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There persists a constant threat from multidrug resistance being acquired by all human pathogens that challenges the well-being of humans. This phenomenon is predominantly led by Pseudomonas aeruginosa which is already resistant to the current generations of antibiotic by altering its metabolic pathways to survive. Specifically for this microbe the phenomenon of quorum sensing (QS) plays a crucial role in acquiring virulence and pathogenicity. QS is simply the cross talk between the bacterial community driven by signals that bind to receptors, enabling the entire bacterial microcosm to function as a single unit which has led to control P. aeruginosa cumbersome even in presence of antibiotics. Inhibition of QS can, therefore, be of a significant importance to curb such virulent and pathogenic strains of P. aeruginosa . Natural compounds are well known for their antimicrobial properties, of which, information on their mode of action is scarce. There can be many antimicrobial phytochemicals that act by hindering QS-pathways. The rationale of the current study is to identify such natural compounds that can inhibit QS in P. aeruginosa driven by LasR, PhzR, and RhlR dependent pathways. To achieve this rationale, in silico studies were first performed to identify such natural compounds which were then validated by in vitro experiments. Gingerol and Curcumin were identified as QS-antagonists (QSA) which could further suppress the production of biofilm, EPS, pyocyanin, and rhamnolipid along with improving the susceptibility to antibiotics.

The health of the plant and soil fertility is dependent on the plant–microbes interaction in the rhizosphere. Microbial life tends to endure various rhizosphere plant–microbe interactions. Phytohormones such as auxins, cytokinins, gibberellic acid, ethylene and abscisic acid are termed as the classical group of hormones. Out of the 70 rhizobacterial strains isolated from the Coleus rhizosphere, three different rhizobacterial strains Pseudomonas stutzeri MTP40, Stenotrophomonas maltophilia MTP42 and Pseudomonas putida MTP50 having plant growth-promoting attributes were isolated and characterized for its phytohormone-producing ability. The phytohormones such as indole 3-acetic acid (IAA), gibberellic acid and cytokinin (kinetin and 6-benzyladenosine) were affirmed in culture supernatant of the above isolates. IAA was detected in all the three isolates, where in highest production was found in S. maltophilia MTP42 (240 µg/mL) followed by P. stutzeri MTP40 (250 µg/mL) and P. putida MTP50 (233 µg/mL). Gibberellic acid production was found maximum in MTP40 (34 µg/mL), followed by MTP42 (31 µg/mL) and MTP50 (27 µg/mL). The cytokinin production from the isolates, namely, MTP40, MTP42 and MTP50 were 13, 11 and 7.5 µg/mL, respectively. The isolates showing the production of plant growth enhancing phytohormones can be commercialized as potent bioformulations.

It is the acquisition of unique traits that adds to the enigma of microbial capabilities to carry out extraordinary processes. One such ecosystem is the soil exposed to radionuclides, in the vicinity of atomic power stations. With the aim to study thorium (Th) tolerance in the indigenous bacteria of such soil, the bacteria were isolated and screened for maximum thorium tolerance. Out of all, only one strain AM3, found to tolerate extraordinary levels of Th (1500 mg L −1 ), was identified to be belonging to genus Providencia and showed maximum genetic similarity with the type strain P. vermicola OP1T. This is the first report suggesting any bacteria to tolerate such high Th and we propose to term such microbes as ‘ thoriotolerant ’. The medium composition for cultivating AM3 was optimized using response surface methodology (RSM) which also led to an improvement in its Th-tolerance capabilities by 23%. AM3 was found to be a good producer of EPS and hence one component study was also employed for its optimization. Moreover, the EPS produced by the strain showed interaction with Th, which was deduced by Fourier Transform Infrared (FTIR) spectroscopy.

