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Synthetic Biology: Cellular Xdna Readers

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Synthetic Biology: Cellular Xdna Readers research highlights DRUG DISCOVERY this state, Ooi et al. treated cells with dimethyl Science, published online 17 November 2011, fumarate and found increased expression Malaria under arrest doi:10.1126/science.1211936 of NRF2 and its target genes, suggesting that KEAP1, which is known to control the The malaria parasites from Plasmodium species have both a liver stage (EEF or sporozoite stability of NRF2, is sensitive to fumarate. MS stage) and a blood stage in human hosts. Because EEFs of certain Plasmodium strains can in both studies confirmed the modification of remain dormant for long periods and disease symptoms originate during the blood stage, several residues in KEAP1 to S-(2-succinyl)- therapeutics that can eliminate parasites of both stages are needed, yet most drugs target cysteine (2SC) in fumarate-accumulating only the blood-stage parasites. To find drugs that might inhibit multiple parasite stages, conditions. Ooi et al. further demonstrated Meister et al. screened a library of 5,697 compounds known to be active against P. falciparum that ubiquitinated KEAP1 was elevated in blood stages. In a high-content imaging assay of sporozoite-infected cultured liver cells, the FH-deficient cells compared to controls; authors found 275 compounds that are structurally unrelated to known antimalarial scaffolds additional experiments using proteasomal and decrease parasite size within cells after infection. They then used a hypergeometric inhibitors led to a model where 2SC-modified mean function to determine which of the 2,715 independent chemical-scaffold clusters KEAP1 is ubiquitinated and degraded by a in the original library were fully represented among the hits, identifying quinazoline, the proteasome. This is the first HIF-1 – pyrazolopyrimidine and imidazolopiperazine scaffold clusters as promising. A structure- independent mechanism proposed to explain activity relationship analysis of the imidazolopiperazine scaffold yielded compounds that are tumorigenesis resulting from FH mutation; active against both parasite stages and have high potencies and desirable pharmacokinetic however, it remains to be determined how properties. By sequencing resistance mutations, the authors identified one target for three activation of the NRF2 antioxidant-response of the imidazolopiperazine compounds as an uncharacterized seven-transmembrane- pathway contributes to oncogenesis in domain–containing protein. As targets of other hits are also most likely distinct from known hereditary renal cancer. AD drug targets, as shown by the authors, these may represent new opportunities for eradicating MICROBIAL ECOLOGY malarial infections by arresting parasite development. MB When things go bad J. Am. Chem. Soc. , 18343–18349 (2011) SYNTHETIC BIOLOGY xDNA-containing plasmids by replicative and 133 Y-family polymerases. Though additional Small molecules often define the interactions Cellular xDNA readers experiments may reveal the mechanistic between bacteria and other species. J. Am. Chem. Soc. 133, 18447–18451 (2011) details of x-base replication, the current study Seyedsayamdost et al. had previously identified H highlights a new opportunity to explore the chemical components of a marine parasitic N N H O alternative coding schemes in cells. TLS interaction, in which the microalga Emiliania huxleyi releases a lignin component—p-coumaric N N H N N CANCER acid—into the environment, and the N O a-proteobacterium Phaeobacter gallaeciensis xA T KEAPing NRF in check BS107 responds by producing two toxic Cancer Cell , 511–523 (2011); Synthetic nucleobase analogs have proven 20 roseobacticides. To explore the generality of Cancer Cell , 524–537 (2011) useful for developing non-natural DNA coding 20 this phenomenon, the authors tested the impact © 2011 Nature America, Inc. All rights reserved. All rights Inc. America, Nature © 2011 systems. For example, ‘size-expanded DNA’ 2SC of p-coumaric acid along with four additional (xDNA) nucleotides—in which purine or lignin components and related biosynthetic KEAP1 KEAP1 pyrimidine bases are structurally extended intermediates on roseobacticide production by a benzene ring fusion—retain their by P. gallaeciensis BS107. Four of the five lignin ability to pair with natural bases but form NRF2 NRF2 molecules elicited a chemical response, the expanded double helices. DNA polymerases components of which could be grouped into four can replicate many alternative base pairs with The Krebs cycle enzyme fumarate hydratase families of roseobacticide analogs, including reasonable fidelity in vitro, but completion (FH) is mutated in a hereditary renal cancer phenyl-, phenol- and indole-modified structures of DNA synthesis is often impaired, limiting syndrome, where FH mutation stabilizes as well as two dimeric roseobacticides. The the cellular applications of synthetic genetic expression of HIF-1a, a transcription factor authors further observed that treatment with systems. Krueger et al. now show that xDNA that promotes cell survival in hypoxic each of the four E. huxleyi elicitors yielded modifications can undergo DNA replication conditions. Because other HIF-1α–stabilizing different combinations of the roseobacticides in in Escherichia coli. The authors created a series mutations lead to distinct tumor phenotypes, different proportions. Extension of these tests to of tagged expression plasmids containing two groups set out to determine whether additional species identified P. gallaeciensis 2.10 xDNA modifications in the coding region of FH mutation could promote tumorigenesis as similarly responsive to the lignin elicitors with a GFP gene. Transformation of E. coli with independently of HIF1α. Using genetic additional diversity in roseobacticide production: modified plasmids with up to four adjacent approaches, Ooi et al. and Adam et al. for P. gallaeciensis BS107, p-coumaric acid and xDNA substitutions yielded green bacterial now link disruption of FH with loss of sinapic acid yielded the strongest responses, colonies; DNA sequencing revealed that, activity of KEAP1, an electrophile-sensitive whereas for P. gallaeciensis 2.10, ferulic acid and after transformation, xDNA templates are component of an E3 ubiquitin ligase, and cinnamic acid were favored. These results help copied faithfully into plasmids with natural increased activity of the antioxidant response to define a parasitic system and stimulate further base pairs. Mutational analysis ruled out transcription factor NRF2. Both groups questions regarding the role of the individual DNA repair pathway involvement in this demonstrated that the link between FH roseobacticides. CG conversion, but biochemical experiments mutation and KEAP1 or NRF2 is independent showed that GFP production from xDNA of HIF-1a. Fumarate, the substrate for FH, Written by Mirella Bucci, Amy Donner, templates was dependent on the copying of accumulates in FH-deficient cells; to mimic Catherine Goodman & Terry L. Sheppard NATURE CHEMICAL BIOLOGY | VOL 8 | JANUARY 2012 | www.nature.com/naturechemicalbiology 21.
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