Julie A. Maupin-Furlow, Heather L. Wilson, Steven J. Kaczowka, and Mark S. Ou

Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611-0700

TABLE OF CONTENTS

1. Abstract

2. Introduction

3. Proteasomes and the 20S proteolytic core

3.1. Architecture of the 20S proteasome
3.2. Catalytic mechanism of peptide bond hydrolysis
3.3. Distribution and subunit composition of 20S proteasomes
3.4. Assembly of 20S proteasomes

4. Proteasome-associated AAA⁺ ATPases

4.1. AAA⁺ superfamily
4.2. Rpt (AAA⁺) subunits of eucaryal 26S proteasomes
4.3. Archaeal proteasome-activating nucleotidase (PAN)
4.4. Eubacterial AAA ATPase-forming ring-shaped complexes (ARC)
4.5. Chaperone activity of AAA⁺ proteins

5. Substrate targeting and signal recognition

5.1. Ubiquitin-dependent
5.2. Ubiquitin-independent

6. Archaeal genomics

6.1. 20S proteasome and PAN operons
6.2. Additional energy-dependent proteases

6.2.1. Rpt/FtsH ATPase
6.2.2. Lon protease
6.2.3. Clp ATPase and HtrA (DegP)

7. Role of proteasomes in stress responses

7.1. Eucaryal 26S proteasome and stress
7.2. Eubacterial HslUV proteases and stress
7.3. Prokaryotic 20S proteasomes and AAA⁺ proteins and stress

8. Perspective

9. Acknowledgments

10. References

1. ABSTRACT

Survival of cells is critically dependent on their ability to rapidly adapt to changes in the natural environment no matter how 'extreme'the habitat. An interplay between protein folding and hydrolysis is emerging as a central mechanism for stress survival and proper cell function. In eucaryotic cells, most proteins destined for destruction are covalently modified by the ubiquitin-system and then degraded in an energy-dependent mechanism by the 26S proteasome, a multicatalytic protease. The 26S proteasome is composed of a 20S proteolytic core and 19S cap (PA700) regulator which includes six AAA⁺ ATPase subunits. Related AAA⁺ proteins and 20S proteasomes are found in the archaea and Gram positive actinomycetes. In general, 20S proteasomes form a barrel-shaped nanocompartment with narrow openings which isolate rather non-specific proteolytic active-sites to the interior of the cylinder and away from interaction with cytosolic proteins. The proteasome-associated AAA⁺ proteins are predicted to form ring-like structures which unfold substrate proteins for entry into the central proteolytic 20S chamber resulting in an energy-dependent and processive destruction of the protein. Detailed biochemical and biophysical analysis as well as identification of proteasomes in archaea with developed genetic tools are providing a foundation for understanding the biological role of the proteasome in these unusual organisms.