DNA photolyase of enterococci: possible explanation for its low sunlight inactivation rate

DNA photolyase is perhaps the most ancient and direct arsenal in curing the UV-induced dimers formed in the microbial genome. Out of two cofactors of the enzyme, catalytic and light harvesting, differences in the latter have provided basis for categorizing photolyases of prokaryotes as folate and deazaflavin types. In the present study, the homology modeling of DNA photolyase of Enterococcus faecalis was undertaken. The predicted models were structurally compared with the crystal structure coordinates of photolyases from Escherichia coli (folate type) and Anacystis nidulans (deazaflavin type). Discrepancies present in the multiple sequence alignment and tertiary structures, particularly at the light harvesting cofactor (methenyltetrahydrofolic acid, MTHF; 8-hydroxy-5-deazaflavin, 8-HDF) binding sites indicated the mechanistic nature of enterococcal photolyase. Concisely, despite the greater holistic homology with folate-type photolyase, enterococcal photolyase was characterized as deazaflavin-type. The presence of 8-HDF binding sites and groove architecture of substrate binding sites were also found supportive in this regard. The inter cofactor distance and/or orientation also implied to the efficient energy transfer in photolyase of Enterococcus in comparison with E. coli. In addition, we observed relatively high protein deformability in the enterococcal genome, which may favors the repair action of photolyase. The findings are expected to provide molecular insights into the difference in sunlight inactivation rate of two important fecal contamination indicators, namely Enterococcus and E. coli.     

The Mating System in Saccharomyces

Many, but not all, Saccharomyces species are heterothallic.The mating types in heterothallic species are determined bytwo allelic genes. The mating-type genes occasionally mutatefrom one to the other. Vegetative cells of opposite mating typewere found in some single ascospore colonies. They show conjugationtubes, stimulated by the proximity of cells of the other matingtype. The cultures alao show zygotes, which on sporulation yieldplus(+) and minus(–) progenies. The zygotes bud off diploid vegetative cells which grow fasterthan the original haploid cells and so tend to replace them.If mutation occurs early, replacement is complete and the culturegives no mating reaction but sporulates. If it occurs late,the culture is a mixture of haploid cells giving a mating reactionand diploid cells that will sporulate.     

The Interactive Approach of Rhizobacteria and l-tryptophan on Growth,Physiology, Tuber Characteristics,and Iron Concentration of Potato (Solanum tuberosum L.)

Iron deficiency is one of the most prevailing micronutrient deficiencies throughout the globe. Iron malnutrition affects billions of people around the world especially children and pregnant women. Its deficiencies can be overcome through microbial biofortification: a process of deliberately increasing desirable nutrients in crop plants. Plant growth-promoting rhizobacteria (PGPR) can improve iron content in edible plant tissues through different direct and indirect mechanisms. Adding plant growth regulators along with rhizobacteria makes it a novel fortification approach. In the current experiment, the interactive effect of two bacterial isolates (O-13 & K-10) alone and in consortium with l-tryptophan in the presence of iron sulfate was evaluated on growth, physiology, tuber characteristics, and iron concentration in potato (Solanum tuberosum L.). Results revealed that inoculation with PGPR and plant growth regulator (PGR) significantly improved the plant height, straw yield, and the number of tubers per plant. Potato (Solanum tuberosum L.) tuber characteristics (starch content, vitamin-C, relative water content) were also improved significantly. O-13, K-10, and l-tryptophan had significantly improved the iron concentration up to 20.59, 33.12, and 28.95%, respectively. However, inoculation with the microbial consortium and l-tryptophan showed a significant increase of up to one-fold in the iron concentration of potato (Solanum tuberosum L.) as compared with uninoculated control. The results suggest that rhizobacteria can help the plant to uptake nutrients from the soil. These findings concluded on the fact that the interactive effect of microbial assisted biofortification and plant growth regulator is a novel, promising, and cost-effective approach to mitigate micronutrient deficiencies especially in resource-limited countries.

