Identification and characterisation of a novel EhOrc1/Cdc6 from the human pathogen Entamoeba histolytica: an in silico approach.

The onset of a pre-replication complex on origin commences DNA replication. The Origin recognition complex (Orc), Cell division cycle protein 6 (Cdc6), and the minichromosome maintenance (Mcm) replicative helicase, along with Chromatin licensing and DNA replication factor 1 (Cdt1), make up the pre-replication complex in eukaryotes. Eukaryotic Orc is made up of six subunits, designated Orc1-6 while monomeric Cdc6 has sequence similarity with Orc1. However, Orc has remained unexplored in the protozoan parasite Entamoeba histolytica. Here we report a single functional Orc1/Cdc6 protein in E. histolytica. Its structural and functional aspects have been highlighted by a detailed in silico analysis that reflects physicochemical characteristics, predictive 3D structure modelling, protein-protein interaction studies, molecular docking and simulation. This in silico study provides insight into EhOrc1/Cdc6 and points out that E. histolytica carries pre-replication machinery that is less complex than higher eukaryotes and closer to archaea. Additionally, it lays the groundwork for future investigations into the methods of origin recognition, and anomalies of cell cycle observed in this enigmatic parasite.Communicated by Ramaswamy H. Sarma.

Characterizations of novel broad-spectrum lytic bacteriophages Sfin-2 and Sfin-6 infecting MDR Shigella spp. with their application on raw chicken to reduce the Shigella load.

The evidence and prevalence of multidrug-resistant (MDR) Shigella spp. poses a serious global threat to public health and the economy. Food- or water-borne MDR Shigella spp. demands an alternate strategy to counteract this threat. In this regard, phage therapy has garnered great interest from medical practitioners and researchers as a potential way to combat MDR pathogens. In this observation, we isolated Shigella phages from environmental water samples and tested against various clinically isolated MDR Shigella spp. In this study, we have defined the isolation and detailed physical and genomic characterizations of two phages Sfin-2 and Sfin-6 from environmental water samples. The phages exhibited potent lytic activity against Shigella flexneri, Shigella dysenteriae, and Shigella sonnei. They showed absorption within 5-10 min, a burst size ranging from ~74 to 265 PFU/cell, and a latent period of 5-20 min. The phages were stable at a broad pH range and survived an hour at 50°C. The purified phages Sfin-2 and Sfin-6 belong to the Siphoviridae family with an isometric head (64.90 ± 2.04 nm and 62.42 ± 4.04 nm, respectively) and a non-contractile tail (145 ± 8.5 nm and 148.47 ± 14.5 nm, respectively). The in silico analysis concluded that the size of the genomic DNA of the Sfin-2 phage is 50,390 bp with a GC content of 44.90%, while the genome size of the Sfin-6 phage is 50,523 bp with a GC content of 48.30%. A total of 85 and 83 putative open reading frames (ORFs) were predicted in the Sfin-2 and Sfin-6 phages, respectively. Furthermore, a comparative genomic and phylogenetic analysis revealed that both phages represented different isolates and novel members of the T1-like phages. Sfin-2 and Sfin-6 phages, either individually or in a cocktail form, showed a significant reduction in the viable Shigella count on raw chicken samples after 72 h of incubation. Therefore, these results indicate that these phages might have a potential role in therapeutic approaches designed for shigellosis patients as well as in the biological control of MDR Shigella spp. in the poultry or food industry during the course of meat storage.

Two novel low molecular weight gelator-driven supramolecular metallogels efficient in antimicrobial activity applications.

A remarkable ultrasonication technique was successfully employed to create two novel metallogels using citric acid as a low molecular weight gelator, in combination with cadmium(ii)-acetate and mercury(ii)-acetate dissolved in N,N-dimethyl formamide at room temperature and under ambient conditions. The mechanical properties of the resulting Cd(ii)- and Hg(ii)-metallogels were rigorously examined through rheological analyses, which revealed their robust mechanical stability under varying angular frequencies and shear strains. Detailed characterization of the chemical constituents within these metallogels was accomplished through EDX mapping experiments, while microstructural features were visualized using field emission scanning electron microscope (FESEM) images. Additionally, FT-IR spectroscopic analysis was employed to elucidate the metallogel formation mechanism. Significantly, the antimicrobial efficacy of these novel metallogels was assessed against a panel of bacteria, including Gram-positive strains such as Bacillus subtilis and Staphylococcus epidermidis, as well as Gram-negative species like Escherichia coli and Pseudomonas aeruginosa. The results demonstrated substantial antibacterial activity, highlighting the potential of Cd(ii) and Hg(ii)-based citric acid-mediated metallogels as effective agents against a broad spectrum of bacteria. In conclusion, this study provides a comprehensive exploration of the synthesis, characterization, and antimicrobial properties of Cd(ii) and Hg(ii)-based citric acid-mediated metallogels, shedding light on their promising applications in combating both Gram-positive and Gram-negative bacterial infections. These findings open up exciting prospects for the development of advanced materials with multifaceted industrial and biomedical uses.

