Pangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family

Lactobacillaceae represent a large family of important microbes that are foundational to the food industry. Many genome sequences of Lactobacillaceae strains are now available, enabling us to conduct a comprehensive pangenome analysis of this family. We collected 3591 high-quality genomes from public sources and found that: 1) they contained enough genomes for 26 species to perform a pangenomic analysis, 2) the normalized Heap's coefficient λ (a measure of pangenome openness) was found to have an average value of 0.27 (ranging from 0.07 to 0.37), 3) the pangenome openness was correlated with the abundance and genomic location of transposons and mobilomes, 4) the pangenome for each species was divided into core, accessory, and rare genomes, that highlight the species-specific properties (such as motility and restriction-modification systems), 5) the pangenome of Lactiplantibacillus plantarum (which contained the highest number of genomes found amongst the 26 species studied) contained nine distinct phylogroups, and 6) genome mining revealed a richness of detected biosynthetic gene clusters, with functions ranging from antimicrobial and probiotic to food preservation, but ∼93% were of unknown function. This study provides the first in-depth comparative pangenomics analysis of the Lactobacillaceae family.

Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic pathogen and major cause of hospital-acquired infections. The virulence of P. aeruginosa is largely determined by its transcriptional regulatory network (TRN). We used 411 transcription profiles of P. aeruginosa from diverse growth conditions to construct a quantitative TRN by identifying independently modulated sets of genes (called iModulons) and their condition-specific activity levels. The current study focused on the use of iModulons to analyze the biofilm production and antibiotic resistance of P. aeruginosa. Our analysis revealed: (i) 116 iModulons, 81 of which show strong association with known regulators; (ii) novel roles of regulators in modulating antibiotics efflux pumps; (iii) substrate-efflux pump associations; (iv) differential iModulon activity in response to beta-lactam antibiotics in bacteriological and physiological media; (v) differential activation of 'Cell Division' iModulon resulting from exposure to different beta-lactam antibiotics and (vi) a role of the PprB iModulon in the stress-induced transition from planktonic to biofilm lifestyle. In light of these results, the construction of an iModulon-based TRN provides a transcriptional regulatory basis for key aspects of P. aeruginosa infection, such as antibiotic stress responses and biofilm formation. Taken together, our results offer a novel mechanistic understanding of P. aeruginosa virulence.

Machine Learning Uncovers a Data-Driven Transcriptional Regulatory Network for the Crenarchaeal Thermoacidophile Sulfolobus acidocaldarius

Dynamic cellular responses to environmental constraints are coordinated by the transcriptional regulatory network (TRN), which modulates gene expression. This network controls most fundamental cellular responses, including metabolism, motility, and stress responses. Here, we apply independent component analysis, an unsupervised machine learning approach, to 95 high-quality Sulfolobus acidocaldarius RNA-seq datasets and extract 45 independently modulated gene sets, or iModulons. Together, these iModulons contain 755 genes (32% of the genes identified on the genome) and explain over 70% of the variance in the expression compendium. We show that five modules represent the effects of known transcriptional regulators, and hypothesize that most of the remaining modules represent the effects of uncharacterized regulators. Further analysis of these gene sets results in: (1) the prediction of a DNA export system composed of five uncharacterized genes, (2) expansion of the LysM regulon, and (3) evidence for an as-yet-undiscovered global regulon. Our approach allows for a mechanistic, systems-level elucidation of an extremophile's responses to biological perturbations, which could inform research on gene-regulator interactions and facilitate regulator discovery in S. acidocaldarius. We also provide the first global TRN for S. acidocaldarius. Collectively, these results provide a roadmap toward regulatory network discovery in archaea.

Growth promotion and yield enhancement of peanut (Arachis hypogaea L.) by application of plant growth-promoting rhizobacteria

