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Abstract Background Rhodopsin is a seven-transmembrane protein covalently linked with retinal chromophore that absorbs photons for energy conversion and intracellular signaling in eukaryotes, bacteria, and archaea. Haloarchaeal rhodopsins are Type-I microbial rhodopsin that elicits various light-driven functions like proton pumping, chloride pumping and Phototaxis behaviour. The industrial application of Ion-pumping Haloarchaeal rhodopsins is limited by the lack of full-length rhodopsin sequence-based classifications, which play an important role in Ion-pumping activity. The well-studied Haloarchaeal rhodopsin is a proton-pumping bacteriorhodopsin that shows promising applications in optogenetics, biosensitized solar cells, security ink, data storage, artificial retinal implant and biohydrogen generation. As a result, a low-cost computational approach is required to identify Ion-pumping Haloarchaeal rhodopsin sequences and its subtype. Results This study uses a support vector machine (SVM) technique to identify these ion-pumping Haloarchaeal rhodopsin proteins. The haloarchaeal ion pumping rhodopsins viz., bacteriorhodopsin, halorhodopsin, xanthorhodopsin, sensoryrhodopsin and marine prokaryotic Ion-pumping rhodopsins like actinorhodopsin, proteorhodopsin have been utilized to develop the methods that accurately identified the ion pumping haloarchaeal and other type I microbial rhodopsins. We achieved overall maximum accuracy of 97.78%, 97.84% and 97.60%, respectively, for amino acid composition, dipeptide composition and hybrid approach on tenfold cross validation using SVM. Predictive models for each class of rhodopsin performed equally well on an independent data set. In addition to this, similar results were achieved using another machine learning technique namely random forest. Simultaneously predictive models performed equally well during five-fold cross validation. Apart from this study, we also tested the own, blank, BLAST dataset and annotated whole-genome rhodopsin sequences of PWS haloarchaeal isolates in the developed methods. The developed web server ( https://bioinfo.imtech.res.in/servers/rhodopred ) can identify the Ion Pumping Haloarchaeal rhodopsin proteins and their subtypes. We expect this web tool would be useful for rhodopsin researchers. Conclusion The overall performance of the developed method results show that it accurately identifies the Ionpumping Haloarchaeal rhodopsin and their subtypes using known and unknown microbial rhodopsin sequences. We expect that this study would be useful for optogenetics, molecular biologists and rhodopsin researchers.

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In India, north-east region holds a special position of having diverse range of plants belonging to endemic species with widespread ethnomedicinal properties which remain unexplored till date. In the present study, Eriobotrya bengalensis (Roxb.) Hook. f. extract was evaluated for its radical scavenging activity and ability to combat quorum sensing regulated bacterial virulence in Pseudomonas aeruginosa PAO1. The ethanolic leaf extract of E. bengalensis (Roxb.) Hook. f. exhibited a concentration dependent radical scavenging of highly reactive DPPH and hydroxyl radicals with a scavenging percentage of 76.84 ± 4.72 and 67.37 ± 4.35 % respectively at a concentration of 500 µg/ml. E. bengalensis (Roxb.) Hook. f. also showed significant reducing power and relatively high ascorbic acid equivalent. The plant extract was also evaluated for its ability to down-regulate the production of quorum sensing (QS) regulated pathogenic determinants in P. aeruginosa PAO1. The violacein production in Chromobacterium violaceum and pyocyanin production in P. aeruginosa PAO1 was greatly inhibited on treatment with sub-MIC of E. bengalensis (Roxb.) Hook. f. with an inhibition of 79.58 ± 4.13 and 76.31 ± 4.03 % respectively. The anti-biofilm activity was further confirmed by confocal laser scanning microscopic (CLSM) analysis. The anti QS activity of E. bengalensis (Roxb.) Hook. f. was further corroborated by molecular docking studies which provides an insight into the mechanism of QS inhibition. The present result will provide novel leads to the application of unexplored plant species towards the development of novel anti-infectives in the post-antibiotic era.

Objective: To investigate the antioxidant and anti-infective potential of Phrynium capitatum and Dryptes indica extract. Methods: The antioxidant potentials were determined by DPPH radical scavenging, reducing power, hydroxyl radical scavenging and total antioxidant assays. We further examined anti-quorum sensing activity and inhibition of synthesis of pathogenic factor of Chromobacterium violaceum and Pseudomonas aeruginosa PAO1. Bioactive compounds were determined using gas chromatography–mass spectrometry analysis. In silico analysis was conducted to determine the binding affinity of bioactive compounds of plant extracts for the quorum sensing regulatory receptor LasR. Results: DPPH assay showed that the ethanolic extract of Phrynium capitatum and Dryptes indica at 500 μg/mL showed (86.96 ± 4.07)% and (74.83 ± 3.47)% inhibition, respectively. Hydroxyl radical scavenging assay showed (73.17 ± 3.03)% and (62.63 ± 4.59)% activity, respectively. The ethanolic extract of Phrynium capitatum and Dryptes indica showed high level of attenuation of quorum sensing regulated pyocyanin production. Confocal laser scanning microscopic analysis revealed that the extracts had the potential to effectively inhibit biofilm formation of Pseudomonas aeruginosa. Molecular docking analysis showed a better binding affinity of bioactive compounds from the extracts for the structure of LasR protein of Pseudomonas aeruginosa. Conclusions: The ethanolic extracts of Phrynium capitatum and Dryptes indica possess antioxidant activity and the potential to inhibit the quorum sensing system and its regulatory irulence traits in Pseudomonas aeruginosa PAO1.

