Valyl-tRNA synthetase (ValRS) strictly discriminates the cognate L-valine from the larger L-isoleucine and the isosteric L-threonine by the tRNA-dependent "double sieve" mechanism. In this study, we determined the 2.9 A crystal structure of a complex of Thermus thermophilus ValRS, tRNA(Val), and an analog of the Val-adenylate intermediate. The analog is bound in a pocket, where Pro(41) allows accommodation of the Val and Thr moieties but precludes the Ile moiety (the first sieve), on the aminoacylation domain. The editing domain, which hydrolyzes incorrectly synthesized Thr-tRNA(Val), is bound to the 3' adenosine of tRNA(Val). A contiguous pocket was found to accommodate the Thr moiety, but not the Val moiety (the second sieve). Furthermore, another Thr binding pocket for Thr-adenylate hydrolysis was suggested on the editing domain.

Bacterial persister cells constitute a small portion of a culture which is tolerant to killing by lethal doses of bactericidal antibiotics. These phenotypic variants are formed in numerous bacterial species, including those with clinical relevance like the opportunistic pathogen Pseudomonas aeruginosa. Although persisters are believed to contribute to difficulties in the treatment of many infectious diseases, the underlying mechanisms affecting persister formation are not well understood. Here we show that even though P. aeruginosa cultures have a significantly smaller fraction of multidrug-tolerant persister cells than cultures of Escherichia coli or Staphylococcus aureus, they can increase persister numbers in response to quorum-sensing-related signaling molecules. The phenazine pyocyanin (and the closely related molecule paraquat) and the acyl-homoserine lactone 3-OC12-HSL significantly increased the persister numbers in logarithmic P. aeruginosa PAO1 or PA14 cultures but not in E. coli or S. aureus cultures.Over the last 50 years, Pseudomonas aeruginosa has emerged as a major cause of nosocomial infections in immunocompromised patients, including those relying on mechanical ventilation and suffering from neutropenia or severe burns, and is perhaps most well known as the agent primarily responsible for the decline in lung function leading to death in cystic fibrosis (CF) patients (8,14,16,23,38). P. aeruginosa possesses a multiplicity of virulence factors that are elicited upon access to susceptible individuals, including various toxins, secretion systems, siderophores, surface appendages, endotoxin (lipopolysaccharide [LPS]), alginate, and phenazines. These can generate acute toxicity/injury, leading P. aeruginosa to be labeled as the "hyena" of the bacterial world (15). Treatment of infections by P. aeruginosa is hindered by its high level of intrinsic resistance to antibiotics due primarily to a combination of the impermeable outer membrane and a number of broad-spectrum efflux pumps (50, 51). P. aeruginosa is also thought to enter into a biofilm mode of growth in CF lung infections (36,48,63), contributing both to pathogenicity/colonization and resistance to therapeutic intervention.In P. aeruginosa, global regulation, mediated by at least 3 quorum-sensing (QS) systems, controls population behaviors and synthesis of the majority of these pathogenicity factors (59, 66). This bacterium possesses two N-acyl-homoserine lactone (HSL)-mediated quorum-sensing systems, las and rhl (26,43,46,47), and a Pseudomonas quinolone signal (PQS) system mediated by 2-heptyl-3-hydroxy-4-quinolone (49). In the HSL-mediated systems, the HSL synthases LasI and RhlI are responsible for the synthesis of the autoinducers N-(3-oxododecanoyl)-L-HSL (3-OC12-HSL) and N-butyryl-L-HSL (C4-HSL), respectively. Expressions of the lasI and rhl genes are regulated by the transcriptional activators LasR and RhlR in response to their cognate HSL signal molecules. Among the numerous cellular and secreted virulence factors in P. aeruginosa whose...

