Pathogen Sensing: Boost to Antimicrobial Immunity

A recent article published in Science Advances sheds light on the mechanisms which the host cells use to eliminate invading pathogens.

The researchers describe how cells use pattern recognition receptors (PRRs) to recognize microbial molecular structures, known as pathogen-associated molecular patterns (PAMPs), and induce a variety of immune responses that trigger pathogen clearance. The study, An innate pathogen sensing strategy involving ubiquitination of bacterial surface proteins, published in Science Advances on March 22nd, details how several classes of PRRs, including Toll-like receptors, Retinoic acid-inducible gene I (RIG-I)–like receptors, NOD-like receptors, and DNA receptors, have been discovered and characterized.

The article highlights the importance of surveillance mechanisms that monitor the intracellular environment to prevent pathogen proliferation. The ubiquitination system plays a pivotal role in pathogen recognition and elimination by decorating intracellular pathogens with poly-ubiquitin (Ub) chains, ultimately leading to their degradation by the proteasomal or autophagic machinery.

Ubiquitination is a process in which a small protein called ubiquitin is attached to target proteins by a series of reactions. This modification can affect the function, stability, localization, and interactions of the target protein, and can serve as a signal for its destruction by the immune system. Ubiquitination is a highly regulated and versatile mechanism that plays a central role in a variety of cellular processes, including protein quality control, DNA repair, immune response, cell signaling, and cell cycle progression.

The scientists identified a variety of host E3 ubiquitin ligases that are responsible for pathogen marking, including LRSAM1, Parkin, RNF166, RNF213, ARIH1, Smurf1, and SCFFBXO2.

Ligase: an enzyme that can help the joining (ligation) of two large molecules by forming a new chemical bond

The article then describes how the researchers identified degron motifs in surface proteins of phylogenetically diverse bacteria of both Gram-positive and Gram-negative origin.

A degron is a short sequence of amino acids found in a protein that signals for its degradation
Gram-positive and Gram-negative are terms used to describe two types of bacteria based on their cell wall structure, which can be identified using a laboratory staining technique called the Gram stain.
Gram-positive bacteria have a thick cell wall made up of a layer of peptidoglycan that is tightly packed together. This peptidoglycan layer is stained purple by the Gram stain, indicating that the bacteria are Gram-positive. The thick cell wall helps to protect the bacteria from environmental stresses such as osmotic pressure and provides structural support.
In contrast, Gram-negative bacteria have a thinner layer of peptidoglycan that is surrounded by an outer membrane composed of lipopolysaccharides (LPS) and proteins. The outer membrane of Gram-negative bacteria makes them more resistant to antibiotics and host immune responses. When stained with the Gram stain, the thinner layer of peptidoglycan and the outer membrane of Gram-negative bacteria prevent the stain from being retained, causing the bacteria to appear pink or red under the microscope, indicating that they are Gram-negative.

The targeting of such substrates by ubiquitination machinery propels efficient pathogen elimination from the host cell. The researchers demonstrated the conversion of a impregnable surface protein into an ubiquitin substrate by engineering degron insertion to promote bacterial clearance. This simple yet generic principle for identifying bacterial substrate potentially serves as a conserved mechanism of cytosolic pathogen recognition, promising to be efficient and multipurpose in fending off bacterial infections.

The study further demonstrated the central role of SCF E3 ligase in bacterial ubiquitination augmenting pathogen degradation. Heterozygous mutations in FBXW7, particularly R505C variant, trigger multiple carcinomas and lymphocytic leukemia in humans. The study provides an unexpected molecular explanation of the enhanced risk of infections in patients with chronic lymphocytic leukemia (CLL). The findings suggest a noteworthy contribution of E3 ligases in host immunity against bacterial infections and maintenance of cellular steady state.

The researchers shed light on a key fundamental cellular immune processes that could be harnessed to intensify the antibacterial immunity. By identifying common motifs for substrate recognition and subsequent ubiquitination, they discovered a smart strategy for resource optimization that could be exploited by the host to present microbial protein antigens to induce a strong response directed against intracellular pathogens. The findings also suggest that genetic polymorphism in E3 ligase genes could play a role in susceptibility to bacterial infections, highlighting the importance of the ubiquitin-mediated alarm arousal as a central mechanism for host defenses against invading pathogens.

The understanding of the immune system's ability to recognize and eliminate pathogens via ubiquitination and other strategies has significant potential applications and benefits, which include:

Development of novel therapeutic strategies: The identification of degron motifs in surface proteins of bacteria and the demonstration of their targeting by ubiquitination machinery can help develop innovative therapies for combating bacterial infections. These could involve designing molecules that enhance ubiquitination or interfere with bacteria's ability to evade this mechanism.
Enhancing vaccines: Knowledge of the ubiquitination process and the role of specific E3 ligases in pathogen recognition can help improve the design of vaccines against bacterial infections. By introducing degron-like sequences in bacterial antigens, vaccines may stimulate stronger immune responses, offering better protection against a wide range of pathogens.
Precision medicine: Understanding the role of specific E3 ligases and their genetic mutations in bacterial infection susceptibility can pave the way for personalized medicine. Genetic screening for polymorphisms in E3 ligase genes could help identify individuals at higher risk for bacterial infections, enabling tailored prevention and treatment strategies.
Antimicrobial resistance mitigation: The identification of conserved mechanisms of cytosolic pathogen recognition may offer alternative approaches to counteract the growing problem of antimicrobial resistance. By targeting bacterial clearance mechanisms that are less prone to resistance development, new therapies could provide a more sustainable solution to infectious diseases.
Diagnostics: The discovery of specific degron motifs and ubiquitination patterns in bacteria may lead to the development of diagnostic tools that rapidly detect and identify pathogens based on their unique molecular signatures.
Enhanced understanding of immune system function: The research into ubiquitination and other pathogen recognition mechanisms contributes to a deeper understanding of the immune system's function, which can inform future immunological research and the development of novel immunotherapies.
Evolutionary insights: Studying the presence or absence of eukaryotic-like functional domains or motifs in bacteria and their role in evading or modulating host immune responses can provide valuable insights into the co-evolution of pathogens and hosts. This knowledge could help anticipate future pathogen adaptations and develop preemptive countermeasures.

In conclusion, the investigation of pathogen recognition and elimination strategies, particularly ubiquitination, can offer numerous applications and benefits in the fight against bacterial infections. These findings can help develop novel therapeutics, enhance existing vaccines, and improve diagnostics, contributing to better public health outcomes and a deeper understanding of host-pathogen interactions.