Engineering Soluble Human Paraoxonase 2 for Quorum Quenching

Anti-biofilm potential of human senescence marker protein 30 against Mycobacterium smegmatis

Human senescence marker protein 30 (huSMP30) has been characterized as a multifaceted protein consisting of various enzymatic and cellular functions. It catalyzes the interconversion of L-gulonate and L-gulono-γ-lactone in the ascorbate biosynthesis pathway. Therefore, we hypothesized that it could be a potential anti-biofilm agent against pathogenic bacteria due to its lactonase activity. In order to corroborate this, the huSMP30 was recombinantly expressed, purified, and analyzed for its ability to inhibit Mycobacterium smegmatis biofilm formation, which showed a concentration-dependent inhibition as compared to the untreated control group. Further, in silico analysis was performed to redesign the huSMP30 with enhanced lactonase activity. Molecular docking analysis of the huSMP30 and lactone substrates facilitated the selection of three single amino acid substitutions (E18H, N154Q, and D204V), which were created using a PCR-based site-directed mutagenesis reaction. These mutant proteins and the wild-type huSMP30 were purified, and the effects on the enzymatic activity and biofilm formation were studied. The mutants E18H and D204V showed non-significant effects on specific lactonase activity, catalytic efficiency, and anti-biofilm property; however, the mutant N154Q showed significant improvement in the specific lactonase activity, catalytic efficiency, and inhibition in the biofilm formation. The protein stability analysis revealed that the wild-type huSMP30 and its designed mutants were stable at 37 °C for up to 4 days. In conclusion, the anti-biofilm property of the huSMP30 has been established, and an engineered version, N154Q, inhibits biofilm formation with greater efficiency. Human SMP30 is a versatile protein with multiple cellular and enzymatic functions, however, its anti-biofilm potential has not been explored. Our work presents the method to produce soluble and active huSMP30 in the E. coli expression system and establishes its role as an anti-biofilm agent against Mycobacterium smegmatis owing to its lactonase activity. Our results provide support for the future advancement of huSMP30 as a potential anti-biofilm agent targeting pathogenic Mycobacterium species.

Quorum-quenching enzymes: Promising bioresources and their opportunities and challenges as alternative bacteriostatic agents in food industry

The problems of spoilage, disease, and biofilm caused by bacterial quorum-sensing (QS) systems have posed a significant challenge to the development of the food industry. Quorum-quenching (QQ) enzymes can block QS by hydrolyzing or modifying the signal molecule, making these enzymes promising new candidates for use as antimicrobials. With many recent studies of QQ enzymes and their potential to target foodborne bacteria, an updated and systematic review is necessary. Thus, the goals of this review were to summarize what is known about the effects of bacterial QS on the food industry; discuss the current understanding of the catalytic mechanisms of QQ enzymes, including lactonase, acylase, and oxidoreductase; and describe strategies for the engineering and evolution of QQ enzymes for practical use. In particular, this review focuses on the latest progress in the application of QQ enzymes in the field of food. Finally, the current challenges limiting the systematic application of QQ enzymes in the food industry are discussed to help guide the future development of these important enzymes.

Targeting Multidrug-Recalcitrant Pseudomonas aeruginosa Biofilms: Combined-Enzyme Treatment Enhances Antibiotic Efficacy