Antibiotics are chemical compounds that are used to treat and prevent disease in humans and animals. They have been used in animal feed for over 60 years and are widely used in industrial farming. Antibiotics can have negative environmental impacts, including the potential to contribute to the development of antibiotic-resistant organisms. They can enter the environment through various pathways, including the manufacturing process, the direct application of antibiotic-laden manure to fields, and through grazing animals. Antibiotics that are given to animals can be excreted from where they can enter soil and groundwater which enable their entry in plants. Streptomycin is an antibiotic that is used against a range of gram-positive and gram-negative bacteria, but its use has led to the development of antibiotic resistance in some pathogens. It has also been shown to have negative impacts on a range of plant species, including tobacco, tomato, and wheat. Although, the major effect of streptomycin on plant physiology have been studied, the molecular mechanisms at play are barely understood in plant body. In current study, we examined the impact of streptomycin on germination of Brassica napus and then using docking, MM-GBBSA and MD simulations identified key proteins that interact with streptomycin by performing rigorous computational screening of 106 different proteins. Our finding suggest that streptomycin might be interacting with acyl-CoA oxidases, protochlorophyllide reductase B and leucoanthocyanidin dioxygenase based on simulation and docking analysis.

Quorum sensing in bacteria is a cell density-dependent phenomenon in which, a community of cells communicate with each other using signalling molecules belonging to various families of which N-acyl homoserine lactone (AHL) is one. AHL acts via ligand–receptor interaction where receptors of AHL differ from species to species, and possess great degree of similarity in conformation at the active site. A macromolecule, LasR, is a receptor protein that binds to N-(3-oxododecanoyl)-l-homoserinelactone (OdDHL), a type of AHL, viz. responsible for biofilm formation in Pseudomonas aeruginosa. Similar macromolecule LuxR, like LasR, found in Vibrio sp. identifies a different AHL, N-(3-oxohexanoyl)-l-homoserine lactone (OhHSL), responsible for the phenomenon of bioluminescence. In silico study depicted that curcumin could bind to both LasR and LuxR by unique sets of hydrogen bonding and hydrophobic interactions that can lead to the inactivation of these proteins, enabling this plant-derived organic AHL antagonist to be categorized as a quorum sensing inhibitor (QSI). To prove this hypothesis, curcumin was treated on P. aeruginosa to access the reduction in biofilm formation and on V. alginolyticus to check its efficacy to reduction in bioluminescence by inhibition of QS. The results of these studies proved curcumin to be an efficient QSI.

The non-structural protein (nsp)-3 of SARS-CoV2 coronavirus is sought to be an essential target protein which is also named as papain-like protease (PLpro). This protease cleaves the viral polyprotein, but importantly in human host it also removes ubiquitin-like interferon-stimulated gene 15 protein (ISG15) from interferon responsive factor 3 (IRF3) protein which ultimately downregulates the production of type I interferon leading to weakening of immune response. GRL0617 is the most potent known inhibitor for PLpro that was initially developed for SARS outbreak of 2003. The PLpro of SARS-CoV and CoV2 share 83% sequence identity but interestingly have several identical conserved amino acids that suggests GRL0617 to be an effective inhibitor for PLpro of SARS-CoV2. GRL0617 is a naphthalene-based molecule and interacts with Tyr268 of SARS-CoV2-PLpro (and Tyr269 of SARS-CoV-PLpro). To identify PLpro inhibitors, we prepared a library of secondary metabolites from fungi with aromatic nature and docked them with PLpro of SARS-CoV and SARS-CoV2. We found six hits which interacts with Tyr268 of SARS-CoV2-PLpro (and Tyr269 of SARS-CoV-PLpro). More surprisingly the top hit, Fonsecin, has naphthalene moiety in its structure, which recruits Tyr268 of SARS-CoV2-PLpro (and Tyr269 of SARS-CoV-PLpro) and has binding energy at par with control (GRL0617). Molecular dynamics (MD) simulation showed Fonsecin to interact with Tyr268 of SARS-CoV2-PLpro more efficiently than control (GRL0617) and interacting with a greater number of amino acids in the binding cleft of PLpro.Graphic abstract

Phytohormones are the main regulatory molecules of core signalling networks associated with plant life cycle regulation. Manipulation of hormone signalling cascade enables the control over physiological traits of plant, which has major applications in field of agriculture and food sustainability. Hence, stable analogues of these hormones are long sought after and many of them are currently known, but the quest for more effective, stable and economically viable analogues is still going on. This search has been further strengthened by the identification of the components of signalling cascade such as receptors, downstream cascade members and transcription factors. Furthermore, many proteins of phytohormone cascades are available in crystallized forms. Such crystallized structures can provide the basis for identification of novel interacting compounds using in silico approach. Plenty of computational tools and bioinformatics software are now available that can aid in this process. Here, the metadata of all the major phytohormone signalling cascades are presented along with discussion on major protein–ligand interactions and protein components that may act as a potential target for manipulation of phytohormone signalling cascade. Furthermore, structural aspects of phytohormones and their known analogues are also discussed that can provide the basis for the synthesis of novel analogues.

