Reversible Assembly and Amyloidogenesis of The
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Reversible assembly and amyloidogenesis of the staphylococcal biofilm protein, Aap A dissertation submitted to the Graduate School of the University of Cincinnati In partial fulfillment of the requirements for the degree of Doctor of Philosophy In the Department of Molecular Genetics, Biochemistry and Microbiology of the College of Medicine 2019 Alexander E. Yarawsky B.S. Biological Sciences and Chemistry Northern Kentucky University 2013 Committee Chair: Andrew B. Herr, Ph.D. Abstract The human skin commensal, Staphylococcus epidermidis, is the bacterium most commonly responsible for hospital-acquired infections. This microbe has a very strong capacity for forming bacterial communities known as biofilms. These communities are well-structured and often involve a slime-like matrix of extracellular polysaccharide which assists in bacterial accumulation. A well-known protein factor, the accumulation- associated protein (Aap), can also mediate intercellular adhesion, contributing the biofilm formation. Interestingly, Aap has been shown to be critical for infection in a rat catheter model, whereas the extracellular polysaccharide was irrelevant in infection. Aap is a large, multi-functional, cell wall-anchored protein expressed by S. epidermidis. The N-terminus of the protein contains a region of short repeats called the A-repeats, followed by a globular lectin domain. The lectin domain can mediate attachment of bacteria to a surface. A proteolytic cleavage site downstream of the lectin domain leads to the release of the A-repeats and lectin domain, allowing Aap to function in accumulation. There are 5 - 17 B-repeats downstream of the cleavage site, which can assembly with Aap on adjacent cells in the presence of Zn2+. At the C-terminus of Aap lies a region of low complexity, which is rich in proline and glycine residues. After this region is a cell wall-anchoring motif that results in the covalent attachment of Aap to the bacterial cell wall. Much of the progress made toward understanding the structure and biological function of the B-repeats has utilized a minimal construct containing one and a half B- repeats (Brpt1.5). Previous members of the Herr Lab have determined that Brpt1.5 can ii assemble into an anti-parallel dimer in the presence of Zn2+. Interestingly, while the Brpt1.5 dimer would disassociate in the presence of Zn2+-chelator, mature biofilms were unaffected by addition of the chelator. This led members of the Herr Lab to express and characterize longer B-repeat constructs, which more closely resemble the number of B- repeats observed in Aap and show Zn2+-dependent assembly beyond dimer, eventually forming amyloid-like fibers. Amyloid fibers are often associated with toxicity, however, the fibers formed by Aap's B-repeats are utilized by the bacterium in a functionally beneficial way. In several other bacteria, functional amyloids have been shown to provide added strength to the biofilm structure. In the work presented here, we show Aap forms fibers in S. epidermidis biofilms and are responsible for the biofilm's resistance toward Zn2+-chelator. We also characterize a recently discovered protein, small basic protein (Sbp), which is able to reduce the amount of Zn2+ required for B- repeat aggregation. We propose that Sbp is a nucleating or accessory protein for Aap- amyloidogenesis. Finally, a secondary interest of this dissertation work is to characterize the structure of the proline/glycine-rich stalk-like region of Aap and other cell wall-anchored proteins. Interestingly, several of these regions have a very high propensity to remain extended in solution, primarily due to the high polyproline type II helix propensity. Overall, this dissertation work has led to an increased understanding of the mechanism of Aap-dependent accumulation in biofilm formation. iii iv Acknowledgements I would like to thank my advisor, Dr. Andrew Herr for always being enthusiastic about my data and inspiring me to continue down the path of biophysics. I thank my fellow lab members for constant discussions about various aspects of my research, as well as for entertaining outings. I also owe the previous lab members who had set the stage for my projects, especially Deb Conrady and Stefanie Johns. I would also like to thank my undergraduate advisor at Northern Kentucky University, Dr. Heather Bullen, for showing me the excitement of research and being an inspirational mentor. I am grateful for my many trips to the Gibbs Conference on Biological Thermodynamics, which are always inspiring me to maintain a high degree of rigor in my work, and have led to me reading many papers from the influential biophysicists that are or once were associated with this meeting. I would like to thank Beckman Coulter for awarding me a full travel grant to attend the 23rd International Analytical Ultracentrifugation Workshop and Symposium (AUC 2017) where I learned a great deal from many experts in the field, particularly in regards to Walter Stafford's SEDANAL software. I must acknowledge my family and friends as well, especially my wife Danille, who have supported my journey and who have encouraged me to pursue the highest of goals. v Table of Contents Title Page ........................................................................................................................ i Abstract .......................................................................................................................... ii Acknowledgements ....................................................................................................... v Table of Contents ......................................................................................................... vi List of Figures and Tables ............................................................................................ x Chapter I. Literature Review ......................................................................................... 1 A. The importance of staphylococcal biofilms in the healthcare industry ..................... 1 B. Molecular pathways of staphylococcal biofilm formation ......................................... 2 i. Steps of biofilm formation ...................................................................................... 3 ii. PNAG-dependent accumulation ............................................................................ 8 iii. Protein-dependent accumulation ........................................................................ 10 C. The accumulation-associated protein .................................................................... 13 i. Aap domain architecture ...................................................................................... 14 ii. Role of Aap in attachment ................................................................................... 14 iii. Zn2+-mediated self-assembly of Aap (role in accumulation) ............................... 17 D. Considerations in Protein Folding and Stability ..................................................... 21 i. The hydrophobic effect ........................................................................................ 22 ii. Solvent-solute interactions .................................................................................. 23 iii. Solute-solute interactions ................................................................................... 27 E. Protein misfolding and natively unfolded proteins .................................................. 31 i. Protein aggregation and amyloid formation ......................................................... 31 a. Amyloid stability ............................................................................................... 32 b. Pathogenic vs. functional amyloid ................................................................... 33 ii. Intrinsically disordered proteins ........................................................................... 34 a. Factors determining conformational propensities ............................................ 34 b. Functional roles of IDPs .................................................................................. 36 F. Goals of dissertation work...................................................................................... 39 References ................................................................................................................. 42 Chapter II. The biofilm adhesion protein Aap from Staphylococcus epidermidis forms zinc-dependent amyloid fibers ........................................................................ 54 Abstract ...................................................................................................................... 55 Author Summary ........................................................................................................ 57 Introduction ................................................................................................................ 58 Solution characterization of tandem B-repeats from Aap ........................................... 62 Tandem B-repeats assemble into multiple higher-order species in the presence of Zn2+ ............................................................................................................................ 64 2D size-and-shape sedimentation analysis indicates formation of fiber-like species . 67 Tandem B-repeats form amyloid fibers in the presence of Zn2+ ................................. 71 vi B-repeat fiber assembly is time- and temperature-dependent ..................................