Engineering Whole-Cell Biosensors for Enhanced Detection of Environmental Antibiotics Using a Synthetic Biology Approach.

Bacterial Two component systems have evolved with many intricate sensory apparatuses for external stimuli like light, temperature, oxygen, pH and chemical compounds. Recent studies have shown the potential of two-component regulatory systems (TCSs) of bacteria in creating synthetic regulatory circuits for several applications. Antimicrobial resistance is increasing globally in both developing and developed countries and it is one of the foremost global threats to public health. The resistance level to a broad spectrum of antibiotics is rising every year by 5-10%. In this context, TCSs controlling microbial physiology at the transcriptional level could be an appropriate candidate for monitoring the antibiotics present in the environment. This review provided a wide opportunity to gain knowledge about the TCSs available in diverse species to sense the antibiotics. Further, this review explored the EMeRALD (Engineered Modularized Receptors Activated via Ligand-induced Dimerization) based biosensors to repurpose the sensing modules from the microbial TCSs using the synthetic biology approach.

Noninvasive Biomarkers for Alcohol-Related Liver Disease-A Proteomic Related Preliminary Report.

Increased alcohol intake over decades leads to progressive alcohol-related liver disease (ALD) and contributes to increased mortality. It is characterized by reduced platelet count. Platelets have a role in protecting vascular integrity and involved in liver regeneration. Alcohol affects the platelet count and its function. Platelet function is regulated by their proteins, released during pathophysiological conditions. Therefore, platelet proteome plays a vital role during ALD. This preliminary study consists of 10 patients with ALD. It includes the preparation of human platelets for the proteomic approach. We performed liquid chromatography-mass spectrometry for the samples. A total of 536 proteins were identified in patients with ALD of which 31 proteins were mentioned as a candidate based on their clinical significance. The advancement of diagnostic or therapeutic tools based on the application of platelet proteins in ALD is still far off. Platform for platelet and its proteome research may give diagnostic and prognostic insights into ALD. Platelet proteomes could possibly be concluded as therapeutic and potential diagnostic or prognostic markers in ALD. Supplementary Information: The online version contains supplementary material available at 10.1007/s12291-023-01120-9.

In Silico Characterization of Pathogenic Homeodomain Missense Mutations in the PITX2 Gene.

Paired homologous domain transcription factor 2 (PITX2) is critically involved in ocular and cardiac development. Mutations in PITX2 are consistently reported in association with Axenfeld-Rieger syndrome, an autosomal dominant genetic disorder and atrial fibrillation, a common cardiac arrhythmia. In this study, we have mined missense mutations in PITX2 gene from NCBI-dbSNP and Ensembl databases, evaluated the pathogenicity of the missense variants in the homeodomain and C-terminal region using five in silico prediction tools SIFT, PolyPhen2, GERP, Mutation Assessor and CADD. Fifteen homeodomain mutations G42V, G42R, R45W, S49Y, R53W, E53D, E55V, R62H, P65S, R69H, G75R, R84G, R86K, R87W, R91P were found to be highly pathogenic by both SIFT, PolyPhen2 were further functionally characterized using I-Mutant 2.0, Consurf, MutPred and Project Hope. The findings of the study can be used for prioritizing mutations in the context of genetic studies.

Noncoding RNAs associated with IgA nephropathy.

IgA nephropathy (IgAN) is one of the most common glomerulonephritides. The disease is characterized by haematuria, proteinuria, deposition of galactose-deficient IgA1 in the glomerular mesangium and mesangial hypercellularity, further leading to extracellular matrix expansion. Kidney biopsy is the gold standard for IgAN diagnosis. Due to the invasiveness of renal biopsy, there is an unmet need for noninvasive biomarkers to diagnose and estimate the severity of IgAN. Understanding the role of RNA molecules as genetic markers to target diseases may allow developing therapeutic and diagnostic markers. In this review we have focused on intrarenal, extrarenal and extracellular noncoding RNAs involved in the progression of IgAN. This narrative review summarizes the pathogenesis of IgAN along with the correlation of noncoding RNA molecules such as microRNAs, small interfering RNAs, circular RNAs and long non-coding RNAs that play an important role in regulating gene expression, and that represent another type of regulation affecting the expression of specific glycosyltranferases, a key element contributing to the development of IgAN.