Insight into the 4-nitrophenol reduction, supercapacitive behavior, and antimicrobial activity of ZnCo2O4-rGO nanocomposite fabricated by the simple reflux method.

In this article, binary oxide ZnCo2O4 nanoparticles (NPs) have been developed on reduced graphene oxide surface by simple reflux condensation method. The physicochemical characteristics of the synthesized nanocomposite were computed using X-ray diffraction (XRD), transmission electron microscopy (TEM), scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), and UV-Visible spectroscopy. The average size of ZnCo2O4 NPs is found to be about 9 nm. The synthesized nanocomposite was found to be an extremely efficient catalyst for reduction of 4-nitrophenol (4-NP) to produce 4-aminophenol (4-AP) and it is exhibited that about 98% 4-nitrophenol can be reduced in only 20 min. The nanocomposite behaves as supercapacitor due to possessing the specific capacitance value up to 609 F/g and excellent capacitance retention over 1000 cycles. The Brunauer-Emmett-Teller (BET) surface area analysis has been conducted to evaluate surface area and pore size of the synthesized material. The antimicrobial activity of this nanocomposite was performed against bacterial strains of Escherichia coli (E. coli), Bacillus subtilis (B. subtilis), and Staphylococcus aureus (S. aureus) and it is noticed to be a good antimicrobial agent against different bacterial strains.

EhSir2c, a Sir2 homolog from the human pathogen Entamoeba histolytica interacts with a DNA repair protein, EhRAD23: Protein-protein interaction, docking and functional study.

Chromosome segregation is a crucial phenomenon in the cell cycle and defects in genome segregation result in an abnormality in various cellular events. Unlike higher eukaryotes, chromosome segregation and a number of cell cycle events are unusual in the protozoan parasite Entamoeba histolytica (E. histolytica). Characterization of Sir2 proteins from E. histolytica may reveal its unique cellular events as they play role in diverse cellular processes including chromosome segregation. E. histolytica has four homologs of Sir2 proteins. EhSir2a and EhSir2b show sequence similarity towards eukaryotic Sir2 homologs, whereas EhSir2c and EhSir2d are more like prokaryotic sirtuins. Using both computational and experimental methods, EhSir2c has been characterized in this study. The three-dimensional structure of EhSir2c is predicted by homology modelling. The protein interactors of EhSir2c have been identified by yeast-two-hybrid screening against the cDNA library of E. histolytica. We have identified a novel interactor, EhRAD23 which is a homolog of UV excision repair protein RAD23. The interaction of EhSir2c and EhRAD23 was validated by pull-down assay. UV-C irradiation up-regulates the relative expression of EhSir2c, suggesting the necessity of EhSir2c in UV-induced stress in this parasite.Communicated by Ramaswamy H. Sarma.

In silico analysis of a Skp1 protein homolog from the human pathogen E. histolytica.

SCF complex consisting of Skp1, Cullins, F-box proteins, is the largest family of E3 ubiquitin ligases that promotes ubiquitination of many substrate proteins and controls numerous cellular processes. Skp1 is an adapter protein that binds directly to the F-box proteins. In this study, we have presented the first comprehensive analysis of the presence of peptides or proteins in the human pathogen Entamoeba histolytica having homology to Skp1protein. The occurrence of other protein components of the SCF complex has been identified from protein-protein interaction network of EhSkp1A. Studying the role of Skp1protein in this pathogen would help to understand its unique chromosome segregation and cell division which are different from higher eukaryotes. Further, owing to the development of resistance over several drugs that are currently available, there is a growing need for a novel drug against E. histolytica. Proteins from ubiquitin-proteasome pathway have received attention as potential drug targets in other parasites. We have identified four homologs of Skp1 protein in E. histolytica strain HM-1: IMSS. Molecular docking study between EhSkp1A and an F-box/WD domain-containing protein (EhFBXW) shows that the F-box domain in the N-terminal region of EhFBXW interacts with EhSkp1A. Therefore, the results of the present study shall provide a stable foundation for further research on the cell cycle regulation of E. histolytica and this will help researchers to develop new drugs against this parasite. Supplementary Information: The online version contains supplementary material available at 10.1007/s12639-022-01523-0.

