The copper-linked Escherichia coli AZY operon: Structure, metal binding, and a possible physiological role in copper delivery

Unraveling the genetic basis of microbial metal resistance: Shift from mendelian to systems biology

Microbial metal resistance, a trait that enables microorganisms to withstand high levels of toxic metals, has been studied for over a century. The significance of uncovering these mechanisms goes beyond basic science as they have implications for human health through their connection to microbial pathogenesis, metal bioremediation, and biomining. Recent advances in analytical chemistry and molecular biology have accelerated the discovery and understanding of genetic mechanisms underlying microbial metal resistance, identifying specific metal resistance genes and their operons. The emergence of omics tools has further propelled research towards a comprehensive understanding of how cells respond to metal stress at the systemic level, revealing the complex regulatory networks and evolutionary dynamics that drive microbial adaptation to metal-rich environments. In this article, we present a historical overview of the evolving understanding of the genetic determinants of metal resistance in microbes. Through multiple narrative threads, we illustrate how our knowledge of microbial metal resistance and genetics has interacted with genetic tools and concept development. This review also discusses how our understanding of microbial metal resistance has progressed from the Mendelian perspective to the current systems biology viewpoint, particularly as omics approaches have considerably enhanced our understanding. This system-level understanding has opened new possibilities for genetically engineered microorganisms to regulate metal homeostasis.

The Escherichia coli AZY operon links copper uptake to antibiotic resistance

Copper import to the bacterial cytoplasm has been underinvestigated as bacterial cuproenzymes are extracytoplasmic. However, copper must access the cytoplasm to interact with metal-dependent transcription factors. In particular, the multiple drug antibiotic resistance (mar) operon is induced by a copper signal, the source of which has not been established. Here we show that the Escherichia coli AZY operon, which encodes the copper-binding periplasmic proteins YobA and YebY and the putative copper importer YebZ, mediates copper uptake. Copper uptake by YebZ depends on two conserved histidine residues and is modulated by YobA and YebY. Moreover, the AZY proteins are necessary for activation of the mar operon and mediate resistance to multiple antibiotics in a copper-dependent fashion. AZY-like operons are widespread in gram-negative bacteria, suggesting that this previously unknown link between copper and antibiotic resistance is a general mechanism that may offer an alternative therapeutic target for multidrug resistance.

Insights into bacterial metabolism from small RNAs

The study of small, regulatory RNAs (sRNA) that act by base-pairing with target RNAs in bacteria has been steadily advancing, particularly with the availability of more and more transcriptome and RNA-RNA interactome datasets. While the characterization of multiple sRNAs has helped to elucidate their mechanisms of action, these studies also are providing insights into protein function, control of metabolic flux, and connections between metabolic pathways as we will discuss here. In describing several examples of the metabolic insights gained, we will summarize the different types of base-pairing sRNAs including mRNA-derived sRNAs, sponge RNAs, RNA mimics, and dual-function RNAs as well as suggest how information about sRNAs could be exploited in the future.

Unique underlying principles shaping copper homeostasis networks

Abstract

Copper is essential in cells as a cofactor for key redox enzymes. Bacteria have acquired molecular components that sense, uptake, distribute, and expel copper ensuring that cuproenzymes are metallated and steady-state metal levels are maintained. Toward preventing deleterious reactions, proteins bind copper ions with high affinities and transfer the metal via ligand exchange, warranting that copper ions are always complexed. Consequently, the directional copper distribution within cell compartments and across cell membranes requires specific dynamic interactions and metal exchange between cognate holo-apo protein partners. These metal exchange reactions are determined by thermodynamic and kinetics parameters and influenced by mass action. Then, copper distribution can be conceptualized as a molecular system of singular interacting elements that maintain a physiological copper homeostasis. This review focuses on the impact of copper high-affinity binding and exchange reactions on the homeostatic mechanisms, the conceptual models to describe the cell as a homeostatic system, the various molecule functions that contribute to copper homeostasis, and the alternative system architectures responsible for copper homeostasis in model bacteria.

Graphical Abstract