A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies—a whole-genome assembly and a regional chromosome assembly—were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional ∼12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

An important mechanism by which the tumor suppressor p53 maintains genomic stability is to induce cell cycle arrest through activation of the cyclin-dependent kinase inhibitor p21 WAF1/Cip1 gene. We show that the gene encoding the gut-enriched Krü ppel-like factor (GKLF, KLF4) is concurrently induced with p21 WAF1/Cip1during serum deprivation and DNA damage elicited by methyl methanesulfonate. The increases in expression of both Gklf and p21 WAF1/Cip1 due to DNA damage are dependent on p53. Moreover, during the first 30 min of methyl methanesulfonate treatment, the rise in Gklf mRNA level precedes that in p21, suggesting that GKLF may be involved in the induction of p21 Indeed, GKLF activates p21WAF1/Cip1 through a specific Sp1-like cis-element in the p21 WAF1/Cip1 proximal promoter. The same element is also required by p53 to activate the p21 WAF1/Cip1 promoter, although p53 does not bind to it. Potential mechanisms by which p53 activates the p21 WAF1/Cip1 promoter include a physical interaction between p53 and GKLF and the transcriptional induction of Gklf by p53. Consequently, the two transactivators cause a synergistic induction of the p21 WAF1/Cip1 promoter activity. The physiological relevance of GKLF in mediating p53-dependent induction of p21 WAF1/Cip1 is demonstrated by the ability of antisense Gklf oligonucleotides to block the production of p21 WAF1/Cip1 in response to p53 activation. These findings suggest that GKLF is an essential mediator of p53 in the transcriptional induction of p21 WAF1/Cip1 and may be part of a novel pathway by which cellular responses to stress are modulated.

Most studies of the impact of vibrational excitation on molecular reactivity have focused on reactions with a late barrier (that is, a transition state resembling the products). For an early barrier reaction, conventional wisdom predicts that a reactant's vibration should not couple efficiently to the reaction coordinate and thus should have little impact on the outcome. We report here an in-depth experimental study of the reactivity effects exerted by reactant C-H stretching excitation in a prototypical early-barrier reaction, F + CHD3. Rather counterintuitively, we find that the vibration hinders the overall reaction rate, inhibits scission of the excited bond itself (favoring the DF + CHD2 product channel), and influences the coproduct vibrational distribution despite being conserved in the CHD2 product. The results highlight substantial gaps in our predictive framework for state-selective polyatomic reactivity.

The gut-enriched Krü ppel-like factor (GKLF) is a newly identified zinc finger-containing transcription factor. Recent studies indicate that GKLF binds to a core DNA sequence of 5-(G/A)(G/A)GG(C/T)G(C/T)-3, which is found in an endogenous cis element, the basic transcription element (BTE) of the cytochrome P-450IA1 (CYP1A1) promoter. The present study characterizes the ability of GKLF to regulate CYP1A1 expression. By electrophoretic mobility gel shift assay (EMSA) and methylation interference assay, GKLF was found to bind BTE in a manner similar to several other transcription factors known to interact with BTE including Sp1 and BTEB. Cotransfection studies in Chinese hamster ovary cells showed that GKLF inhibited the CYP1A1 promoter in a dose-and BTE-dependent manner. The same experiments also revealed that BTE was responsible for a significant portion of the CYP1A1 promoter activity. EMSA of nuclear extracts from Chinese hamster ovary cells showed that Sp1 and Sp3 were two major proteins that interacted with BTE. Additional cotransfection studies showed that GKLF inhibited Sp1-mediated activation of the CYP1A1 promoter. In contrast, GKLF enhanced Sp3-dependent suppression of the same promoter. Moreover, the ability of GKLF to inhibit Sp1-dependent transactivation was in part due to physical interaction of the two proteins. These findings indicate that GKLF is a negative regulator of the CYP1A1 promoter in a BTE-dependent fashion and that this inhibitory effect is in part mediated by physical interaction with Sp1.