Although plant growth-promoting rhizobacteria (PGPR) have been reported to influence plant growth, yield and nutrient uptake by an array of mechanisms, the specific traits by which PGPR promote plant growth, yield and nutrient uptake were limited to the expression of one or more of the traits expressed at a given environment of plant-microbe interaction. We selected nine different isolates of PGPR from a pool of 233 rhizobacterial isolates obtained from the peanut rhizosphere on the basis of ACC-deaminase activity. The nine isolates were selected, initially, on the basis of germinating seed bioassay in which the root length of the seedling was enhanced significantly over the untreated control. All the nine isolates were identified as Pseudomonas spp. Four of these isolates, viz. PGPR1, PGPR2, PGPR4 and PGPR7 (all fluorescent pseudomonads), were the best in producing siderophore and indole acetic acid (IAA). In addition to IAA and siderophore-producing attributes, Pseudomonas fluorescens PGPR1 also possessed the characters like tri-calcium phosphate solubilization, ammonification and inhibited Aspergillus niger and A. flavus in vitro. P. fluorescens PGPR2 differed from PGPR1 in the sense that it did not show ammonification. In addition to the traits exhibited by PGPR1, PGPR4 showed strong in vitro inhibition to Sclerotium rolfsii. The performances of these selected plant growth-promoting rhizobacterial isolates were repeatedly evaluated for 3 years in pot and field trials. Seed inoculation of these three isolates, viz. PGPR1, PGPR2 and PGPR4, resulted in a significantly higher pod yield than the control, in pots, during rainy and post-rainy seasons. The contents of nitrogen and phosphorus in soil, shoot and kernel were also enhanced significantly in treatments inoculated with these rhizobacterial isolates in pots during both the seasons. In the field trials, however, there was wide variation in the performance of the PGPR isolates in enhancing the growth and yield of peanut in different years. Plant growth-promoting fluorescent pseudomonad isolates, viz. PGPR1, PGPR2 and PGPR4, significantly enhanced pod yield (23-26%, 24-28% and 18-24%, respectively), haulm yield and nodule dry weight over the control in 3 years. Other attributes like root length, pod number, 100-kernel mass, shelling out-turn and nodule number were also enhanced. Seed bacterization with plant growth-promoting P. fluorescens isolates, viz. PGPR1, PGPR2 and PGPR4, suppressed the soil-borne fungal diseases like collar rot of peanut caused by A. niger and PGPR4 also suppressed stem rot caused by S. rolfsii. Studies on the growth patterns of PGPR isolates utilizing the seed leachate as the sole source of C and N indicated that PGPR4 isolate was the best in utilizing the seed leachate of peanut, cultivar JL24. Studies on the rhizosphere competence of the PGPR isolates, evaluated on the basis of spontaneous rifampicin resistance, indicated that PGPR7 was the best rhizoplane colonizer and PGPR1 was the best rhizosphere colonizer. Although the presence of growth-promoting traits in vitro does not guarantee that an isolate will be plant growth promoting in nature, results suggested that besides ACC-deaminase activity of the PGPR isolates, expression of one or more of the traits like suppression of phytopathogens, solubilization of tri-calcium phosphate, production of siderophore and/or nodulation promotion might have contributed to the enhancement of growth, yield and nutrient uptake of peanut.

Regioselective biomimetic oxidation of etodolac with iodosylbenzene catalyzed by halogenated and perhalogenated metalloporphyrins in dichloromethane

The biomimetic oxidation of etodolac, an anti-inflammatory drug (1) with iodosylbenzene catalyzed by 5,10,15,20-tetraarylporphyrinatoiron(III) chlorides TAPFe(III)Cl (7a-e) in dichloromethane gives 4-hydroxyetodolac (6) and 4-oxoetodolac (5) regioselectively in moderate yields.

Formation of 6-formyl-7-hydroxy-8-methoxycoumarin and 5,8-dioxopsoralen by reaction of 8-methoxypsoralen with H2O2 and potassium superoxide (KO2) catalyzed by halogenated or perhalogenated 5,10,15,20-tetraarylporphyrinatoiron(III) chlorides

The oxidation of 8-methoxypsoralen (2) with hydrogen peroxide and potassium superoxide catalyzed by 5,10,15,20-(2,4,6-trimethylphenyl)porphyrinatoiron(III) chlorides [Me12TPPFe(III)Cl] (1a) and 5,10,15,20-(2,6-dichlorophenyl)porphyrinatoiron(III) chlorides [Cl8TPPFe(III)Cl] (1b) in dichloromethane gives 6-formyl-7-hydroxy-8-methoxycoumarin (3) in moderate yields, whereas the oxidation of (2) with H2O2 catalyzed by 5,10,15,20-(2,6-dichlorophenyl)-beta-octahaloporphyrinatoiron(III) chlorides [Cl8betaX8TPPFe(III)Cl] (X=Cl, Br) (1c, 1d) gives specifically 5,8-dioxopsoralen (4) in moderate yields.

Biomimetic oxidation of ibuprofen with hydrogen peroxide catalysed by horseradish peroxidase (HRP) and 5,10,15,20-tetrakis-(2',6'-dichloro-3'-sulphonatophenyl)porphyrinatoiro n(III) and manganese(III) hydrates in AOT reverse micelles

The oxidation of ibuprofen with H2O2 catalysed by Horseradish peroxidase (HRP), Cl8TPPS4Fe(III)(OH2)2 and Cl8TPPS4Mn(III)(OH2)2 in AOT reverse micelles gives 2-(4'-isobutyl-phenyl)ethanol (5) and p-isobutyl acetophenone (6) in moderate yields. The reaction of ibuprofen (2) with H2O2 catalysed by HRP form carbon radicals by the oxidative decarboxylation, which on reaction with molecular oxygen to form hydroperoxy intermediate, responsible for the formation of the products 5 and 6. The yields of different oxidation products depend on the pH, the water to surfactant ratio (Wo), concentration of Cl8TPPS4Fe(III)(OH2)2 and Cl8TPPS4Mn(III)(OH2)2 and amount of molecular oxygen present in AOT reverse micelles. The formation of 2-(4'-isobutyl phenyl)ethanol (5) may be explained by the hydrogen abstraction from ibuprofen by high valent oxo-manganese(IV) radical cation, followed by decarboxylation and subsequent recombination of either free hydroxy radical or hydroxy iron(III)/manganese(III) porphyrins. The over-oxidation of 5 with high valent oxo-manganese, Mn(IV)radical cation intermediate form 6 in AOT reverse micelles by abstraction and recombination mechanism.