     

Genome-Wide Relatedness of Treponema pedis,from Gingiva and Necrotic Skin Lesions of Pigs,with the Human Oral Pathogen Treponema denticola

Treponema pedis and T. denticola are two genetically related species with different origins of isolation. Treponema denticola is part of the human oral microbiota and is associated with periodontitis while T. pedis has been isolated from skin lesions in animals, e.g., digital dermatitis in cattle and necrotic ulcers in pigs. Although multiple Treponema phylotypes may exist in ulcerative lesions in pigs, T. pedis appears to be a predominant spirochete in these lesions. Treponema pedis can also be present in pig gingiva. In this study, we determined the complete genome sequence of T. pedis strain T A4, isolated from a porcine necrotic ear lesion, and compared its genome with that of T. denticola. Most genes in T. pedis were homologous to those in T. denticola and the two species were similar in general genomic features such as size, G+C content, and number of genes. In addition, many homologues of specific virulence-related genes in T. denticola were found in T. pedis. Comparing a selected pair of strains will usually not give a complete picture of the relatedness between two species. We therefore complemented the analysis with draft genomes from six T. pedis isolates, originating from gingiva and necrotic ulcers in pigs, and from twelve T. denticola strains. Each strain carried a considerable amount of accessory genetic material, of which a large part was strain specific. There was also extensive sequence variability in putative virulence-related genes between strains belonging to the same species. Signs of lateral gene-transfer events from bacteria known to colonize oral environments were found. This suggests that the oral cavity is an important habitat for T. pedis. In summary, we found extensive genomic similarities between T. pedis and T. denticola but also large variability within each species.     

Identification of QTLs for Yield and Associated Traits in F₂ Population of Rice

Identification of quantitative trait loci (QTLs) controlling yield and yield-related traits in rice was performed in the F₂ mapping population derived from parental rice genotypes DHMAS and K343. A total of 30 QTLs governing nine different traits were identified using the composite interval mapping (CIM) method. Four QTLs were mapped for number of tillers per plant on chromosomes 1 (2 QTLs), 2 and 3; three QTLs for panicle number per plant on chromosomes 1 (2 QTLs) and 3; four QTLs for plant height on chromosomes 2, 4, 5 and 6; one QTL for spikelet density on chromosome 5; four QTLs for spikelet fertility percentage (SFP) on chromosomes 2, 3 and 5 (2 QTLs); two QTLs for grain length on chromosomes 1 and 8; three QTLs for grain width on chromosomes1, 3 and 8; three QTLs for 1000-grain weight (TGW) on chromosomes 1, 4 and 8 and six QTLs for yield per plant (YPP) on chromosomes 2 (3 QTLs), 4, 6 and 8. Most of the QTLs were detected on chromosome 2, so further studies on chromosome 2 could help unlock some new chapters of QTL for this cross of rice variety. Identified QTLs elucidating high phenotypic variance can be used for marker-assisted selection (MAS) breeding. Further, the exploitation of information regarding molecular markers tightly linked to QTLs governing these traits will facilitate future crop improvement strategies in rice.     

Antifungal effect of Penicillium metabolites against some fungi

Microorganisms are increasingly exploited as a source of new biological control agents. Genus Penicillium is a source of novel bioactive molecules which can be used as antifungal agents. The objective of this study was to evaluate the antifungal potential of Penicillium strains. Culture filtrates of two Penicillium species were tested for their antifungal potential by well diffusion assays. Filtrate of Penicillium isolates showed high antifungal effects on mycelial growth of Fusarium oxysporum, Fusarium solani, Macrophomina phaseolina, Aspergillus japonicus var aculeatus and Cladosporium cladosporioides. But Penicillium italicum inhibit the fungal growth from 45 to 68% as compared to Penicillium simplissimum (25–68%). However in case of A. japonicus var aculeatus, Penicillium spp. extracts were equally effective and reduce the colony growth up to 68%. However, P. simplissimum extract was least effective in case of M. phaseolina, where it decreased the colony growth only 25%.     

A case of primary amenorrhea with 46+XY genotype from Kashmir Valley

Primary amenorrhea is one of the common reproductive disorder affecting females. It leads to the absence of menarche in the reproductive age group in females and/or complete absence of reproductive organs. There are many causes which lead to PA, including genetic aberrations which are the leading factors.