Polyhydroxyalkanoates (PHAs) are bio-polyesters of hydroxyalkanoates that accumulate intracellularly in case of prokaryotes, as cytoplasmic granules, under carbon rich and paucity of nitrogen, phosphorous, sulphur and oxygen where it can serve as carbon and energy source under nutrient limiting condition and/or environmental stress conditions. In adverse growth conditions, many bacteria have ability to store nutrients in form of PHA granules using their specific metabolic pathways during stationary growth phase, in the presence of high levels of carbon containing nutrient sources. Bacterial PHAs have generated attention as an alternative to petroleum derived synthetic plastics. It possesses the characteristic physico-chemical properties comparable to the synthetic plastics. These properties of PHAs can be improved by blending of PHAs with other natural polymer like starch, cellulose and semisynthetic polymers like poly lactic acids and polycaprolactones. Being eco-friendly, biodegradable and biocompatible; major PHAs such as, Polyhydroxybutyrate (PHB) and Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) have found numerous vital applications in pharmaceutical, biomedical, textile, cosmetic, agricultural, treatment of waste water and have been successfully employed for Food packaging industries. This review provides a comprehensive knowledge about the world of PHAs covering its major aspects, namely its chemical nature and structure, biosynthesis, various methods of screening of potential PHA producing bacteria along with properties, several techniques used for its recovery and further characterization.

Exopolysaccharides (EPS) are organic macromolecules naturally secreted by many microorganisms. EPS is increasingly used for agriculture and industrial purposes. This study focuses on isolate  Klebsiella   pneumonia SSN1, Klebsiella quasipeumonniae SGM81 isolated from rhizosphere to explore its water retention efficiency under drought conditions. Neutron Radiography was used to visualise water distribution in the sand under normal and drought conditions in the presence and absence of EPS producing bacteria. The EPS production was studied by applying Box Behnken design (BBD) under drought stress which was artificially induced by using polyethene glycol 6000 under osmotic stress condition 3.65% w/v of EPS dry weight was obtained. The relative water content (RWC) is used to calculate the amount of water present in the sand and was further studied by Neutron Radiography imaging with appropriate controls. FTIR and HPLC were also carried out for the characterisation of the extracted EPS. The sand experiments revealed that after 24 h of evaporation, the highest RWC was maintained by SSN1 at 29.7% compared to SGM81 (19.06%). SSN1 was found to release L-arabinose as the main sugar of its EPS under drought stress conditions by HPLC method. The FTIR data indicated the presence of β-glucans and polysaccharide α-pyranose between wavenumber 700 cm −1 –1500 cm −1 and 1017 cm −1 –1200 cm −1 respectively. The HPLC characterization of extracted EPS from osmotic stressed cells (run 3) displayed a peak designated to L-arabinose at 10.3 retention time (RT) for 132.4 mM concentration. While from run 5 with the controlled condition indicated the presence of L-rhamnose at 7.3 RT for 87 mM concentration. Neutron radiography enables the visualisation of water distribution in the sand as well as water transport in root-soil systems in situ. SSN1 has elicited EPS production in drought conditions with a low level of nitrogen and carbon.

Peptide Nucleic Acid (PNA) serves as an artificial functional analog of DNA. Being immune to enzymatic degradation and possessing strong affinity towards DNA and RNA, it is an ideal candidate for many medical and biotechnological applications that are of antisense and antigene in nature. PNAs are anticipated to have its application in DNA and RNA detection as well as quantification, to serve as antibacterial and antiviral agents, and silencing gene for developing anticancer strategies. Although, their restricted entry in both eukaryotic and prokaryotic cells limit their applications. In addition, aggregation of PNA in storage containers reduces the quality and quantity of functional PNA that makes it inadequate for their mass production and storage. To overcome these limitations, researchers have modified PNA either by the addition of diverse functional groups at various loci on its backbone, or by synthesizing chimeras with other moieties associated with various delivery agents that aids their entry into the cell. Here, this review article summarizes few of the structural modifications that are performed with PNA, methods used to improve their cellular uptake and shedding light on the applications of PNA in various prospects in biological sciences.