Vesicle formation by amphiphilic 10-alkyl-3-methyl isoalloxazine in aqueous medium

The synthetic 10-alkyl isoalloxazines have been found to form vesicles in aqueous and binary solvent systems and confirmed by UV-visible, fluorescence,transmission electron microscopy and quasi elastic light scattering experiments. The mean external diameters of vesicles have been calculated for isoalloxazine with different carbon atom chain at position 10 by transmission electron microscopy and quasi elastic laser light scattering. The gel to liquid phase transition of liposomes measured by differential scanning calorimetry shows reproducible endothermic peak which lies well in the range of typical aqueous vesicles.

Incorporation of synthetic tetramethylene diamine 8,8'-bis(riboflavin tetraacetate) in DMPC vesicles

The tetramethylene diamine 8,8'-bis(riboflavin tetraacetate) is synthesized by condensation of 8 alpha-bromo riboflavin tetraacetate and 1,4 diaminobutane. The incorporation of bis(riboflavin tetraacetate) in bilayer of DMPC vesicles has been studied by gel permeation chromatography, UV-visible and fluorescence spectroscopy.

Characterization of alkyldinitrogen species implicated in the carcinogenic, mutagenic and anticancer activities of N-nitroso compounds

The syntheses of certain specifically 15N-labelled E and Z alkyldiazotates and alkylnitrosoamines, together with related dinitrogen species, including diazoalkanes, are reported. A study of their conformational and configurational equilibria by 15N and 13C nuclear magnetic resonance spectrometry has revealed: (1) corresponding pairs of E and Z alkyldiazotates do not interconvert at ambient temperatures in aprotic solvents; (2) a preferential Z conformer of the alkylnitrosamines; (3) a fast interchange of metal counterion between oxygen and nitrogen in the Z-diazotates, but a slow interchange of metal ion between oxygen and nitrogen in the corresponding E diazotates; (4) interconversion of Z aryldiazotates, via detectable Z and E diazohydroxides, to the E diazotates; and (5) rapid stereoelectronically-assisted decomposition of Z-alkyldiazotates to diazoalkanes, in contrast with the behaviour of the more stable E diazotates. Self-Consistent Field calculations ab initio show that Z methyl diazohydroxide is the higher energy and more reactive form, while the carbon is relatively soft. In contrast, the E isomer is the more stable (by congruent to 18.0 kcal/mol) and the carbon harder. These data are in accord with the view that the Z form (from N-nitrosodimethylamine) attacks G-O6 (softer center) preferentially by SN1, while the E form prefers to react at the harder G-N7 and by an SN2 mechanism. These data provide a rationale for the known propylation of G-N7 without rearrangement, for propylation of G-O6 with rearrangement and possibly for the origin of the characteristic G-O6 alkylation carcinogenic lesion.

Mechanism of action of (2-haloethyl)nitrosoureas on DNA. Isolation and reactions of postulated 2-(alkylimino)-3-nitrosooxazolidine intermediates in the decomposition of 1,3-bis(2-chloroethyl)-, 1-(2-chloroethyl)-3-cyclohexyl-, and 1-(2-chloroethyl)-3-(4'-trans-methylcyclohexyl)-1-nitrosourea

Three examples of the postulated but hitherto unisolated 2-(alkylimino)-3-nitrosooxazolidines (2) have been prepared containing cyclohexyl, trans-4-methylcyclohexyl, and 2-chloroethyl groups at the 2 position, respectively. These compounds correspond to intermediates previously postulated to be formed in the aqueous decomposition of the antitumor agents 1-(2-chloroethyl)-3-cyclohexyl- (CCNU), 1-(2-chloroethyl)-3-(4'-trans-methylcyclohexyl)- (MeCCNU), and 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU), respectively, Compounds 2 decompose under physiological conditions to give a range of products similar to those formed from the corresponding (2-chloroethyl)nitrosoureas, including the hitherto unrecognized 2-hydroxyethl N-alkylcarbamates (9). Compounds 2a and 2b are converted with hydrochloric acid into CCNU and MeCCNU, respectively, suggesting that 2a and 2b may be reaction intermediates of decomposition. The corresponding 3-alkyl-1-nitroso-1-(2-hydroxyethyl)ureas (4) were characterized and, since they also decompose to give the same products as 2, may arise from the ring opening of 2. The intermediacy of compounds 4 can explain the formation of hydroxyethylated nucleosides isolated by other workers from the reaction of (2-chloroethyl)nitrosoureas on polynucleotides.