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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

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Phylogenetic analysis predicts structural divergence for proteobacterial ClpC proteins.

Justin M Miller¹, Hamza Chaudhary¹, Justin D Marsee¹

¹Middle Tennessee State University, Department of Chemistry, 1301 East Main Street, Murfreesboro, TN 37132, United States.

Journal of Structural Biology

|November 14, 2017

Summary

Bacterial ATP-dependent proteases like ClpA and ClpC are vital for cellular quality control. Phylogenetic analysis reveals ClpA evolved from ClpC, with ClpE/ClpL as intermediates, and some ClpC proteins may not be functional.

Keywords:

AAA+ ATPases ATP-dependent proteases Clp/Hsp100 ClpA ClpC ClpE ClpK ClpL ClpP Phylogenetic analysis Protein evolution molecular motors

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Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

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Published on: June 11, 2015

Area of Science:

Molecular Biology
Cellular Biology
Evolutionary Biology

Background:

Regulated proteolysis is essential for cellular quality control, removing misfolded or tagged proteins.
ATP-dependent proteases, such as ClpAP and ClpCP, are the molecular machines catalyzing protein degradation.
Clp/Hsp100 proteins form ring structures that unfold proteins for degradation by the ClpP protease.

Purpose of the Study:

To clarify the evolutionary relationships among bacterial Clp/Hsp100 proteins (ClpA, ClpC, ClpE, ClpK, ClpL).
To investigate the functional implications of identified structural differences within bacterial ClpC proteins.

Main Methods:

Comprehensive phylogenetic analysis of bacterial Clp/Hsp100 protein sequences.
Comparative analysis of protein structures and conserved domains.

Main Results:

Phylogenetic analysis suggests ClpA evolved from an ancestral ClpC protein.
ClpE and ClpL appear to represent intermediate evolutionary forms between ClpA and ClpC.
A subset of proteobacterial ClpC proteins were identified as potentially non-functional in regulated proteolysis.

Conclusions:

The bacterial Clp/Hsp100 family evolved through divergent evolution from ancestral ClpC.
Significant structural variations exist among bacterial ClpC proteins, impacting their function.
It is cautioned against assuming uniform function across all bacterial ClpC proteins.