The relationship between translational initiation and messenger RNA inactivation in down-shifted Escherichia coli

The parameters of protein synthesis and functional inactivation of global messenger RNA (mRNA) were examined in a Tic+ strain of Escherichia coli during the 30-min period following a shift-down from glucose-minimal to succinate-minimal medium. The rate of mRNA inactivation and the relative translational initiation frequency were both most severely depressed immediately after the shift-down and increased slowly thereafter. If glucose was restored to the medium at any time after shift-down, mRNA inactivation immediately resumed its normal (preshift) rate and the protein-forming capacity was increased. These changes in mRNA inactivation rate do not reflect an altered mRNA composition in the down-shifted cells. The relative rate of mRNA inactivation was linearly proportional to the relative translational initiation frequency over a 10-fold range of initiation frequencies. Low initiation frequencies represent increased "dwell" of the ribosomes at the initiation site before the commencement of polypeptide chain initiation. We propose that initiating ribosomes protect mRNA from an inactivating endonucleolytic cleavage at or near the ribosome binding site.     

The relationship between precursor and mature forms of the 23 S ribosomal RNA

Summary Oligonucleotide fingerprinting shows the precursor form of the 23S ribosomal RNA fromBacillus megaterium to be larger than its mature counterpart, by some 8 percent, or approximately 250 nucleotides. It can further be shown that the 23SrRNA precursor doesnot contain the 5SrRNA sequence, as had been previously suggested.     

The relationship between HIV-1 genome RNA dimerization, virion maturation and infectivity

The relationship between virion protein maturation and genomic RNA dimerization of human immunodeficiency virus type 1 (HIV-1) remains incompletely understood. We have constructed HIV-1 Gag cleavage site mutants to enable the steady state observation of virion maturation steps, and precisely study Gag processing, RNA dimerization, virion morphology and infectivity. Within the virion maturation process, the RNA dimer stabilization begins during the primary cleavage (p2-NC) of Pr55 Gag. However, the primary cleavage alone is not sufficient, and the ensuing cleavages are required for the completion of dimerization. From our observations, the increase of cleavage products may not put a threshold on the transition from fragile to stable dimeric RNA. Most of the RNA dimerization process did not require viral core formation, and particle morphology dynamics during viral maturation did not completely synchronize with the transition of dimeric RNA status. Although the endogenous virion RT activity was fully acquired at the initial step of maturation, the following process was necessary for viral DNA production in infected cell, suggesting the maturation of viral RNA/protein plays critical role for viral infectivity other than RT process.     

Ultrafast catalytic processes in enzymes

The study of biocatalysis and biotransformation in the transition-state region has been challenging and difficult, but recent advances on two important photoenzymes in nature, DNA photolyase and protochlorophyllide oxidoreductase, have enabled the investigation of their catalytic processes in real time. By following the entire evolution of substrate transformation, the functional dynamics constituting a series of elementary reactions have been mapped out. The five fundamental reactions in the enzymes, namely electron transfer, bond breaking and making, proton and hydride transfer, all occur ultrafast within subnanosecond. The direct clocking of catalytic transition states probes central, unmasked chemical processes and provides mechanistic insights into the role of the dynamics in enzyme function, which not only facilitates the formation of the enzyme-substrate complex in the transition-state configurations, but also modulates the subsequent catalytic reactions for maximum biotransformation efficiency.     

On the relationship between thermal stability and catalytic power of enzymes

The possible relationship between the thermal stability and the catalytic power of enzymes is of great current interest. In particular, it has been suggested that thermophilic or hyperthermophilic (Tm) enzymes have lower catalytic power at a given temperature than the corresponding mesophilic (Ms) enzymes, because the thermophilic enzymes are less flexible (assuming that flexibility and catalysis are directly correlated). These suggestions presume that the reduced dynamics of the thermophilic enzymes is the reason for their reduced catalytic power. The present paper takes the specific case of dihydrofolate reductase (DHFR) and explores the validity of the above argument by simulation approaches. It is found that the Tm enzymes have restricted motions in the direction of the folding coordinate, but this is not relevant to the chemical process, since the motions along the reaction coordinate are perpendicular to the folding motions. Moreover, it is shown that the rate of the chemical reaction is determined by the activation barrier and the corresponding reorganization energy, rather than by dynamics or flexibility in the ground state. In fact, as far as flexibility is concerned, we conclude that the displacement along the reaction coordinate is larger in the Tm enzyme than in the Ms enzyme and that the general trend in enzyme catalysis is that the best catalyst involves less motion during the reaction than the less optimal catalyst. The relationship between thermal stability and catalysis appears to reflect the fact that to obtain small electrostatic reorganization energy it is necessary to invest some folding energy in the overall preorganization process. Thus, the optimized catalysts are less stable. This trend is clearly observed in the DHFR case.     