CRISPR-Cas9: Taming protozoan parasites with bacterial scissor.

The invention of CRISPR-Cas9 technology has opened a new era in which genome manipulation has become precise, faster, cheap and more accurate than previous genome editing strategies. Despite the intricacies of the genomes associated with several protozoan parasites, CRISPR-Cas9 has made a substantial contribution to parasitology. The study of functional genomics through CRISPR-Cas9 mediated gene knockout, insertion, deletion and mutation has helped in understanding intrinsic parasite biology. The invention of CRISPR-dCas9 has helped in the programmable control of protozoan gene expression and epigenetic engineering. CRISPR and CRISPR-based alternatives will continue to thrive and may aid in the development of novel anti-protozoan strategies to tame the protozoan parasites in the imminent future.

In silico analysis and molecular identification of an anaphase-promoting complex homologue from human pathogen Entamoeba histolytica.

BACKGROUND: Amoebiasis, being endemic worldwide, is the second leading cause of parasite-associated morbidity and mortality after malaria. The human parasite Entamoeba histolytica is responsible for the disease. Metronidazole is considered as the gold standard for the treatment of amoebiasis, but this antibiotic is carcinogenic and the development of antibiotic resistance against E. histolytica is a major health concern. Chromosome segregation is irregular in this parasite due to the absence of a few cell cycle checkpoint proteins. Anaphase-promoting complex (APC/C or cyclosome) is an E3 ubiquitin ligase that synchronizes chromosome segregation and anaphase progression via the ubiquitin-proteasome system. Proteasome is considered to be an attractive drug target for protozoan parasites. For the present study, EhApc11 from E. histolytica, a homologue of Apc11 in humans, is selected for elucidating its structural and functional aspects by detailed in silico analysis and molecular methods. Its physicochemical characteristics, identification of probable interactors, 3D model and quality analysis are done using standard bioinformatics tools. cDNA sequence of EhAPC11 has been further cloned for molecular characterization. RESULT: Conserved domain analysis revealed that EhApc11 belongs to the RING (really interesting new gene) superfamily and has ligand binding capacity. Expression study in Escherichia coli BL21 (DE3) revealed that the molecular weight of glutathione S-transferase (GST)-tagged protein is ~ 36 kDa. CONCLUSION: EhApc11 is a hydrophilic, thermostable, extracellular protein with potent antigenicity. The study will serve as a groundwork for future in-depth analysis regarding the validation of protein-protein interaction of EhApc11 with its substrates identified by STRING analysis and the potential of EhApc11 to serve as an anti-amoebic drug target.

Transformation of CuS/ZnS nanomaterials to an efficient visible light photocatalyst by 'photosensitizer' graphene and the potential antimicrobial activities of the nanocomposites.

We report the growth of CuS/ZnS (CZS) nanoparticles (NPs) on the graphene sheet by a facile green synthesis process. The CuS/ZnS-graphene (CZSG) nanocomposites exhibit enhanced visible light photocatalytic activity towards organic dye (methylene blue) degradation than that of CZS nanoparticles. To find the reason for the enhanced photo-activity, we propose a new photocatalytic mechanism where graphene in the CZSG nanocomposites acts as a 'photosensitizer' for CZS nanoparticles. This distinctive photocatalytic mechanism is noticeably different from all other previous research works on semiconductor-graphene hybrid photocatalysts where graphene behaves as an electron reservoir to capture the electrons from photo-excited semiconductor. This novel idea of the photocatalytic mechanism in semiconductor-graphene photocatalysts could draw a new track in thinking for designing of graphene-based photocatalysts for solving environmental pollution problems and they also show remarkable antimicrobial activities.

A new half-condensed Schiff base platform: structures and sensing of Zn2+ and H2PO4- ions in an aqueous medium.

A newly designed and synthesized half-condensed organic moiety 2-hydroxy-5-methyl-3-[(2-phenylamino-phenylimino)-methyl]-benzaldehyde (HL') and a Zn2L4 complex sequentially detect Zn2+ and H2PO4- ions as low as 1.13 nM and1.23 µM, respectively. HL' and a dinuclear Zn(ii) complex of in situ generated L- in a solution formulated as Zn2L4 under investigation were characterized by physicochemical and spectroscopic studies along with detailed structural analyses by single-crystal X-ray crystallography. The selectivity and sensitivity of HL' towards Zn2+ ions and of the Zn2L4 complex towards H2PO4- ions are based on CHEF and via displacement pathways, respectively. Dual sensing of Zn2+ ions and H2PO4-ions in an aqueous medium via "Green-Blue-Green" emission with the reversible transformation of in situ formed HL' to HL was established by detailed electronic absorption and emission spectroscopic studies. This non-cytotoxic probe (HL', i.e. produced HL in solution) and Zn2L4 complexes are able to monitor the subcellular distribution changes of Zn2+ and H2PO4- ions, respectively, by fluorescence microscopy using the human semen sample.

