Besides linear RNAs, pre-mRNA splicing generates three forms of RNAs: lariat introns, Y-structure introns from trans-splicing, and circular exons through exon skipping. To study the persistence excised in total cellular RNA, we used Escherichia coli 3' to 5' exoribonucleases. Ribonuclease R (RNase R) thoroughly degrades abundant RNAs while preserving loop portion a RNA. II II) polynucleotide phosphorylase (PNPase) also preserve loop, but are less efficient degrading RNAs. RNase digestion RNA...

vacB, a gene previously shown to be required for expression of virulence in Shigella and enteroinvasive Escherichia coli, has been found encode the 3′–5′ exoribonuclease, RNase R. Thus, cloning E. coli vacB led overexpression R activity, partial deletion or interruption cloned abolished this overexpression. Interruption chromosomal copy ofvacB eliminated endogenous activity; however, absence by itself had no effect on cell growth. In contrast, cells lacking both polynucleotide phosphorylase...

Significance As RNA polymerase (RNAP) translocates along the DNA template for repetitive nucleotide additions, its active site opens and closes NTP association catalysis, a pyrophosphate ion (PPi) is generated after each incorporation. Understanding role of PPi release important elucidating mechanism. The structures σ S -containing transcription initiation complexes (σ -TICs) provide insights into mechanism -dependent selective gene expression. In addition, highly stressed -TICs trap at RNAP...

Significance Transcription is the first and most regulated step of gene expression. During transcription, RNA polymerase (RNAP) translocates along DNA while processively synthesizing molecules hundreds nucleotides long. Excessive translocation in either direction halts synthesis. Here, we present a structure Escherichia coli complex with ATPase RapA, large translocase that involved transcriptional reactivation. The structural insights gained from this study suggest an alternative mechanism...

We investigated digestion responses to conventional and low oligosaccharide soybean meal (SBM) incorporation into diets for dogs. Five female dogs were fitted with T-type cannulas at the terminal ileum fed five in a 5 × Latin square design. Corn grain + poultry meal-based containing different levels types of SBM (0% SBM, 18.55% 37.1% SBM) formulated. Each period consisted 11 d (7-d diet adaptation; 4-d collection ileal digesta feces). Intakes DM, OM, CP, fat, GE not affected (P > .10) by...

Escherichia coli RNase T, the enzyme responsible for end-turnover of tRNA and 3′ maturation 5 S 23 rRNAs many other small, stable RNAs, was examined in detail with respect to its substrate specificity. The found be a single-strand-specific exoribonuclease that acts 5′ direction non-processive manner. However, although otherEscherichia exoribonucleases stop several nucleotides downstream an RNA duplex, T can digest up first base pair. presence free 3′-hydroxyl group is required initiate...

Mycoplasma genitalium , a small bacterium having minimal genome size, has only one identified exoribonuclease, RNase R (MgR). We have purified MgR to homogeneity, and compared its RNA degradative properties those of Escherichia coli homologs (EcR) II (EcII). is active on number substrates including oligoribonucleotides, poly(A), rRNA, precursors tRNA. Unlike EcR, which degrades rRNA pre-tRNA without formation intermediate products, appears sensitive certain structural features forms specific...

P. L. Boulas, Y. Zuo and Echegoyen, Chem. Commun., 1996, 1547 DOI: 10.1039/CC9960001547

TATB as an insensitive high explosive, has wide applications in both civil and military areas. High performance liquid chromatography (HPLC) is a crucial tool to analyze the purity for quality control of TATB. However, current HPLC method several drawbacks resulted by its poor solubility. A deep eutectic solvent (CS-1) solubility toward TATB, so it been used pretreatment mobile phase develop new this work. When CS-1 was prior analysis, displayed greater efficiency, less dosage, shorter time...

Escherichia coli RNase T, an RNA-processing enzyme and a member of the DEDD exonuclease superfamily, was examined using sequence analysis site-directed mutagenesis. Like other exonucleases, T found to contain three conserved Exo motifs that included four invariant acidic residues. Mutagenesis these revealed they are essential for activity, indicating probably form catalytic center in manner similar exonucleases. We also identified by short, but highly conserved, segments rich positively...

During transcription, RNA polymerase moves downstream along the DNA template and maintains a transcription bubble. Several recent structural studies of complexes with complete bubble provide new insights into how RNAP couples nucleotide addition reaction to its directional movement.

RNase T is one of eight distinct 3′→5′ exoribonucle-ases present in Escherichia coli. The enzyme plays an important role stable RNA metabolism, including tRNA end turnover and 3′ maturation most RNAs because it the only that can efficiently remove residues near a double-stranded (ds) stem. In course study its specificity mechanism, we found also has single-strand-specific DNase activity. Purified degrades both single-stranded (ss)RNA ssDNA non-processive manner. However, contrast to action...

A detailed structural and functional model of E. coli RNase T was generated based on sequence analysis, homology modeling, experimental observation. In the accompanying article, three short segments (nucleic acid binding sequences (NBS)) important for substrate were identified. model, these cluster to form a positively charged surface patch. However, this patch is face monomer opposite DEDD catalytic center. We propose that by dimerization, NBS from one subunit brought vicinity center second...