Pseudomonas aeruginosa is an important opportunistic pathogen which causes bacterial keratitis, cyctic fibrosis and other hospital acquired infections. Its ability to form biofilm provides resistance to conventional antibiotics and further corroborates the global health concerns. The antibiotic resistance by P. aeruginosa is due to highly complex cellular signaling system called quorum sensing (QS). As QS controls bacterial pathogenicity and plays a crucial role in biofilm formation, it is a promising alternative target to combat the bacterial virulence. The present study aims to determine the inhibitory activity of Plectranthus tenuiflorus extract on QS and biofilm development in P. aeruginosa PAO1. The crude plant extract inhibited the production of pyocyanin, elastase, protease and chitinase by 71.96 ± 1.82, 38.74 ± 1.29, 30.84 ± 1.20 and 44.75 ± 1.40 % respectively at sub-MIC concentration of 500 µg/ml. The production of biofilm aggravating phenotypes such as exopolysaccharides, alginate and rhamnolipid were also significantly reduced. The biofilm inhibition capability of P. tenuiflorus was further supported by light microscopic and confocal laser scanning microscopic analysis. The phytochemicals such as phytol and mosloflavone were identified from the crude extract using gas chromatography–mass spectrometry (GC-MS). The role of these phytochemicals in down regulation of QS in P. aeruginosa was further confirmed by in silico studies targeting transcriptional receptors, LasR and RhlR of the QS regulatory network. The in vitro and docking studies suggest the anti QS potential of P. tenuiflorus in combating the bacterial pathogenesis.

Haloarchaea inhabit high salinity environments worldwide. They are a potentially rich source of crucial biomolecules like carotenoids and industrially useful proteins. However, diversity in haloarchaea present in Indian high salinity environments is poorly studied. In the present study, we isolated 12 haloarchaeal strains from hypersaline Kottakuppam, Tamil Nadu solar saltern in India. 16S rRNA based taxonomic characterization of these isolates suggested that nine of them are novel strains that belong to genera Haloarcula, Halomicrobium, and Haloferax. Transmission electron microscopy suggests the polymorphic nature of these haloarchaeal isolates. Most of the haloarchaeal species are known to be high producers of carotenoids. We were able to isolate carotenoids from all these 12 isolates. The UV-Vis spectroscopy-based analysis suggests that bacterioruberin and lycopene are the major carotenoids produced by these isolates. Based on the visual inspection of the purified carotenoids, the isolates were classified into two broad categories i.e., yellow and orange, attributed to the differences in the ratio of bacterioruberin and lycopene as confirmed by the UV-Vis spectral analysis. Using a PCR-based screening assay, we were able to detect the presence of the bacteriorhodopsin gene (bop) in 11 isolates. We performed whole-genome sequencing for three bop positive and one bop negative haloarchaeal isolates. Whole-genome sequencing, followed by pan-genome analysis identified multiple unique genes involved in various biological functions. We also successfully cloned, expressed, and purified functional recombinant bacteriorhodopsin (BR) from one of the isolates using Escherichia coli as an expression host. BR has light-driven proton pumping activity resulting in the proton gradient across the membrane, which is utilized by V-Type ATPases to produce ATP. We analyzed the distribution of bop and other accessory genes involved in functional BR expression and ATP synthesis in all the representative haloarchaeal species. Our bioinformatics-based analysis of all the sequenced members of genus Haloarcula suggests that bop, if present, is usually inserted between the genes coding for B and D subunits of the V-type ATPases operon. This study provides new insights into the genomic variations in haloarchaea and reports expression of new BR variant having good expression in functional form in E. coli.

Background Rise in the number of healthcare associated or hospital acquired infections is a major problem affecting the global healthcare sector. We evaluated superior antibacterial and antibiofilm photodynamic therapy (aPDT) using malachite green encapsulated mesoporous silica nanoparticles (MG-MSN) against Staphylococcus aureus and Escherichia coli, which are known to be major causative agents of nosocomial infections. Methods Malachite green (MG) was encapsulated on mesoporous silica nanoparticles (MSN). Fourier-transform infrared spectroscopy, Transmission electron microscopy, and spectroscopic analysis were performed to characterize the MG-MSN. The antimicrobial efficacies of MSN, MG, and MG-MSN were investigated and the results were recorded. Results MG-MSN was effective against both the tested bacteria. S. aureus was more phototoxic to MG-MSN compared to E. coli. The antibiofilm efficacy of MG-MSN on E. coli and S. aureus was also studied. Biofilm inhibition was 65.68 ± 2.62% in E. coli and 79.66 ± 3.82% in S. aureus. Cell viability assay, exopolysaccharides quantification, and confocal laser scanning microscopy studies also revealed the enhanced antibiofilm activity of MG-MSN when used as a potential photosensitizer for aPDT. This study can be extended to eradicate these strains from localized superficial infections and medical appliances, preventing nosocomial infections.

