Improving the Annotations of JCVI-Syn3a Proteins
- PMID: 39576580
- DOI: 10.1007/978-1-0716-4196-5_9
Improving the Annotations of JCVI-Syn3a Proteins
Abstract
The JCVI-Syn3 organism is a minimal organism derived from Mycoplasma mycoides capri, which is capable of self-replication. While the ancestor has 863 genes, the synthetic progeny has only 473, with 434 of these coding for proteins. Despite initial efforts to understand all functions of the organism, a significant number of these protein-coding genes still have unknown functions, and subsequent studies have been only partially successful in elucidating their roles. In this study, we employ our innovative method PROST to identify homologs and better understand these previously unidentified genes. PROST employs protein language embeddings and enables the identification of remote homologs with as low as 16% sequence identity. PROST successfully finds functionally annotated homologs for 93% of the minimal genome with a high level of accuracy, both confirming previously identified functions, as well as proposing new functions for others. The results of our study can be accessed at https://bit.ly/prost-syn3a .
Keywords: Alphafold2; FATCAT; Functional annotation; JCVI-Syn3 organism; Minimal organism; PROST.
© 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
References
-
- Hutchison CA, Chuang R-Y, Noskov VN et al (2016) Design and synthesis of a minimal bacterial genome. Science 351:aad6253. https://doi.org/10.1126/science.aad6253 - DOI - PubMed
-
- Danchin A, Fang G (2016) Unknown unknowns: essential genes in quest for function. Microb Biotechnol 9:530–540. https://doi.org/10.1111/1751-7915.12384 - DOI - PubMed - PMC
-
- Yang Z, Tsui SK-W (2018) Functional annotation of proteins encoded by the minimal bacterial genome based on secondary structure element alignment. J Proteome Res 17:2511–2520. https://doi.org/10.1021/acs.jproteome.8b00262 - DOI - PubMed
-
- Antczak M, Michaelis M, Wass MN (2019) Environmental conditions shape the nature of a minimal bacterial genome. Nat Commun 10:3100. https://doi.org/10.1038/s41467-019-10837-2 - DOI - PubMed - PMC
-
- Breuer M, Earnest TM, Merryman C et al (2019) Essential metabolism for a minimal cell. eLife 8:e36842. https://doi.org/10.7554/eLife.36842 - DOI - PubMed - PMC
MeSH terms
Substances
LinkOut - more resources
Full Text Sources