The R Protein of SARS-CoV: Analyses of Structure and Function Based on Four Complete Genome Sequences of Isolates BJ01-BJ04

The R (replicase) protein is the uniquely defined non-structural protein (NSP) responsible for RNA replication, mutation rate or fidelity, regulation of transcription in coronaviruses and many other ssRNA viruses. Based on our complete genome sequences of four isolates (BJ01-BJ04) of SARS-CoV from Beijing, China, we analyzed the structure and predicted functions of the R protein in comparison with 13 other isolates of SARS-CoV and 6 other coronaviruses. The entire ORF (open-reading frame) encodes for two major enzyme activities, RNA-dependent RNA polymerase (RdRp) and proteinase activities. The R polyprotein undergoes a complex proteolytic process to produce 15 function-related peptides. A hydrophobic domain (HOD) and a hydrophilic domain (HID) are newly identified within NSP1. The substitution rate of the R protein is close to the average of the SARS-CoV genome. The functional domains in all NSPs of the R protein give different phylogenetic results that suggest their different mutation rate under selective pressure. Eleven highly conserved regions in RdRp and twelve cleavage sites by 3CLP (chymotrypsin-like protein) have been identified as potential drug targets. Findings suggest that it is possible to obtain information about the phylogeny of SARS-CoV, as well as potential tools for drug design, genotyping and diagnostics of SARS

The Genomes of Oryza sativa: A History of Duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family

Screening of Bioactive Ingredients in Ligusticum Chuanxiong Hort for Protection against Myocardial Ischemia

Background/Aims: To study the spectrum-effect relationship and effective components of Ligusticum Chuanxiong Hort. (LCH) on the protection of canine myocardial ischemia. Methods: Fingerprint spectrum of LCH extracts was developed using high performance liquid chromatography (HPLC), and a canine model of acute myocardial ischemia was established by ligating the coronary artery. Bivariate correlation analysis and multivariate regression analysis were used to correlate the pharmacodynamics of LCH extract and its common peaks in HPLC. Results: The bioactive components of LCH were ligustrazine, ferulic acid, cnidilide and ligustilide. Ligustrazine and ferulic acid could significantly reduce serum lactic acid in canine model of acute myocardial ischemia, while ligustilide could significantly reduce the elevation of serum free fatty acid. Conclusions: The spectrum-effect relationship study shows that the effective components of LCH are ligustrazine, ferulic acid, cnidilide and ligustilide, which have protective effect on myocardial ischemia

Evolution and Variation of the SARS-CoV Genome

Knowledge of the evolution of pathogens is of great medical and biological significance to the prevention, diagnosis, and therapy of infectious diseases. In order to understand the origin and evolution of the SARS-CoV (severe acute respiratory syndrome-associated coronavirus), we collected complete genome sequences of all viruses available in GenBank, and made comparative analyses with the SARS-CoV. Genomic signature analysis demonstrates that the coronaviruses all take the TGTT as their richest tetranucleotide except the SARS-CoV. A detailed analysis of the forty-two complete SARS-CoV genome sequences revealed the existence of two distinct genotypes, and showed that these isolates could be classified into four groups. Our manual analysis of the BLASTN results demonstrates that the HE (hemagglutinin-esterase) gene exists in the SARS-CoV, and many mutations made it unfamiliar to us

Functional Classifications from GO, Focused on Plant-Specific Categories Outlined by Gramene

<p>(A) compares predicted genes from <i>Arabidopsis</i> and Beijing <i>indica</i>. (B) compares predicted genes from Beijing <i>indica</i> with nr-KOME cDNAs. We ignore categories with less than 0.1% of the genes.</p

Overlapping FGENESH Predictions in All Three Rice Assemblies

<p>Two predictions are shared when 50% of their coding regions can be aligned. Because of imprecision in the predictions and overlap criteria, we get slightly different numbers for each assembly, and these are encoded through multiple color-coded numbers in the Venn diagram. EST confirmation requires 100 bp of exact match. Unlike the genes, we do not bother to show a different number for each assembly, because they are very similar.</p

Ka/Ks Distribution for Homolog Pairs

<p>Ka and Ks are the fraction of the available nonsynonymous and synonymous sites that are changed in the homolog pairs. Ka/Ks > 1 is an indicator of positive selection. Shown is the Ka/Ks distribution for segmental duplications (A) and for tandem duplications (B).</p

Duplicated Segments in the Beijing <i>indica</i> Assembly

<p>Depicted here are the plots for Chromosomes 2 (A) and 6 (B). Each data point represents the coordinated genomic positions in a homolog pair, consisting of one nr-KOME cDNA and its one and only TBlastN homolog in rice. Shown on the <i>x</i>-axis is the position of a gene on the indicated chromosome, and shown on the <i>y</i>-axis is the position of its homolog on any of the rice chromosomes, with chromosome number encoded by the colors indicated on the legend at the right.</p

A Region on Beijing <i>indica</i> Chromosome 2, Showing Three Gene Islands Separated by Two Intergenic Repeat Clusters of High 20-mer Copy Number

<p>Transposable elements identified by RepeatMasker are classified based on the nomenclature of <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030038#st002" target="_blank">Table S2</a>. Depicted genes include both nr-KOME cDNAs and FGENESH predictions.</p