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Site-Specific Lysine Lactylation via Genetic Code Expansion in E. coli and Mammalian Cells
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Lysine carboxylation: unveiling a spontaneous post-translational modification
David Jimenez-Morales1, Larisa Adamian1, Dashuang Shi2
1Department of Bioengineering, University of Illinois at Chicago, 851 South Morgan Street, Room 218, Chicago, IL 60607, USA.
Acta Crystallographica. Section D, Biological Crystallography
|January 15, 2014
Summary
Lysine carboxylation, a crucial protein modification, is now detectable with a new computational tool. This finding reveals its widespread role in biological regulation and enzyme function.
Area of Science:
- Biochemistry
- Proteomics
- Enzymology
Background:
- Lysine carboxylation is a post-translational modification (PTM) vital for enzyme catalysis.
- This modification occurs spontaneously but is challenging to detect experimentally, limiting understanding of its impact.
- The full functional significance of lysine carboxylation remains largely unknown.
Purpose of the Study:
- To characterize the microenvironment signature of lysine carboxylation sites.
- To develop a computational method for detecting lysine carboxylation in proteins.
- To assess the prevalence of lysine carboxylation in the proteome.
Main Methods:
- Characterization of the microenvironment of lysine carboxylation sites.
- Development of the Predictor of Lysine Carboxylation (PreLysCar) computational tool.
- Large-scale computational analysis to estimate proteome-wide prevalence.
Main Results:
- A signature microenvironment for lysine carboxylation was identified.
- The PreLysCar tool was developed for detecting lysine carboxylation in proteins with 3D structures.
- Approximately 1.3% of large proteins may contain carboxylated lysine residues, suggesting widespread functional roles.
Conclusions:
- Spontaneous PTMs like lysine carboxylation can serve as efficient biological regulatory machinery.
- The unexpected prevalence indicates enrichment of reactions involving carboxylated lysine.
- Physicochemical conditions can be tuned to regulate enzymes via lysine carboxylation.
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