Analysis of Novel Antioxidant Sesquarterpenes (C35 Terpenes) Produced in Recombinant Corynebacterium glutamicum.

Novel synthetic isoprenoids have been synthesized in engineered microbial hosts by evolving terpene synthase or expressing heterologous terpene synthases. Recently, the native operon, crtNaNcM derived from Planococcus sp. PAMC 21323, has isolated for potential industrial applications of C35 carotenoids. For the first time, novel C35 carotenoids (sesquarterpene) were synthesized in Corynebacterium glutamicum expressing the crtNaNcM genes. The recombinant strains accumulate various sesquarterpene including 4-apolycopene (red color), 4-aponeurosporene (yellow color), and no pigmentation, depending on the expression of the genetic elements of the crtNaNcM genes. Subsequently, the carotenoid extract from the cells harboring pCES-H36-CrtNaNcM was analyzed, resulting in significantly higher antioxidant activity than those of other strains harboring pCES-H36-CrtNcM and pCES-H36-CrtNaNc, respectively. This study will promote further engineering of C. glutamicum to increase sesquarterpene productions.

A Chimeric Two-Component Regulatory System-Based Escherichia coli Biosensor Engineered to Detect Glutamate.

In this study, we constructed amino acid biosensors that can be used as a high-throughput system to screen microorganisms that produce glutamate. The biosensors are based on two-component regulatory systems (TCRSs) combined with green fluorescent protein (GFP) as a reporter. A chimeric DegS/EnvZ (DegSZ) TCRS was constructed by fusing the N-terminal domain of the sensor kinase DegS from Planococcus sp. PAMC21323 with the catalytic domain of the osmosensor EnvZ from Escherichia coli to control expression of gfp in response to glutamate. gfp was controlled by the ompC promoter through the activated response regulator OmpR-P. The chimeric TCRS-based biosensors showed a 4-fold increase in the fluorescent signal after adding glutamate. A linear correlation was observed between fluorescence intensity and exogenously added glutamate concentration. The chimeric TCRS-based biosensor was used to determine glutamate concentration at the single-cell level by fluorescence-activated cell sorting. Therefore, this biosensor can be used to isolate novel gene products and optimize pathways involved in amino acid production.

Engineered microbial biosensors based on bacterial two-component systems as synthetic biotechnology platforms in bioremediation and biorefinery.

Two-component regulatory systems (TCRSs) mediate cellular response by coupling sensing and regulatory mechanisms. TCRSs are comprised of a histidine kinase (HK), which serves as a sensor, and a response regulator, which regulates expression of the effector gene after being phosphorylated by HK. Using these attributes, bacterial TCRSs can be engineered to design microbial systems for different applications. This review focuses on the current advances in TCRS-based biosensors and on the design of microbial systems for bioremediation and their potential application in biorefinery.

Good use of fruit wastes: eco-friendly synthesis of silver nanoparticles, characterization, BSA protein binding studies.

A simple and eco-friendly methodology for the green synthesis of silver nanoparticles (AgNPs) using a mango seed extract was evaluated. The AgNPs were characterized by ultraviolet-visible spectrophotometry, Fourier transform infrared spectroscopy, transmission electron microscopy, energy dispersive X-ray spectroscopy, and X-ray diffraction. The interaction between the green synthesized AgNPs and bovine serum albumin (BSA) in an aqueous solution at physiological pH was examined by fluorescence spectroscopy. The results confirmed that the AgNPs quenched the fluorophore of BSA by forming a ground state complex in aqueous solution. This fluorescence quenching data were also used to determine the binding sites and binding constants at different temperatures. The calculated thermodynamic parameters (ΔG°, ΔH° and ΔS°) suggest that the binding process occurs spontaneously through the involvement of electrostatic interactions. The synchronous fluorescence spectra showed a blue shift, indicating increasing hydrophobicity. Copyright © 2015 John Wiley & Sons, Ltd.

Interaction Studies of Greenly Synthesized Gold Nanoparticles with Bovine Serum Albumin (BSA) Using Fluorescence Spectroscopy.

