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Published on: September 15, 2015
Structural and functional diversity of the microbial kinome
Natarajan Kannan1, Susan S Taylor, Yufeng Zhai
1Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America.
Plos Biology
|March 16, 2007
Summary
Eukaryotic protein-like kinases (ELKs) are as common as histidine kinases in bacteria, suggesting a major role in prokaryotic signaling. This diverse enzyme superfamily evolved from a common protein kinase-like fold, revealing significant functional plasticity.
Area of Science:
- Biochemistry
- Molecular Biology
- Evolutionary Biology
Background:
- Eukaryotic protein kinases (ePKs) are central to eukaryotic signaling.
- Bacterial signaling primarily involves histidine kinases, with fewer known ePK-like kinases (ELKs).
- The Global Ocean Sampling (GOS) dataset offers a vast resource for exploring microbial proteomes.
Purpose of the Study:
- To investigate the prevalence and evolutionary significance of ePK-like kinases (ELKs) in bacteria.
- To analyze the diversity and evolutionary history of the protein kinase-like (PKL) superfamily.
- To understand the structural and functional plasticity within this enzyme superfamily.
Main Methods:
- Analysis of the Global Ocean Sampling (GOS) dataset and public databases.
- Phylogenetic and comparative analysis of protein sequences.
- Identification and classification of ELKs and ePKs into distinct families.
- Examination of conserved residues and functional compensation mechanisms.
Main Results:
- ELKs are as prevalent as histidine kinases in prokaryotes, indicating a significant role in bacterial behavior.
- The ePK domain is part of a larger, diverse superfamily built on a common protein kinase-like (PKL) fold.
- GOS data substantially increased the number of known ELK sequences, enabling the discovery of novel families.
- Cataloged 27,677 ePKs and 18,699 ELKs, classifying them into 20 distinct families.
- Identified ten key conserved residues, with evidence of loss and functional compensation in some families, highlighting plasticity.
Conclusions:
- ELKs play a crucial role in prokaryotic signaling, comparable to histidine kinases.
- The protein kinase-like (PKL) superfamily is ancient, diverse, and exhibits remarkable functional plasticity.
- Understanding this superfamily provides insights into enzyme evolution and adaptation.
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