The function of RAD52 N-terminal domain is essential for viability of BRCA-deficient cells

RAD52 is a member of the homologous recombination pathway that is important for survival of BRCA-deficient cells. Inhibition of RAD52 leads to lethality in BRCA-deficient cells. However, the exact mechanism of how RAD52 contributes to viability of BRCA-deficient cells remains unknown. Two major activities of RAD52 were previously identified: DNA or RNA pairing, which includes DNA/RNA annealing and strand exchange, and mediator, which is to assist RAD51 loading on RPA-covered ssDNA. Here, we report that the N-terminal domain (NTD) of RAD52 devoid of the potential mediator function is essential for maintaining viability of BRCA-deficient cells owing to its ability to promote DNA/RNA pairing. We show that RAD52 NTD forms nuclear foci upon DNA damage in BRCA-deficient human cells and promotes DNA double-strand break repair through two pathways: homology-directed repair (HDR) and single-strand annealing (SSA). Furthermore, we show that mutations in the RAD52 NTD that disrupt these activities fail to maintain viability of BRCA-deficient cells.     

Identifying enriched drug fragments as possible candidates for metabolic engineering

Background

Fragment-based approaches have now become an important component of the drug discovery process. At the same time, pharmaceutical chemists are more often turning to the natural world and its extremely large and diverse collection of natural compounds to discover new leads that can potentially be turned into drugs. In this study we introduce and discuss a computational pipeline to automatically extract statistically overrepresented chemical fragments in therapeutic classes, and search for similar fragments in a large database of natural products. By systematically identifying enriched fragments in therapeutic groups, we are able to extract and focus on few fragments that are likely to be active or structurally important.

Results

We show that several therapeutic classes (including antibacterial, antineoplastic, and drugs active on the cardiovascular system, among others) have enriched fragments that are also found in many natural compounds. Further, our method is able to detect fragments shared by a drug and a natural product even when the global similarity between the two molecules is generally low.

Conclusions

A further development of this computational pipeline is to help predict putative therapeutic activities of natural compounds, and to help identify novel leads for drug discovery.

     

The catalytic activity of the translation termination factor methyltransferase Mtq2-Trm112 complex is required for large ribosomal subunit biogenesis

The Mtq2-Trm112 methyltransferase modifies the eukaryotic translation termination factor eRF1 on the glutamine side chain of a universally conserved GGQ motif that is essential for release of newly synthesized peptides. Although this modification is found in the three domains of life, its exact role in eukaryotes remains unknown. As the deletion of MTQ2 leads to severe growth impairment in yeast, we have investigated its role further and tested its putative involvement in ribosome biogenesis. We found that Mtq2 is associated with nuclear 60S subunit precursors, and we demonstrate that its catalytic activity is required for nucleolar release of pre-60S and for efficient production of mature 5.8S and 25S rRNAs. Thus, we identify Mtq2 as a novel ribosome assembly factor important for large ribosomal subunit formation. We propose that Mtq2-Trm112 might modify eRF1 in the nucleus as part of a quality control mechanism aimed at proof-reading the peptidyl transferase center, where it will subsequently bind during translation termination.     

Males and Females Gain Differentially from Sociality in a Promiscuous Fruit Bat Cynopterus sphinx

Sociality emerges when the benefits of group living outweigh its costs. While both males and females are capable of strong social ties, the evolutionary drivers for sociality and the benefits accrued maybe different for each sex. In this study, we investigate the differential reproductive success benefits of group membership that males and females might obtain in the promiscuous fruit bat Cynopterus sphinx. Individuals of this species live in flexible social groups called colonies. These colonies are labile and there is high turnover of individuals. However, colony males sire more offspring within the colony suggesting that being part of a colony may result in reproductive benefits for males. This also raises the possibility that long-term loyalty towards the colony may confer additional advantage in terms of higher reproductive success. We used ten seasons of genetic parentage data to estimate reproductive success and relatedness of individuals in the colony. We used recapture data to identify long and short-term residents in the colony as well as to obtain rates of recapture for males and females. Our results reveal that males have a significantly higher chance of becoming long-term residents (than females), and these long-term resident males gain twice the reproductive success compared to short-term resident males. We also observed that long-term resident females are related to each other and also achieve higher reproductive success than short-term resident females. In contrast, long-term resident males do not differ from short-term resident males in their levels of relatedness. Our results re-iterate the benefits of sociality even in species that are promiscuous and socially labile and possible benefits of maintaining a colony.     

In Silico Analysis of New Potent Anti-hyperglycemic Molecule for Diabetes Type 2 Management

International Journal of Peptide Research and Therapeutics - Diabetes mellitus Type 2 happens to be one of the most challenging health concerns in recent times and has spiked an alarming rise...     

Variance in Female Reproductive Success Differentially Impacts Effective Population Size in the Short-Nosed Fruit Bat, <Emphasis Type="Italic">Cynopterus sphinx</Emphasis>

Effective population size (N _e) quantifies the effects of micro-evolutionary processes and the rate of loss of genetic diversity in a population. Several demographic and mating parameters reduce N _e. Theoretical studies elucidate the impacts of various demographic and mating system parameters on N _e, while empirical studies illustrate realized N _e for species with differing life histories and mating systems. However, effect of intra-specific variation in mating system on effective size remains largely unexplored. In this paper we investigated the effect of promiscuous and polygynous mating on N _e in two wild populations of the short-nosed fruit bat, Cynopterus sphinx. N _e/N (ratio of effective population size to census size) was lower than unity in both populations, and much lower for the polygynous population compared to promiscuous population. Elasticity analyses reveal that N _e/N was sensitive to deviations in the sex ratio. Variance in female reproductive success had a higher impact on N _e compared to variance in male reproductive success in the promiscuous population. However, for the polygynous population, impact of variance in male reproductive success on N _e was higher than that of variance in female reproductive success. Our results suggest that depending on mating system, different populations of the same species could have alternate evolutionary trajectories. The rate of loss of genetic diversity would be lower for the promiscuous population compared to the polygynous population. Our study is the first to highlight which parameters would most significantly impact population specific N _e under different mating systems.     

16S rRNA gene profiling of rhizospheric microbial community of Eichhornia crassipes

Molecular Biology Reports - The rhizosphere of a plant is an important interface for the plant-microbe interaction that plays a significant role in the uptake and removal of heavy metal from...     

Drop-out phagemid vector for switching from phage displayed affinity reagents to expression formats

Affinity reagents that are generated by phage display are typically subcloned into an expression vector for further biochemical characterization. This insert transfer process is time consuming and laborious especially if many inserts are to be subcloned. To simplify the transfer process, we have constructed a “drop-out” phagemid vector that can be rapidly converted to an expression vector by a simple restriction enzyme digestion with MfeI (to “drop-out” the gene III coding sequence), which generates alkaline phosphatase (AP) fusions of the affinity reagents on religation. Subsequently, restriction digestion with AscI drops out the AP coding region and religation generates affinity reagents with a C-terminal six-histidine tag. To validate the usefulness of this vector, four different human single chain Fragments of variable regions (scFv) were tested, three of which show specific binding to three zebrafish (Danio rerio) proteins, namely suppression of tumorigenicity 13, recoverin, and Ppib and the fourth binds to human Lactoferrin protein. For each of the constructs tested, the gene III and AP drop-out efficiency was between 90% and 100%. This vector is especially useful in speeding up the downstream screening of affinity reagents and bypassing the time-consuming subcloning experiments.