In the present study, gold nanoparticles (AuNPs) with an average particle size of -41.23 nm were synthesized using eco-friendly reducing material (i.e., aqueous Nelumbo nucifera root extract). Rapid reduction results in the formation of polydispersed nanoparticles. The formation of AuNPs was characterized by surface plasmon resonance (SPR) which was determined by UV-Vis spectra (band at 544 nm), FTIR, SEM-EDX, TEM, HR-TEM, and XRD. This study aims to investigate the interaction between AuNPs and Bovine Serum Albumin (BSA) using fluorescence spectroscopy. The analysis of fluorescence spectra and intensity at physiological pH in an aqueous solution indicates that AuNPs have a potent ability to quench the BSA fluorescence by both quenching mechanisms. Resonance light scattering spectra indicated the formation of BSA-AuNPs complex. The number of binding sites and binding constants were determined based on fluorescence quenching at different temperatures. The thermodynamic parameters were also calculated at various temperatures that indicate that hydrophobic forces are abundant in the AuNPs-BSA complex. Negative ΔG degrees values suggest that the binding process is spontaneous. Synchronous fluorescence spectra showed a blue shift and CD spectra showed an increase in a-helicity content which is an indication of increasing hydrophobicity.

Construction of a high efficiency copper adsorption bacterial system via peptide display and its application on copper dye polluted wastewater.

For the construction of an efficient copper waste treatment system, a cell surface display strategy was employed. The copper adsorption ability of recombinant bacterial strains displaying three different copper binding peptides were evaluated in LB Luria-Bertani medium (LB), artificial wastewater, and copper phthalocyanine containing textile dye industry wastewater samples. Structural characteristics of the three peptides were also analyzed by similarity-based structure modeling. The best binding peptide was chosen for the construction of a dimeric peptide display and the adsorption ability of the monomeric and dimeric peptide displayed strains were compared. The dimeric peptide displayed strain showed superior copper adsorption in all three tested conditions (LB, artificial wastewater, and textile dye industry wastewater). When the strains were exposed to copper phthalocyanine dye polluted wastewater, the dimeric peptide display [543.27 µmol/g DCW dry cell weight (DCW)] showed higher adsorption of copper when compared with the monomeric strains (243.53 µmol/g DCW).

Construction of malate-sensing Escherichia coli by introduction of a novel chimeric two-component system.

In an attempt to develop a high-throughput screening system for screening microorganisms which produce high amounts of malate, a MalKZ chimeric HK-based biosensor was constructed. Considering the sequence similarity among Escherichia coli (E. coli) MalK with Bacillus subtilis MalK and E. coli DcuS, the putative sensor domain of MalK was fused with the catalytic domain of EnvZ. The chimeric MalK/EnvZ TCS induced the ompC promoter through the cognate response regulator, OmpR, in response to extracellular malate. Real-time quantitative PCR and GFP fluorescence studies showed increased ompC gene expression and GFP fluorescence as malate concentration increased. By using this strategy, various chimeric TCS-based bacteria biosensors can be constructed, which may be used for the development of biochemical-producing recombinant microorganisms.

Evaluation of zraP gene expression characteristics and construction of a lead (Pb) sensing and removal system in a recombinant Escherichia coli.

A ZraP-based lead sensing and removal system was constructed in E. coli. It was regulated by the ZraS/ZraR two-component system. The expression profile of the zraP gene towards extracellular lead was studied via real-time PCR. A dual-function bacterial system was also designed to express GFP and OmpC-lead binding peptide under the control of zraP for the simultaneous sensing and adsorption of environmental lead without additional manipulation. The constructed bacterial system can emit fluorescence and it adsorbed a maximum of 487 µmol lead/g cell DCW. From a study of artificial wastewater, the constructed bacteria adsorbed lead highly selectively (427 µmol lead/g cell DCW) among other metal ions. The newly-constructed dual function bacterial system can be applied for the development of an efficient process for the removal of lead from polluted wastes.

Green synthesized silver nanoparticles using Nelumbonucifera root extract for efficient protein binding, antioxidant and cytotoxicity activities.