Because resistance has developed to mainline antibiotics, including vancomycin, new antibiotics are now being aggressively sought. For this purpose, aminoacyl tRNA synthetases are being pursued as targets for new drugs. These enzymes are universal and are essential for cell viability. The key to their usefulness lies in being able to find drugs that inhibit a pathogen synthetase but not its human cell counterpart. The possibility for species-specific inhibition was originally demonstrated with a natural product and has now been demonstrated with prototypical drugs that are based on the structure of an intermediate of the aminoacylation reaction. Efficacy of a rationally designed inhibitor has been shown in vivo with a pathogen infection established in an animal model. Although many challenges remain, these early results suggest that synthetases will continue to be of major interest for development of new anti-infectives.

A single arginine residue within the basic region of the human immunodeficiency virus Tat protein mediates specific binding of Tat peptides to a three-nucleotide bulge in TAR RNA. It has been proposed that arginine recognizes TAR by forming a network of hydrogen bonds with two structurally distinct phosphates, an interaction termed the "arginine fork." Here it is shown that L-arginine blocks the Tat peptide/TAR interaction, whereas L-lysine and analogs of arginine that remove specific hydrogen bond donors do not.Experiments using an L-argine amnity column do te that argiiine and the Tat peptides bind to the same site in TAR.Modification of two phosphates located at the junction of the double-stranded stem and bulge and modification of two adenine N7 groups in base-paired regions of TAR interfere with specific arginine binding. The results emphasize the importance of RNA structure in RNA-protein recognition and provide methods to identify argininebinding sites in RNAs.The importance of RNA structure in sequence-specific RNA-protein recognition is becoming increasingly apparent. Biochemical studies of the R17 phage coat protein and its RNA-binding site were among the first to suggest a direct role of RNA structure in the interaction (1,2). Subsequent structural studies of glutaminyl-and aspartyl-tRNA synthetase-tRNA complexes have highlighted its importance (3-5). RNA structure is also critical in the interaction of the human immunodeficiency virus (HIV) transcriptional activator, Tat, with TAR, an RNA stem-loop located at the 5' end of viral mRNAs. Studies with Tat peptides have shown that the Tat/TAR interaction is mediated by a short (nine amino acid) region of basic amino acids (6-9). A single arginine residue in the peptide provides the only sequence-specific contact with the RNA (10). Chemical modification experiments identified two phosphates in TAR, located at the junction of the double-stranded stem and a three-nucleotide bulge, that are important in this interaction (10), suggesting that specificity may be derived largely from recognition of a defined backbone conformation of the RNA. Arginine may recognize this structure by forming a specific network of hydrogen bonds with the two phosphates, an interaction termed the "arginine fork" (10). Chemical modification experiments also suggest that N7 groups of two base-paired adenines, one located above the bulge and one located below the bulge, are important in the interaction (6, 11).Because only one arginine in the Tat peptides mediates specific recognition of TAR, it seemed plausible that the free amino acid arginine might also bind specifically to TAR. Here we show that L-arginine does indeed bind specifically to TAR and that the arginine-binding site in TAR requires the same two phosphates and adenine N7 groups that are needed for Tat peptide binding. The results suggest that TAR RNA folds into a specific conformation containing a single argininebinding site and emphasize the importance of RNA structure in an RNA-protein interaction. MATERIALS AN...

High-throughput screening (HTS) is an integral part of early drug discovery. Herein, we focused on those small molecules in a screening collection that have never shown biological activity despite having been exhaustively tested in HTS assays. These compounds are referred to as 'dark chemical matter' (DCM). We quantified DCM, validated it in quality control experiments, described its physicochemical properties and mapped it into chemical space. Through analysis of prospective reporter-gene assay, gene expression and yeast chemogenomics experiments, we evaluated the potential of DCM to show biological activity in future screens. We demonstrated that, despite the apparent lack of activity, occasionally these compounds can result in potent hits with unique activity and clean safety profiles, which makes them valuable starting points for lead optimization efforts. Among the identified DCM hits was a new antifungal chemotype with strong activity against the pathogen Cryptococcus neoformans but little activity at targets relevant to human safety.