A Nuclear-Localized Naphthalimide-Based Fluorescent Light-Up Probe for Selective Detection of Carbon Monoxide in Living Cells.

A nuclear-localized fluorescent light-up probe, NucFP-NO2, was designed and synthesized that can detect CO selectively in an aqueous buffer (pH 7.4, 37 °C) through the CO-mediated transformation of the nitro group into an amino-functionalized moiety. This probe triggered a more than 55-fold "turn-on" fluorescence response to CO without using any metal ions, e.g., Pd, Rh, Fe, etc. The enhanced response is highly selective over a variety of relevant reactive oxygen, nitrogen, and sulfur species and also various biologically important cationic, anionic, and neutral species. The detection limit of this probe for CO is as low as 0.18 µM with a linear range of 0-70 µM. Also, this fluorogenic probe is an efficient candidate for monitoring intracellular CO in living cells (RAW 264.7, A549 cells), and the fluorescence signals predominantly localize in the nuclear region.

Madhuca longifolia plant mediated green synthesis of cupric oxide nanoparticles: A promising environmentally sustainable material for waste water treatment and efficient antibacterial agent.

In current years, the development of efficient green methods for synthesis of metal oxide nanomaterials has attracted a great attention to the researchers since the plant-mediated synthesis is a cost-effective and a good alternative to chemical and physical methods. An efficient and eco-friendly route has been developed for the green synthesis of CuO nanoparticles (NPs) by Madhuca longifolia plant extract which acts as a non-toxic reducing agent. X-ray diffraction studies reveal the good crystallinity of the synthesized NPs and FTIR spectra confirm the synthesis of these NPs. UV-visible absorption spectra showed that the NPs have been reached at different nano scale level depending on their synthesis procedures. TEM images indicate that as-synthesized CuO NPs are spherical in shape with their different size ranges and they show different band gap values which is confirmed by Tauc's formula. The NPs exhibit good photoluminescence property depending on their particle size and they also show excellent photocatalytic activity towards the degradation of methylene blue (MB) in presence of visible light irradiation which will be a promising material for waste water treatment. The synthesized CuO NPs show good antibacterial activity against bacterial strains namely E. coli BL21 DE3 Gram-negative, S. aureus Gram-positive and B.subtilis Gram-positive and the results have been compared against Ampicillin and Tetracycline.

Ammonium induces differential expression of methane and nitrogen metabolism-related genes in Methylocystis sp. strain SC2.

Nitrogen source and concentration are major determinants of methanotrophic activity, but their effect on global gene expression is poorly studied. Methylocystis sp. strain SC2 produces two isozymes of particulate methane monooxygenase. These are encoded by pmoCAB1 (low-affinity pMMO1) and pmoCAB2 (high-affinity pMMO2). We used RNA-Seq to identify strain SC2 genes that respond to standard (10 mM) and high (30 mM) NH4(+) concentrations in the medium, compared with 10 mM NO3(-). While the expression of pmoCAB1 was unaffected, pmoCAB2 was significantly downregulated (log2 fold changes of -5.0 to -6.0). Among nitrogen metabolism-related processes, genes involved in hydroxylamine detoxification (haoAB) were highly upregulated, while those for assimilatory nitrate/nitrite reduction, high-affinity ammonium uptake and nitrogen regulatory protein PII were downregulated. Differential expression of pmoCAB2 and haoAB was independently validated by end-point reverse transcription polymerase chain reaction. Methane oxidation by SC2 cells exposed to 30 mM NH4(+) was inhibited at ≤ 400 ppmv CH4 , where pMMO2 but not pMMO1 is functional. When transferred back to standard nitrogen concentration, methane oxidation capability and pmoCAB2 expression were restored. Given that Methylocystis contributes to atmospheric methane oxidation in upland soils, differential expression of pmoCAB2 explains, at least to some extent, the strong inhibitory effect of ammonium fertilizers on this activity.

Genome analysis coupled with physiological studies reveals a diverse nitrogen metabolism in Methylocystis sp. strain SC2.