Silver nanoparticles (AgNPs) with a mean particle size of ∼ 16.7 nm were synthesized using an eco-friendly reducing material, aqueous Nelumbo nucifera root extract. Rapid reduction resulted in the formation of polydispersed nanoparticles. The formation of AgNPs was characterized by surface plasmon resonance, which was determined by ultraviolet-visible (UV-Vis) spectroscopy (band at 412 nm), Fourier transform infrared spectroscopy, scanning electron microscopy-energy dispersive X-ray spectroscopy, transmission electron microscopy and X-ray diffraction. The interaction of the green synthesized AgNPs with Bovine Serum Albumin (BSA) at various temperatures was investigated. Fluorescence quenching, synchronous and resonance light scattering spectroscopy along with UV-Vis absorption studies revealed the efficient binding between BSA and the AgNPs. In addition, the AgNPs exhibited moderate antioxidant and cytotoxicity activities against HeLa cell lines.

Cortisol effect on heat shock proteins in the C2C12 and 3T3-L1 cells.

The present study was carried out to understand the effect of cortisol on heat shock protein system (Hsps) in the C2C12 and 3T3-L1 cells under co-culture system. Cells were co-cultured by using Transwell inserts with a 0.4-µm porous membrane to separate C2C12 and 3T3-L1 cells. Each cell type was grown independently on the Transwell plates. After cell differentiation, inserts containing 3T3-L1 cells were transferred to C2C12 plates and inserts containing C2C12 cells transferred to 3T3-L1 plates. Ten micrograms per microliter of cortisol was added to the medium. Following 72 h of treatment, the cells in the lower wells were harvested for analysis. Heat shock proteins (Hsps) such as Hsp27, Hsp70, and Hsp90 were selected for the analysis. The qRT-PCR results showed the significant increase in the mRNA expression of as Hsp27, Hsp70, and Hsp90. In addition, confocal microscopical investigation showed the cortisol treatment increases Hsps expressions in the mono and co-cultured C2C12 and 3T3-L1 cells. From the results, we concluded that the cortisol increases Hsps expression in the co-cultured C2C12 and 3T3-L1 cells, which is differed from one-dimensional mono-cultured C2C12 and 3T3-L1 cells.

Effect of cortisol on calpains in the C2C12 and 3T3-L1 cells.

The present study was carried out to understand the effect of cortisol on calpain system in the C2C12 and 3T3-L1 adipocyte cells under co-culture system. Cells were co-cultured by using transwell inserts with a 0.4 µm porous membrane to separate C2C12 and 3T3-L1 preadipocyte cells. Each cell type was grown independently on the transwell plates. Following cell differentiation, inserts containing 3T3-L1 cells were transferred to C2C12 plates. Ten microgram per milliliter of cortisol was added to the medium. Following treatment for 3 days, the cells in the lower well were harvested for analysis. Calpains such as µ-calpain, m-calpain, and calpastatin were selected for the analysis. RT-PCR results indicated the significant increase in the mRNA expression of µ-calpain, m-calpain, and calpastatin. In addition, the confocal microscopical investigation indicated the cortisol treatment increases calpain expression in the C2C12 and 3T3-L1 cells. Taking all these together, cortisol treatment with co-culture system shows most reliable status of calpains expression in the cells, which is quite distinct from one-dimensional monocultured cells.

A new arene-Ru based supramolecular coordination complex for efficient binding and selective sensing of green fluorescent protein.

A new dipyridyl ligand is encoded with 120° angularity between its coordination vectors by using a central pyridine carboxamide scaffold to orient two 4-(pyridin-4-ylethynyl)phenyl moieties. The N,N'-bis(4-(pyridin-4-ylethynyl)phenyl)pyridine-2,6-dicarboxamide ligand undergoes self-assembly with a diruthenium arene complex to furnish a [2 + 2] metallacycle with a wedge-like structure. The metallacycle binds to the enhanced green fluorescent protein (EGFP) variant of GFP, resulting in steady-state spectral changes in UV-Vis absorption and emission experiments. These studies indicate that the metallacycle induces conformation changes to the EGFP, disrupting the tripeptide chromophore. Furthermore, gel electrophoresis, circular dichroism and atomic force microscopy studies indicate that binding ultimately leads to aggregation of the protein. Computational investigations indicate a favorable interaction, predominantly between the metallacycle and the Arg168 residue of the EGFP. An interaction with Arg168 and related residues was previously observed for an emission-attenuating antibody, supporting that these interactions induce changes to the photophysical properties of EGFP by disrupting the tripeptidechromophore in a similar manner. Additionally, we have also described the quenching study of the reporter GFP protein in vivo by a new metal complex using reflected fluorescence microscopy. We anticipate that such metal complexes which can passively diffuse into the cells in vivo can serve as potential tools in molecular and drug targeting based biological studies.