Pseudomonas aeruginosa is an opportunistic pathogen that forms biofilms during infection, resulting in recalcitrance to antibiotic treatment. Biofilm inhibition is a promising research direction for the treatment of biofilm-associated infections. Here, a combined-enzyme biofilm-targeted strategy was put forward for the first time to simultaneously prevent biofilm formation and break down preformed biofilms. The N-acylhomoserine lactonase AidH was used as a quorum-sensing inhibitor and was modified to enhance the inhibitory effect on biofilms by rational design. Mutant AidH_A147G exerted maximum activity at the human body temperature and pH and could reduce the expression of virulence factors as well as biofilm-related genes of P. aeruginosa. Subsequently, the P. aeruginosa self-produced glycosyl hydrolase PslG joined with AidH_A147G to disrupt biofilms. Interestingly, under the combined-enzyme intervention for P. aeruginosa wild-type strain PAO1 and clinical strains, no biofilm was observed on the bottom of NEST glass-bottom cell culture dishes. The combination strategy also helped multidrug-resistant clinical strains change from resistant to intermediate or sensitive to many antibiotics commonly used in clinical practice. These results demonstrated that the combined-enzyme approach for inhibiting biofilms is a potential clinical treatment for P. aeruginosa infection.

Protein Design: From the Aspect of Water Solubility and Stability

Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.

Production of highly soluble native human paraoxonase 2 with potential anti-biofilm property

Paraoxonase 2 (PON2) is considered as a potential anti-biofilm agent due to the highest lactonase activity among the PON family members implicating quorum quenching in gram-negative bacteria. However, PON2 is expressed mostly in insoluble fractions in the bacterial expression host which limits its application as an anti-biofilm agent. Therefore, obtaining the native human PON2 (HuPON2) protein in soluble form, better protein yield, stability, and enzymatic activities is essential. In this study, procedures for obtaining a high yield of the native form of HuPON2 in soluble and active forms were optimized. Guanidinium hydrochloride solubilized the HuPON2 protein, however, it is lethal for several bacteria, and thus a major problem for studying the various downstream application of the protein. Therefore, another refolding process for native HuPON2 was optimized. Owing to the promiscuous nature of HuPON2, we hypothesized that it could inhibit the biofilm formation in Mycobacterium smegmatis also. Interestingly, we observed a significant inhibition of the biofilm formation by HuPON2_Rf. However, the primary target of HuPON2 and the probable mechanism behind the quorum quenching in M. smegmatis need to be further explored, which would help widen the scope of HuPON2 as a potential anti-biofilm agent beyond the gram-negative bacteria.

The Structure and Function of Paraoxonase-1 and Its Comparison to Paraoxonase-2 and -3

Serum paraoxonase-1 (PON1) is the most studied member of the group of paraoxonases (PONs). This enzyme possesses three enzymatic activities: lactonase, arylesterase, and paraoxonase activity. PON1 and its isoforms play an important role in drug metabolism as well as in the prevention of cardiovascular and neurodegenerative diseases. Although all three members of the PON family have the same origin and very similar amino acid sequences, they have different functions and are found in different locations. PONs exhibit substrate promiscuity, and their true physiological substrates are still not known. However, possible substrates include homocysteine thiolactone, an analogue of natural quorum-sensing molecules, and the recently discovered derivatives of arachidonic acid—bioactive δ-lactones. Directed evolution, site-directed mutagenesis, and kinetic studies provide comprehensive insights into the active site and catalytic mechanism of PON1. However, there is still a whole world of mystery waiting to be discovered, which would elucidate the substrate promiscuity of a group of enzymes that are so similar in their evolution and sequence yet so distinct in their function.

Engineering acyl-homoserine lactone-interfering enzymes toward bacterial control

Enzymes able to degrade or modify acyl-homoserine lactones (AHLs) have drawn considerable interest for their ability to interfere with the bacterial communication process referred to as quorum sensing. Many proteobacteria use AHL to coordinate virulence and biofilm formation in a cell density-dependent manner; thus, AHL-interfering enzymes constitute new promising antimicrobial candidates. Among these, lactonases and acylases have been particularly studied. These enzymes have been isolated from various bacterial, archaeal, or eukaryotic organisms and have been evaluated for their ability to control several pathogens. Engineering studies on these enzymes were carried out and successfully modulated their capacity to interact with specific AHL, increase their catalytic activity and stability, or enhance their biotechnological potential. In this review, special attention is paid to the screening, engineering, and applications of AHL-modifying enzymes. Prospects and future opportunities are also discussed with a view to developing potent candidates for bacterial control.

