal of Bacteriology,183(10), 3108--3116.Google ScholarCross Ref
- Kietzman, C. C., Gao, G., Mann, B., Myers, L., & Tuomanen, E. I. (2016). Dynamic capsule restructuring by the main pneumococcal autolysin LytA in response to the epithelium. Nature Communications,7, 10859.Google ScholarCross Ref
Recommendations
Unexpected Predictors of Antibiotic Resistance in Housekeeping Genes of Staphylococcus Aureus
BCB '19: Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health InformaticsMethicillin-resistant Staphylococcus aureus (MRSA) is currently the most commonly identified antibiotic-resistant pathogen in US hospitals. Resistance to methicillin is carried by SCCmec genetic elements. Multilocus sequence typing (MLST) covers ...
Application of Comparative Biosequence Analysis to Understand Antibiotic Resistance in Superbug
BCB '19: Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health InformaticsThe advent of synthetic antibiotics revolutionized the treatment of bacterial infections in humans. Antibiotics are classified into several different families, depending on their mode of action, including beta-lactams, macrolides, and quinolones. Beta-...
In silico Pathogenomic Analysis of Corynebacterium Pseudotuberculosis Biovar Ovis
Advances in Bioinformatics and Computational BiologyAbstractCorynebacterium pseudotuberculosis is a pathogenic bacterium that may transmit caseous lymphadenitis, veterinary infection that severely attacks animals such as goats and sheep. It is known that the toxin Phosholipase D is the major virulence ...
Comments