Impact of stress hormone on adipogenesis in the 3T3-L1 adipocytes.

Stress hormone is known to play a vital role in lipolysis and adipogenesis in fat cells. The present study was carried out to evaluate the effect of epinephrine on adipogenesis in the 3T3-L1 cells. The investigation on adipogenesis was done in both mono and co-cultured 3T3-L1 cells. 3T3-L1 preadipocytes and C2C12 cells were grown independently on transwell plates and transferred to differentiation medium. Following differentiation, C2C12 cells transferred to 3T3-L1 plate and treated with medium containing 10 µg/ml of epinephrine. Adipogenic markers such as fatty acid binding protein 4, peroxisome proliferator activating receptor, CCAAT/enhancer-binding protein, adiponectin, lipoprotein lipase and fatty acid synthase mRNA expressions were evaluated in the 3T3-L1 cells. Epinephrine treatment reduced adipogenesis, evidenced by reducing adipogenic marker mRNA expression in the 3T3-L1 cells. In addition, glycerol accumulation and oil red-O staining supported the reduced rate of adipogenesis. Taking all together, it is concluded that the stress hormone, epinephrine reduces the rate of adipogenesis in the mono and co-cultured 3T3-L1 cells. In addition, the rate of adipogenesis is much reduced in the co-cultured 3T3-L1 cells compared monocultured 3T3-L1 cells.

Engineered fumarate sensing Escherichia coli based on novel chimeric two-component system.

DcuS/DcuR two component system (TCS) was firstly employed for the expression of the gfp gene under the dcuB gene promoter in aerobic condition to develop high throughput screening system able to screen microorganisms producing high amount of fumarate. However, the DcuS/DcuR TCS could not produce a signal strong enough to mediate the expression of the gfp gene responding fumarate concentration. Thus, DcuS/DucR TCS was engineered by recruiting the EnvZ/OmpR system, the most-studied TCS in E. coli. A chimeric DcuS/EnvZ (DcuSZ) TCS was constructed by fusing the sensor histidine kinase of DcuS with the cytoplasmic catalytic domain of EnvZ, in which the expression of the gfp gene or the ompC gene was mediated by the ompC gene promoter through the cognate response regulator, OmpR. The output signals produced by the chimeric DcuSZ TCS were enough to detect fumarate concentration quantatively, in which the expressions of the gfp gene and the ompC gene were proportional to the fumarate concentration in the medium. Moreover, principal component analysis of C4-dicarboxylates showed that DcuSZ chimera was highly specific to fumarate but could also respond to other C4-dicarboxylates, which strongly suggests that TCS-based high throughput screening system able to screen microorganisms producing target chemicals can be developed.

Modification of response behavior of zinc sensing HydHG two-component system using a self-activation loop and genomic integration.

Characterizing the dynamics of HydHG-a two-component transcriptional regulatory network for exogenous zinc in E. coli-is essential in understanding the biology of these regulatory and signaling pathways. Here, we used a synthetic biology strategy to modify the dynamic characteristics of the HydHG network in two ways. First, a self-activation loop for HydHG network was created under the control of zraP promoter, after which the threshold Zn(2+) concentration for the self-activated HydHG network significantly decreased from 200 to 10 µM. Second, the self-activation loop was integrated into the E. coli genome allowing the threshold Zn(2+) concentration to be elevated to 500 µM. As the threshold Zn(2+) concentration could be modified in both directions, the introduction of a self-activation loop and the entire genomic integration strategy may prove useful for the creation of a two-component bacterial biosensor with varying sensitivities.