Anbu Karani Adikesavan

Separation of recombination and SOS response in Escherichia coli RecA suggests LexA interaction sites.

RecA plays a key role in homologous recombination, the induction of the DNA damage response through LexA cleavage and the activity of error-prone polymerase in Escherichia coli. RecA interacts with multiple partners to achieve this pleiotropic role, but the structural location and sequence determinants involved in these multiple interactions remain mostly unknown. Here, in a first application to prokaryotes, Evolutionary Trace (ET) analysis identifies clusters of evolutionarily important surface amino acids involved in RecA functions. Some of these clusters match the known ATP binding, DNA binding, and RecA-RecA homo-dimerization sites, but others are novel. Mutation analysis at these sites disrupted either recombination or LexA cleavage. This highlights distinct functional sites specific for recombination and DNA damage response induction. Finally, our analysis reveals a composite site for LexA binding and cleavage, which is formed only on the active RecA filament. These new sites can provide new drug targets to modulate one or more RecA functions, with the potential to address the problem of evolution of antibiotic resistance at its root.

Prediction and redesign of protein–protein interactions

Understanding the molecular basis of protein function remains a central goal of biology, with the hope to elucidate the role of human genes in health and in disease, and to rationally design therapies through targeted molecular perturbations. We review here some of the computational techniques and resources available for characterizing a critical aspect of protein function - those mediated by protein-protein interactions (PPI). We describe several applications and recent successes of the Evolutionary Trace (ET) in identifying molecular events and shapes that underlie protein function and specificity in both eukaryotes and prokaryotes. ET is a part of analytical approaches based on the successes and failures of evolution that enable the rational control of PPI.

Predicting Future Scientific Discoveries Based on a Networked Analysis of the Past Literature

We present KnIT, the Knowledge Integration Toolkit, a system for accelerating scientific discovery and predicting previously unknown protein-protein interactions. Such predictions enrich biological research and are pertinent to drug discovery and the understanding of disease. Unlike a prior study, KnIT is now fully automated and demonstrably scalable. It extracts information from the scientific literature, automatically identifying direct and indirect references to protein interactions, which is knowledge that can be represented in network form. It then reasons over this network with techniques such as matrix factorization and graph diffusion to predict new, previously unknown interactions. The accuracy and scope of KnITs knowledge extractions are validated using comparisons to structured, manually curated data sources as well as by performing retrospective studies that predict subsequent literature discoveries using literature available prior to a given date. The KnIT methodology is a step towards automated hypothesis generation from text, with potential application to other scientific domains.

Activation of p53 Transcriptional Activity by SMRT: a Histone Deacetylase 3-Independent Function of a Transcriptional Corepressor

ABSTRACT The silencing mediator of retinoic acid and thyroid hormone receptors (SMRT) is an established histone deacetylase 3 (HDAC3)-dependent transcriptional corepressor. Microarray analyses of MCF-7 cells transfected with control or SMRT small interfering RNA revealed SMRT regulation of genes involved in DNA damage responses, and the levels of the DNA damage marker γH2AX as well as poly(ADP-ribose) polymerase cleavage were elevated in SMRT-depleted cells treated with doxorubicin. A number of these genes are established p53 targets. SMRT knockdown decreased the activity of two p53-dependent reporter genes as well as the expression of p53 target genes, such as CDKN1A (which encodes p21). SMRT bound directly to p53 and was recruited to p53 binding sites within the p21 promoter. Depletion of GPS2 and TBL1, components of the SMRT corepressor complex, but not histone deacetylase 3 (HDAC3) decreased p21-luciferase activity. p53 bound to the SMRT deacetylase activation domain (DAD), which mediates HDAC3 binding and activation, and HDAC3 could attenuate p53 binding to the DAD region of SMRT. Moreover, an HDAC3 binding-deficient SMRT DAD mutant coactivated p53 transcriptional activity. Collectively, these data highlight a biological role for SMRT in mediating DNA damage responses and suggest a model where p53 binding to the DAD limits HDAC3 interaction with this coregulator, thereby facilitating SMRT coactivation of p53-dependent gene expression.