Engineering quorum quenching enzymes: progress and perspectives

Quorum sensing is a key contributor to the virulence of many important plant, animal and human pathogens. The disruption of this signalling—a process referred to as ‘quorum quenching’—is a promising new approach for controlling microbial pathogens. In this mini-review, we have focused on efforts to engineer enzymes that disrupt quorum sensing by inactivating acyl-homoserine lactone signalling molecules. We review different approaches for protein engineering and provide examples of how these engineering approaches have been used to tailor the stability, specificity and activities of quorum quenching enzymes. Finally, we grapple with some of the issues around these approaches—including the disconnect between in vitro biochemistry and potential in vivo applications.

Paraoxonases Activities and Polymorphisms in Elderly and Old-Age Diseases: An Overview

Aging is defined as the accumulation of progressive organ dysfunction. There is much evidence linking the involvement of oxidative stress in the pathogenesis of aging. With increasing age, susceptibility to the development of diseases related to lipid peroxidation and tissue injury increases, due to chronic inflammatory processes, and production of reactive oxygen species (ROS) and free radicals. The paraoxonase (PON) gene family is composed of three members (PON1, PON2, PON3) that share considerable structural homology and are located adjacently on chromosome 7 in humans. The most studied member product is PON1, a protein associated with high-density lipoprotein with paraoxonase/esterase activity. Nevertheless, all the three proteins prevent oxidative stress. The major aim of this review is to highlight the importance of the role of PON enzymes in the aging process, and in the development of the main diseases present in the elderly: cardiovascular disease, diabetes mellitus, neurodegenerative diseases, and cancer.

Progress in and promise of bacterial quorum sensing research

This Review highlights how we can build upon the relatively new and rapidly developing field of research into bacterial quorum sensing (QS). We now have a depth of knowledge about how bacteria use QS signals to communicate with each other and to coordinate their activities. In recent years there have been extraordinary advances in our understanding of the genetics, genomics, biochemistry, and signal diversity of QS. We are beginning to understand the connections between QS and bacterial sociality. This foundation places us at the beginning of a new era in which researchers will be able to work towards new medicines to treat devastating infectious diseases, and use bacteria to understand the biology of sociality.

Catalytic Characteristics of New Antibacterials Based on Hexahistidine-Containing Organophosphorus Hydrolase

Catalytic characteristics of hexahistidine-containing organophosphorus hydrolase (His6-OPH) and its enzyme-polyelectrolyte complexes with poly-l-glutamic acid or poly-l-aspartic acid (His6-OPH/PLD50), hydrolyzing organophosphorous compounds, and N-acyl homoserine lactones were studied in the presence of various antibiotics (ampicillin, gentamicin, kanamycin, and rifampicin). The antibiotics at concentrations below 1 g·L−1 had a negligible inhibiting effect on the His6-OPH activity. Mixed inhibition of His6-OPH was established for higher antibiotic concentrations, and rifampicin was the most potent inhibitor. Stabilization of the His6-OPH activity was observed in the presence of antibiotics at a concentration of 0.2 g·L−1 during exposure at 25–41 °C. Molecular docking of antibiotics to the surface of His6-OPH dimer revealed the antibiotics binding both to the area near active centers of the enzyme subunits and to the region of contact between subunits of the dimer. Such interactions between antibiotics and His6-OPH were verified with Fourier-transform infrared (FTIR) spectroscopy. Considering all the results of the study, the combination of His6-OPH/PLD50 with β-lactam antibiotic ampicillin was established as the optimal one in terms of exhibition and persistence of maximal lactonase activity of the enzyme.

Improving Pseudomonas fluorescens esterase for hydrolysis of lactones

Although both acyclic esters and lactones contain ester functional groups, their shapes differ and most esterases are poor catalysts for hydrolysis of lactones.