The relationship between aminoglycosides' RNA binding proclivity and their antiplasmid effect on an IncB plasmid

Bacteria routinely become resistant to antibiotics through the uptake of plasmids that encode resistance-mediating proteins. Such plasmid-based resistance is seen extensively in clinical settings and has been documented for a wide variety of bacterial infections from both Gram-positive and Gram-negative organisms. We recently reported that a small molecule could be used to mimic a natural process of plasmid elimination, called plasmid incompatibility, and that the addition of this compound causes elimination of an IncB plasmid from E. coli and a subsequent resensitization to antibiotics [DeNap, Thomas, Musk, and Hergenrother (2004) J. Am. Chem. Soc. 126, 15402-15404]. Described herein is a further substantiation and validation of the notion that plasmid incompatibility can be mimicked with small molecules that bind to important RNA targets controlling plasmid replication. In this study, the dissociation constant and stoichiometry of RNA binding are determined for 12 aminoglycosides with stem-loop I (SLI) of the IncB replication machinery. Importantly, it is found that compounds that do not bind to this RNA replication control element fail to induce plasmid loss in vivo, whereas those that do bind to the RNA typically cause measurable plasmid loss. These results highlight the potential for targeting key RNA regions for induction of plasmid loss and the subsequent resensitization of bacteria to antibiotics.     

Quantifying the relationship between sequence and three-dimensional structure conservation in RNA

Background  

In recent years, the number of available RNA structures has rapidly grown reflecting the increased interest on RNA biology. Similarly to the studies carried out two decades ago for proteins, which gave the fundamental grounds for developing comparative protein structure prediction methods, we are now able to quantify the relationship between sequence and structure conservation in RNA.     

The big motivational picture: Examining the relationship between positive intrapersonal processes and adolescent health-promoting behaviors

The purpose of the present study was to examine the relationship between positive intrapersonal processes (intrinsic motivation and subjective vitality) at a general level and adolescent physical activity and food intake. Self-report questionnaires were administered to 433 ninth graders to assess their generalized perceptions of autonomy, competence, relatedness, and subjective vitality as well as their physical activity and eating behavior. Cluster analytic procedures resulted in the identification of three groups of adolescents who differed in their positive intrapersonal processes. Furthermore, these groups exhibited significant and contrasting patterns in their health-promoting behaviors. Participants who were in the most positive intrapersonal cluster (high well-being) reported the highest levels of moderate-to-vigorous physical activity and healthy eating patterns when compared to the adolescents in the low and moderate well-being clusters. These findings support a top-down approach to understanding adolescent motivation for and participation in health-promoting behavior. Implications for intervention are discussed.     

The relationship between guanosine tetraphosphate,polysomes and RNA synthesis in amino acid starved escherichia coli

ArelA⁺ strain ofE. coli with four amino acid requirements was starved separately for each amino acid, after which the levels of polysomes, guanosine-5-diphosphate-3-diphosphate and the residual net synthesis of RNA were determined. The polysome level and guanosine-5-diphosphate-3-diphosphate production were coordinately affected by starvation for the different amino acids, whereas no correlation was found between these two parameters and residual RNA synthesis. The main conclusion stemming from these results is that guanosine-5-diphosphate-3-diphosphate cannot act as the sole effector molecule in stringent control of RNA synthesis.     

The relationship between metal-metal distance of two metal ions chelated complex and RNA cleavage activity.

We prepared a series of ligands possessing two binding sites for metal coordination: in each ligand molecule, two binding sites with the same functionality (2,2'-dipicolylamino group) were placed at the of various methyl arenes. Thus, the distances between the metal binding sites were different from ligand to ligand. We examined the rate of the hydrolysis of RNA dimer catalyzed by La3+ ion binuclear complexes of the ligands. The catalytic activity of the binuclear complexes increased as the distance between the metal binding sites was decreased.