SecretoMyc, a web-based database on mycobacteria secreted proteins and structure-based homology identification using bio-informatics tools
Open accessPublished version of a preprint
Abstract
To better understand the interaction between the host and the Mycobacterium tuberculosis pathogen, it is critical to identify its potential secreted proteins. While various experimental methods have been successful in identifying proteins under specific culture conditions, they have not provided a comprehensive characterisation of the secreted proteome. We utilized a combination of bioinformatics servers and in-house software to identify all potentially secreted proteins from six mycobacterial genomes through the three secretion systems: SEC, TAT, and T7SS. The results are presented in a database that can be crossed referenced to selected proteomics and transcriptomics studies (https://secretomyc.cbs.cnrs.fr). In addition, thanks to the recent availability of Alphafold models, we developed a tool in order to identify the structural homologues among the mycobacterial genomes.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Pai, M., Behr, M. A., Dowdy, D., Dheda, K., Divangahi, M., Boehme, C. C., Ginsberg, A., Swaminathan, S., Spigelman, M., Getahun, H., et al. (2016) · Nature Reviews Disease Primers · doi:10.1038/nrdp.2016.76 · Cited by 1,270 · see citing works
Two Nonredundant SecA Homologues Function in Mycobacteria
Braunstein, M., Brown, A. M., Kurtz, S., & Jacobs, W. R. (2001) · Journal of Bacteriology · doi:10.1128/jb.183.24.6979-6990.2001 · Cited by 141 · see citing works
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- Authors
- Gracy, J., Vallejos-Sanchez, K., & Cohen-Gonsaud, M.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Venue
- Tuberculosis
- Publisher
- Elsevier BV
- Published
- 2023-07
- Volume
- 141
- Pages
- 102375
- ISSN
- 1472-9792 (ISSN-L)
- OpenAlex
- W4383466132
- Cited by
- 1
- References
- 3
- Citations by year
- 2025: 1
- FWCI
- 0.21
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (am, 373 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Tuberculosis (acceptedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- HAL (submittedVersion, cc-by-nc)
- Funders
- French Infrastructure for Integrated Structural Biology (ANR-10-INSB-05-01)
- Topics
- Health Sciences › Medicine › Infectious Diseases › Tuberculosis Research and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Mycobacterium tuberculosis, secreted proteins, AlphaFold models, host-pathogen interaction
- MeSH terms
- Bacterial Proteins, Biological Transport, Mycobacterium tuberculosis, Internet, Proteome
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