Selective Transport and Targeted Assembly in the 1,2-Propanediol Bacterial Microcompartment

This dissertation is the culmination of my graduate studies in the laboratory of Todd O. Yeates at UCLA. The research presented here is a study of 1,2-propanediol utilization (Pdu), a scavenger pathway used by common gut bacteria to thrive in the human gut environment. Encapsulating the Pdu pathway is a novel non-membrane, proteinaceous shell (approximately 100-200 nm in diameter) also known as a bacterial microcompartment (BMC) and the focus of investigation in the present work. BMCs are a conserved mechanism for housing metabolic processes that involve volatile or toxic intermediates. They are found in approximately 20% of sequenced bacterial genomes. However, little is known about BMC properties for small molecule transport and assembly. My dissertation work revealed important aspects of selective transport and shell protein organization for the Pdu BMC and other BMC shell proteins through hypothesis-driven research. As an introduction to this dissertation, chapter 1 summarizes the history of research on Pdu BMCs and recent applications in biotechnology. Chapter 2 is a comprehensive review, reprinted with permission from Microbiology and Molecular Biology Reviews (see Acknowledgments), of diverse bacterial microcompartments of known function and their possible applications in bioengineering of fuel and drug biosynthesis. Chapter 3 is an exposition on biochemical and structural characterization on selective transport of small molecules in the shell protein PduA, testing my first hypothesis about substrate entry and toxic intermediate encapsulation. This article is reprinted with permission from Proceedings of the National Academy of Sciences (see Acknowledgments). To follow up on the results of Chowdhury, Chun, et al. (2015), Chapter 4 presents a molecular dynamics approach to study free energy barriers to small molecules through the shell protein PduA, which supported our previous conclusions. This manuscript is in submission for journal peer review. Another type of BMC shell protein, called EutL, is a promising candidate for pore-conducting small molecule transport. In Chapter 5, I describe molecular dynamics studies on EutL, previously reported by several groups in open and closed pore conformations by X-ray crystallography, in order to observe the large structural rearrangements required for conformational transition. Chapter 6 reports on the study of homologous shell protein, PduB, that I hypothesized can also have an open pore structure. Here, I used Tryptophan emission spectroscopy and X-ray crystallography to test this hypothesis. I outline future work for the continuation of this project.Lastly, the latter part of my dissertation focuses on questions of BMC shell assembly, a difficult topic of study due to non-uniform distributions of size and shape among BMCs of a particular system and highly redundant motifs in the BMC shell. Chapter 7 details the structural and in vivo studies of the shell protein PduJ that has 80% amino acid sequence identity to PduA. However, PduJ is found to not be functionally synonymous with PduA and its genic location in the Pdu operon may affect its post-translational assembly. This research was published electronically ahead of print in Molecular Microbiology (June 2016) and is reprinted here with permission (see Acknowledgments). Finally, Chapter 8 chronicles the study of Pdu enzyme N-terminal peptides binding Pdu BMC shell proteins for two reasons. First, the literature on this subject contributed by many research groups is sometimes inconsistent, which may be attributed to the difficulty of studying amphipathic peptides in a biochemical setting. A thorough study of the Pdu enzyme N-terminal peptides using biophysical chemistry has not been carried out prior to this work and would benefit the research community. Second, a more quantitative analysis could be used to mathematically model Pdu BMC assembly and, in combination with data on pore permeability (described in chapter 4) and enzyme kinetics, accurately simulate production efficiency of the Pdu BMC. This information is highly valuable for the industrial scale use of Pdu BMCs, the bioengineering and synthetic biology of which is already an active area of research. I outline the future work for the continuation of this project, with notes in the Appendix, and offer advice for using different techniques.In conclusion, this dissertation work contributes significant findings to the expanding knowledge of the Pdu BMC and details further studies of interest for posterity in the BMC research community