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The highly conserved coadapters CREB binding protein (CBP) and p300 form complexes with CREB as well as other DNA binding transcription factors to modulate chromatin remodeling and thus transcription. Human T-lymphotropic virus type 1 (HTLV-1) transcription is controlled, in part, by the CREB/ATF family of transcription factors which bind promoter sequences and function as complexes with the viral oncogenic protein Tax. We have reported that the nuclear localizing protein p30 II of HTLV-1 functions as a transcription factor, differentially modulates CREB-responsive promoters, and is critical for maintenance of proviral loads in rabbits. In this study, we tested whether p30 II directly interacts with CBP/p300 to modulate gene transcription. Gal4(BD)-p30II -mediated transactivation was enhanced following exogenous expression of p300 and was competitively repressed by the p300 binding protein, adenovirus E1A, and E1ACR2 (mutated for retinoblastoma binding but retaining p300 binding). In contrast, E1ACR1 (mutated for p300 binding) failed to alter Gal4(BD)-p30 II -mediated transactivation. In addition, Gal4(BD)-p30 II -mediated transactivation was competitively inhibited by the cotransfection of CMV-p30 II -HA and CMV-Tax but could be rescued by exogenous p300. Importantly, we demonstrate that p30 II colocalizes with p300 in cell nuclei and directly binds to CBP/p300 in cells. Deletion mutants of CBP/p300 were used to localize the site critical for binding p30 II to a highly conserved KIX region. DNA binding assays confirmed the interference of p30 II with the assembly of CREB-Tax-p300/CBP multiprotein complexes on 21-bp repeat oligonucleotides in vitro. Collectively, our results demonstrate that CBP/p300 is a cellular protein target for HTLV-1 p30 II and mediates its transcriptional effects in vivo.The coactivators CREB binding protein (CBP) and p300 mediate transcriptional control of various cellular and viral DNA binding transcription factors. These coactivators are highly similar in nucleotide sequence, are evolutionarily conserved, and are often referred to together as CBP/p300, despite evidence of divergent functions (10, 25). These proteins bridge transcription factors to relevant promoters, have intrinsic histone acetyltransferase (HAT) activity, and form complexes with proteins such as CBP/p300 binding protein-associated factor, which also exhibits HAT activity (26). Recent reviews provide a growing list of cellular and viral proteins that interact with either CBP or p300, including steroid and retinoid hormone receptors, CREB, c-Jun, c-Myb, Sap-1a, c-Fos, MyoD, p53, Stat-1/2, NF-B, pp90rsk , TATA-binding protein, and TFIIB (4, 25, 29, 30). Among viral regulatory proteins, human T-lymphotropic virus type 1 (HTLV-1) Tax, adenovirus E1A, Kaposi's sarcoma-associated herpesvirus viral interferon regulatory factor protein, and simian virus 40 large T antigen also target and affect CBP and p300 functions (1-3, 17, 32, 38, 41, 52).Complex retroviruses, like HTLV-1, must regulate their gene expression in cooperation...

Based on theoretical evidence, it has been proposed that HIV-1 may encode several selenoprotein modules, one of which (overlapping the env gp41-coding region) has highly significant sequence similarity to the mammalian selenoprotein glutathione peroxidase (GPx; EC 1.11.1.9). The similarity score of the putative HIV-1 viral GPx homolog relative to an aligned set of known GPx is 6.3 SD higher than expected for random sequences of similar composition. Based on that alignment, a molecular model of the HIV-1 GPx was constructed by homology modeling from the bovine GPx crystal structure. Despite extensive truncation relative to the cellular GPx gene, the structural core and the geometry of the catalytic triad of selenocysteine, glutamine, and tryptophan are well conserved in the viral GPx. All of the insertions and deletions predicted by the alignment proved to be structurally feasible. The model is energetically favorable, with a computed molecular mechanics strain energy close to that of the bovine GPx structure, when normalized on a per-residue basis. However, considering the remote homology, this model is intended only to provide a working hypothesis allowing for a similar active site and structural core. To validate the theoretical predictions, we cloned the hypothetical HIV-1 gene and found it to encode functional GPx activity when expressed as a selenoprotein in mammalian cells. In transfected canine kidney cells, the increase in GPx activity ranged from 21% to 43% relative to controls (average 30%, n ‫؍‬ 9, P < 0.0001), whereas, in transfected MCF7 cells, which have low endogenous GPx activity, a near 100% increase was observed (average 99%, n ‫؍‬ 3, P < 0.05).A s various genome projects have continued to expand the number of entries in nucleic acid sequence databases, there has been an increasing demand for computational biology and computational chemistry methods capable of solving several fundamental problems (1). The latter include the prediction of (i) the existence, location and architecture of genes, (ii) the functions of the encoded proteins, and, ultimately, (iii) the structures of the encoded proteins. Advances in comparative sequence analysis, including methods for the identification of remote homologs (1, 2), coupled with advances in protein structure prediction and molecular mechanics (3-5), have now brought all of these objectives within reach, at least when there is some degree of homology between a novel gene and known examples in databases. The ability to identify remote homologs and predict their protein structures is still a major challenge for computational chemists and biologists.The need for such advanced computational methods should not be underestimated, because their use can lead to the identification of genes whose existence or function is not obvious and which can be missed even after extensive analysis by conventional methods.

Metallic nanocrystals (NCs) with well-defined sizes and shapes represent a new family of model systems for establishing structure-function relationships in heterogeneous catalysis. Here in this study, we show that catalyst poisoning can be utilized as an efficient strategy for nanocrystals shape and composition control, as well as a way to tune the catalytic activity of catalysts. Lead species, a well-known poison for noble-metal catalysts, was investigated in the growth of Pd NCs. We discovered that Pb atoms can be incorporated into the lattice of Pd NCs and form Pd-Pb alloy NCs with tunable composition and crystal facets. As model catalysts, the alloy NCs with different compositions showed different selectivity in the semihydrogenation of phenylacetylene. Pd-Pb alloy NCs with better selectivity than that of the commercial Lindlar catalyst were discovered. This study exemplified that the poisoning effect in catalysis can be explored as efficient shape-directing reagents in NC growth, and more importantly, as a strategy to tailor the performance of catalysts with high selectivity.