Expanded versions of the Ribosomal RNA Mutation Databases provide lists of mutated positions in 16S and 16S-like ribosomal RNA (16SMDBexp) and 23S and 23S-like ribosomal RNA (23SMDBexp) and the identity of each alteration. Alterations from organisms other than Escherichia coli are reported at positions according to the E.coli numbering system. Information provided for each mutation includes: (i...

Low-resolution molecular models can provide appropriate and efficient ways for studying large biomolecular systems such as the ribosome. We have developed computer codes that use the Yammp Under Python modeling package to assemble low-resolution force fields for RNA-protein complexes, and that connect these to the Amber molecular simulation package. This pipeline combines many of the complement...

We have isolated and partially characterized an endonuclease involved in processing the 5' end of 16S rRNA of Escherichia coli. A mutant strain that is deficient in this enzyme accumulates a new precursor of 16S rRNA, named 16.3S rRNA. This rRNA has the 3' end of mature 16S rRNA but is about 60 nucleotides longer at the 5' end. In vitro, the enzyme preparation cleaves an RNA fragment of about 6...

BACKGROUND Ribosomal RNAs contain many modified nucleotides. The functions of these nucleotides are poorly understood and few of them are strongly conserved. The final stem loop in 16S-like rRNAs is an exception in both regards. In both prokaryotes and eukaryotes, the tetranucleotide loop that caps the 3'-terminal stem contains two N6, N6-dimethyladenosine residues. The sequence and pattern of ...

For prokaryotes in vitro, 16S rRNA and 20 ribosomal proteins are capable of hierarchical self- assembly yielding a 30S ribosomal subunit. The self-assembly is initiated by interactions between 16S rRNA and three key ribosomal proteins: S4, S8, and S7. These proteins also have a regulatory function in the translation of their polycistronic operons recognizing a specific region of mRNA. Therefore...

Doi, Roy H. (Syracuse University, Syracuse N.Y.), and Richard T. Igarashi. Ribonucleic acids of Bacillus subtilus spores and sporulating cells. J. Bacteriol. 87:323-328. 1964.-The ribonucleic acids (RNA) of Bacillus subtilis spores were analyzed for their size and base composition. Soluble and ribosomal RNA identical to those found in vegetative cells were present in spores. A base ratio differ...

The 16S ribosomal RNA mutation database (16SMDB) provides a list of mutated positions in 16S ribosomal RNA from Escherichia coli and the identity of each alteration. Information provided for each mutation includes: (i) a brief description of the phenotype(s) associated with each mutation; (ii) whether a mutant phenotype has been detected by in vivo or in vitro methods; (iii) relevant literature...

A short treatment with ethylenedinitrilotetraacetic acid to permeabilize bacteria for various antibiotics or treatment with the ribonucleic acid (RNA) synthesis inhibitor rifampin causes a slow degradation of 50S and 30S ribosomal particles and of the corresponding 23S and 16S ribosomal RNA species (about 25 percent in 1 h). The effects are additive such that the decay is about 50 percent/h if ...