BACKGROUND: Methylocystis sp. strain SC2 can adapt to a wide range of methane concentrations. This is due to the presence of two isozymes of particulate methane monooxygenase exhibiting different methane oxidation kinetics. To gain insight into the underlying genetic information, its genome was sequenced and found to comprise a 3.77 Mb chromosome and two large plasmids. PRINCIPAL FINDINGS: We report important features of the strain SC2 genome. Its sequence is compared with those of seven other methanotroph genomes, comprising members of the Alphaproteobacteria, Gammaproteobacteria, and Verrucomicrobia. While the pan-genome of all eight methanotroph genomes totals 19,358 CDS, only 154 CDS are shared. The number of core genes increased with phylogenetic relatedness: 328 CDS for proteobacterial methanotrophs and 1,853 CDS for the three alphaproteobacterial Methylocystaceae members, Methylocystis sp. strain SC2 and strain Rockwell, and Methylosinus trichosporium OB3b. The comparative study was coupled with physiological experiments to verify that strain SC2 has diverse nitrogen metabolism capabilities. In correspondence to a full complement of 34 genes involved in N2 fixation, strain SC2 was found to grow with atmospheric N2 as the sole nitrogen source, preferably at low oxygen concentrations. Denitrification-mediated accumulation of 0.7 nmol (30)N2/hr/mg dry weight of cells under anoxic conditions was detected by tracer analysis. N2 production is related to the activities of plasmid-borne nitric oxide and nitrous oxide reductases. CONCLUSIONS/PERSPECTIVES: Presence of a complete denitrification pathway in strain SC2, including the plasmid-encoded nosRZDFYX operon, is unique among known methanotrophs. However, the exact ecophysiological role of this pathway still needs to be elucidated. Detoxification of toxic nitrogen compounds and energy conservation under oxygen-limiting conditions are among the possible roles. Relevant features that may stimulate further research are, for example, absence of CRISPR/Cas systems in strain SC2, high number of iron acquisition systems in strain OB3b, and large number of transposases in strain Rockwell.

Complete genome sequence of Methylocystis sp. strain SC2, an aerobic methanotroph with high-affinity methane oxidation potential.

Methylocystis sp. strain SC2 is an aerobic type II methanotroph isolated from a highly polluted aquifer in Germany. A specific trait of the SC2 strain is the expression of two isozymes of particulate methane monooxygenase with different methane oxidation kinetics. Here we report the complete genome sequence of this methanotroph that contains not only a circular chromosome but also two large plasmids.

Complete sequence analysis of two methanotroph-specific repABC-containing plasmids from Methylocystis sp. strain SC2.

The complete nucleotide sequences of two large, low-copy-number plasmids of 229.6 kb (pBSC2-1) and 143.5 kb (pBSC2-2) were determined during assembly of the whole-genome shotgun sequences of the methane-oxidizing bacterium Methylocystis sp. strain SC2. The physical existence of the two plasmids in strain SC2 was confirmed by pulsed-field gel electrophoresis followed by Southern hybridization. Both plasmids have a conserved replication module of the repABC system and carry genes involved in their faithful maintenance and conjugation. In addition, they contain genes that might be involved in essential metabolic processes. These include several heavy metal resistance genes and copper transport genes in pBSC2-1 and a complete nitrous oxide reductase operon and a pmoC singleton in pBSC2-2, the latter encoding the PmoC subunit of particulate methane monooxygenase.

Entamoeba histolytica sirtuin EhSir2a deacetylates tubulin and regulates the number of microtubular assemblies during the cell cycle.

We have discovered four sirtuin genes in Entamoeba histolytica, two of which are similar to eukaryotic sirtuins and two to bacterial and archaeal sirtuins. The eukaryotic sirtuin homologue, EhSir2a, showed NAD(+)-dependent deacetylase activity and was sensitive to class III HDAC inhibitors. Localization of EhSir2a at different cellular sites suggested that this deacetylase could have multiple targets. Using an E. histolytica cDNA library in the yeast two-hybrid genetic screen, we identified several proteins that bound to EhSir2a. These proteins included Eh alpha-tubulin, whose interaction with EhSir2a was validated in E. histolytica. We have shown that EhSir2a deacetylated tubulin and localized with microtubules in E. histolytica. Increased expression levels of EhSir2a in stable transformants led to reduced number of microtubular assemblies in serum synchronized cells. This effect was abrogated by mutations in the deacetylase domain of EhSir2a, showing that EhSir2a deacetylase activity affected the stability and number of microtubular assemblies during the cell cycle of E. histolytica. Our results suggest that epigenetic modification of tubulin by EhSir2a is one of the mechanisms that regulates microtubular assembly in E. histolytica.