The persistence of multidrug resistance among microorganisms has directed a mandate towards a hunt for the development of alternative therapeutic modalities. In this context, antimicrobial photodynamic therapy (aPDT) is sprouted as a novel strategy to mitigate biofilms and planktonic cells of pathogens. Nanoparticles (NPs) are reported with unique intrinsic and antimicrobial properties. Therefore, silver NPs (AgNPs) were investigated in this study to determine their ability to potentiate the aPDT of photosensitizer against Staphylococcus aureus and Pseudomonas aeruginosa. Biologically synthesized AgNPs were surface coated with methylene blue (MB) and studied for their aPDT against planktonic cells and biofilms of bacteria. The nano-conjugates (MB-AgNPs) were characterized for their size, shape and coated materials. MB-AgNPs showed significant phototoxicity against both forms of test bacteria and no toxicity was observed in the dark. Moreover, activity of MB-AgNPs was comparatively higher than that of the free MB, which concludes that MB-AgNPs could be an excellent alternative to combat antibiotic resistant bacteria.

The application of nanotechnology in medicine is gaining popularity due to its ability to increase the bioavailability and biosorption of numerous drugs. Chrysin, a flavone constituent of Orocylumineicum vent is well-reported for its biological properties. However, its therapeutic potential has not been fully exploited due to its poor solubility and bioavailability. In the present study, chrysin was encapsulated into chitosan nanoparticles using TPP as a linker. The nanoparticles were characterized and investigated for their anti-biofilm activity against Staphylococcus aureus. At sub-Minimum Inhibitory Concentration, the nanoparticles exhibited enhanced anti-biofilm efficacy against S. aureus as compared to its bulk counterparts, chrysin and chitosan. The decrease in the cell surface hydrophobicity and exopolysaccharide production indicated the inhibitory effect of the nanoparticles on the initial stages of biofilm development. The growth curve analysis revealed that at a sub-MIC, the nanoparticles did not exert a bactericidal effect against S. aureus. The findings indicated the anti-biofilm activity of the chrysin-loaded chitosan nanoparticles and their potential application in combating infections associated with S. aureus.

Methanotrophs are bacteria that consume methane (CH4) as their sole carbon and energy source. These microorganisms play a crucial role in the carbon cycle by metabolizing CH4 (the greenhouse gas), into cellular biomass and carbon dioxide (CO2). Polyhydroxyalkanoates (PHAs) are biopolymers produced by various microorganisms, including methanotrophs. PHA production using methanotrophs is a promising strategy to address growing concerns regarding plastic pollution and the need for sustainable, biodegradable materials. Various factors, including nutrient availability, environmental conditions, and metabolic engineering strategies, influence methanotrophic production. Nutrient limitations, particularly those of nitrogen or phosphorus, enhance PHA production by methanotrophs. Metabolic engineering approaches, such as the overexpression of key enzymes involved in PHA biosynthesis or the disruption of competing pathways, can also enhance PHA yields by methanotrophs. Overall, PHA production by methanotrophs represents a sustainable and versatile approach for developing biomedical materials with numerous potential applications. Additionally, alternative feedstocks, such as industrial waste streams or byproducts can be explored to improve the economic feasibility of PHA production. This review briefly describes the potential of methanotrophs to produce PHAs, with recent updates and perspectives. [ABSTRACT FROM AUTHOR]

Soil pollution is one of the serious global threats causing risk to environment and humans. The major cause of accumulation of pollutants in soil are anthropogenic activities and some natural processes. There are several types of soil pollutants which deteriorate the quality of human life and animal health. They are recalcitrant hydrocarbon compounds, metals, antibiotics, persistent organic compounds, pesticides and different kinds of plastics. Due to the detrimental properties of pollutants present in soil on human life and ecosystem such as carcinogenic, genotoxic and mutagenic effects, alternate and effective methods to degrade the pollutants are recommended. Bioremediation is an effective and inexpensive method of biological degradation of pollutants using plants, microorganisms and fungi. With the advent of new detection methods, the identification and degradation of soil pollutants in different ecosystems were made easy. Metagenomic approaches are a boon for the identification of unculturable microorganisms and to explore the vast bioremediation potential for different pollutants. Metagenomics is a power tool to study the microbial load in polluted or contaminated land and its role in bioremediation. In addition, the negative ecosystem and health effect of pathogens, antibiotic and metal resistant genes found in the polluted area can be studied. Also, the identification of novel compounds/genes/proteins involved in the biotechnology and sustainable agriculture practices can be performed with the integration of metagenomics. Highlights: Soil carries diverse microorganisms which maintain plant and soil health. The different types of recalcitrant soil pollutants affect the ecosystem and human health. Complex pollutants can be degraded through bioremediation using microorganisms/plants Metagenomic approaches help to explore novel organisms and enzymes involved in bioremediation. [ABSTRACT FROM AUTHOR]