In vivo role of NAD(P)H: quinone oxidoreductase 1 in metabolic activation of mitomycin C and bone marrow cytotoxicity

NAD(P)H:quinone oxidoreductase 1(-/-) (NQO1(-/-)), NQO1(+/-) along with NRH:quinone oxidoreductase 2(-/-) (NQO2(-/-)), and wild-type (WT) mice were exposed to five once weekly doses of mitomycin C. The mice were euthanized 15 weeks after the first dose. Blood cell counts and histologic analyses were done. WT and NQO2(-/-) mice showed hypocellularity and a significant increase in adipocytes in bone marrow. They also showed anemia because of the loss of RBC and hemoglobin. The neutrophils and platelets were reduced, whereas other blood cell types and tissues were normal. Interestingly, NQO1(-/-) mice showed a complete resistance to mitomycin C-induced bone marrow cytotoxicity and reduction in RBC, hemoglobin, and neutrophils. NQO1(+/-) mice also showed limited resistance to mitomycin C-induced bone marrow cytotoxicity. These data show a major in vivo role of NQO1 in metabolic activation of mitomycin C with implications in mitomycin C chemotherapy.

Overlapping signal sequences control nuclear localization and endoplasmic reticulum retention of GRP58

This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). The University of Maryland, Baltimore conducted an internal investigation which found that the article was compromised and a preponderance of evidence supports retraction of the publication in order to correct the scientific record and ensure its integrity. The Editor-in-Chief has decided to retract this article. This article has been found to contain manipulated and enhanced figures, namely figures 1D and 1E, 4A and 4B.

Si RNA inhibition of GRP58 associated with decrease in mitomycin C-induced DNA cross-linking and cytotoxicity.

This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This article has been retracted at the request of the Office of Integrity of the University of Maryland due to data entered in Fig 3 of the publication that were not supported by raw data, in addition to the fact that the statistical evaluations were adultered.

Literature-based automated discovery of tumor suppressor p53 phosphorylation and inhibition by NEK2.

Significance We adapted natural language processing to the biological literature and demonstrated end-to-end automated knowledge discovery by exploring subtle word connections. General text mining scanned 21 million publication abstracts and selected a reliable 130,000 from which hypothesis generation algorithms predicted kinases not known to phosphorylate p53, but likely to do so. Six of these p53 kinase candidates passed experimental validation. Among them NEK2 was examined in depth and shown to repress p53 and promote cell division. This work demonstrates the possibility of integrating a vast corpora of written knowledge to compute valuable hypotheses that will often test true and fuel discovery. Scientific progress depends on formulating testable hypotheses informed by the literature. In many domains, however, this model is strained because the number of research papers exceeds human readability. Here, we developed computational assistance to analyze the biomedical literature by reading PubMed abstracts to suggest new hypotheses. The approach was tested experimentally on the tumor suppressor p53 by ranking its most likely kinases, based on all available abstracts. Many of the best-ranked kinases were found to bind and phosphorylate p53 (P value = 0.005), suggesting six likely p53 kinases so far. One of these, NEK2, was studied in detail. A known mitosis promoter, NEK2 was shown to phosphorylate p53 at Ser315 in vitro and in vivo and to functionally inhibit p53. These bona fide validations of text-based predictions of p53 phosphorylation, and the discovery of an inhibitory p53 kinase of pharmaceutical interest, suggest that automated reasoning using a large body of literature can generate valuable molecular hypotheses and has the potential to accelerate scientific discovery.

Retraction notice to “Si RNA inhibition of GRP58 associated with decrease in mitomycin C-induced DNA cross-linking and cytotoxicity”: [Chem. Biol. Interact. 162/1 (2006) 81–87]

This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This article has been retracted at the request of the Office of Integrity of the University of Maryland due to data entered in Fig 3 of the publication that were not supported by raw data, in addition to the fact that the statistical evaluations were adultered.

Retraction notice to "Overlapping signal sequences control nuclear localization and endoplasmic reticulum retention of GRP58" [Biochemical and Biophysical Research Communications 377 (2) (2008) 407–412]

This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). The University of Maryland, Baltimore conducted an internal investigation which found that the article was compromised and a preponderance of evidence supports retraction of the publication in order to correct the scientific record and ensure its integrity. The Editor-in-Chief has decided to retract this article. This article has been found to contain manipulated and enhanced figures, namely figures 1D and 1E, 4A and 4B.