Aaron T. Smith

Post-Doc, Northwestern University, 2016

M. Sc., Ph. D., University of Wisconsin—Madison, 2012

B. A., Boston University, 2007

Research in my lab focuses on understanding the structure and function of metalloproteins involved in crucial biological processes such as protein translation, peptide posttranslational modification, nutrient uptake, and protein regulation. My laboratory sits at the interface of inorganic chemistry, biochemistry, and biophysics, and members of my lab have the opportunity to learn a wide array of techniques from molecular biology and protein expression and purification (both soluble and membrane), to structural biology, spectroscopy, and anaerobic techniques. We are a proud and diverse group, and welcome chemists, biochemists, and molecular biologists alike who are interested in understanding the role of inorganic elements in biological settings!

There are three major projects currently in the lab:

The Mechanism and Regulation of Post-Translational Arginylation 

Proteins are a versatile group of biological macromolecules that are responsible for undertaking many indispensable functions within the cell. However, when constrained to only the 20 canonical amino acids, not every necessary cellular function may be fulfilled. Thus, the encoding capacity of the genome must be expanded, and such augmentation is achieved by the ability of proteins to be co- and/or post-translationally modified. A lesser-studied but essential eukaryotic PTM is arginylation, which is the covalent addition of the amino acid arginine (Arg) to an acceptor protein, catalyzed by the enzyme arginyltransferase 1 (ATE1). Arginylation is emerging as a global regulator of eukaryotic cellular homeostasis through its degradative and non-degradative effects on the proteome. Arginylation has a major role within the N-degron pathway, a hierarchal determinant of intracellular protein half-life. However, degradation is not the only fate for proteins and enzymes that have be post-translationally arginylated and recent and important research has shown that proteins may also be stabilized and oligomerize differently once arginylated. Examples of some proteins that change their oligomeric state in response to arginylation include β-actin and calreticulin, while recent studies have even shown that arginylation even affects viruses such as the human immunodeficiency virus (HIV) and SARS-CoV-2, the causitive agent of the COVID-19 pandemic. Despite its physiological importance, the structural and the biophysical properties of ATE1 are poorly understood, and research in the Smith laboratory is attempting to answer these pressing questions.

This research project aims to understand how the mechanism and regulation of ATE1-catalyzed post-translational arginylation, which affects normal eukaryotic development and is linked to cardiovascular disease, development disease, and some forms of cancers.

Pathogenic Ferrous Iron Uptake and Delivery

Iron is an essential element for virtually every living organism and has been adopted to serve in major biological processes such as nitrogen fixation, methane oxidation, hydrogen production, aerobic cellular respiration, oxygen transport, DNA biosynthesis, and even gene regulation. However, iron-based life represents a double-edged sword, as Fe(II) is bioavailable but highly reactive, whereas Fe(III) is intractable but generally chemically inert. Every organism that utilizes iron employs biological pathways to obtain this element from the environment, to regulate its bioavailable concentration, and to sequester its excess. In order to establish infection in humans, pathogenic bacteria have evolved several responses to manage iron acquisition and utilization. The ability to acquire and utilize iron aids in the proliferation of numerous infectious bacteria. One important route for the uptake of Fe(II) for bacteria is via the ferrous iron uptake (Feo) system However, the mechanism of iron uptake through this pathway is poorly understood by comparison to Fe(III) and heme uptake pathways. In an era of increasing antibacterial resistance, understanding and targeting the routes of bacterial nutrient uptake are crucial to stem bacterial virulence. We are using a multifaceted approach to understand the structure and function of proteins involved in bacterial Fe(II) uptake.

This research project aims to understand how pathogenic bacteria acquire ferrous iron, with the goal of targeting this system for novel antibiotic developments.

Bacterial Ferrous Iron Sensing and Generation

There is an emerging connection between Feo and additional membrane-bound proteins that function more broadly in bacterial Fe(II) homeostasis through: 1) sensing Fe(II) as part of a mechanism to control biofilm formation in antibiotic-resistant pathogens and 2) using Fe(III)-siderophores to supply Fe(II) to the Feo system for hyper iron accumulation in select bacteria. For example, studies have identified a two-component signal transduction system, BqsR-BqsS, that regulates biofilm formation and quorum sensing in Pseudomonas aeruginosa through the sensing of periplasmic Fe(II), and these proteins appear to be conserved in many bacteria. Moreover, there is an increasing consensus that a family of small membrane proteins known as membrane ferric reductases (mFRs) contribute to the Fe(II) pool in bacteria through the reductive dissociation of iron from Fe(III)-siderophores, which could explain why the Feo system is expressed even under O₂-replete conditions. We hypothesize that mFRs are heme b-containing proteins of the enigmatic cytb₅₆₁ family that couple Fe(III) reduction to Feo-mediated Fe(II) transport in bacteria. Using structural, biochemical, and biophysical methods coupled with in vivo approaches, we are working to uncover the complex interplay of these membrane proteins in maintaining Fe(II) homeostasis in both pathogenic prokaryotes as well as magnetotactic bacteria that are capable of synthesizing complex iron nanoparticles.

This research project aims to understand how pathogenic bacteria acquire sense and generate ferrous iron, with the goal of targeting this system for attenuating bacterial virulence and for new material developments aided by hyper iron accumulating bacteria.

Selected Publications (last 3 years)