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PubMed1964

[THE POLYSOME].

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Nucleotides↗
PubMed2006

Crystal structure of TTHA0252 from Thermus thermophilus HB8, a RNA degradation protein of the metallo-beta-lactamase superfamily.

In bacterial RNA metabolism, mRNA degradation is an important process for gene expression. Recently, a novel ribonuclease (RNase), belonging to the beta-CASP family within the metallo-beta-lactamase superfamily, was identified as a functional homologue of RNase E, a major component for mRNA degradation in Escherichia coli. Here, we have determined the crystal structure of TTHA0252 from Thermus thermophilus HB8, which represents the first report of the tertiary structure of a beta-CASP family protein. TTHA0252 comprises two separate domains: a metallo-beta-lactamase domain and a "clamp" domain. The active site of the enzyme is located in a cleft between the two domains, which includes two zinc ions coordinated by seven conserved residues. Although this configuration is similar to those of other beta-lactamases, TTHA0252 has one conserved His residue characteristic of the beta-CASP family as a ligand. We also detected nuclease activity of TTHA0252 against rRNAs of T. thermophilus. Our results reveal structural and functional aspects of novel RNase E-like enzymes with a beta-CASP fold.

Amino Acid Sequence↗
PubMed2004

Forward translocation is the natural pathway of RNA release at an intrinsic terminator.

Intrinsic terminators of bacterial RNA polymerase are small (< approximately 30 bp) sequences containing a dyad symmetry that encodes a hairpin in the RNA, followed immediately by a uridine-rich stretch of 5-9 nucleotides just before the site of RNA release. Formation of the RNA hairpin destabilizes the elongation complex, leading to transcript release. We test a model in which hair-pin formation drives RNA polymerase and the melted DNA bubble downstream without transcript elongation, thus releasing the transcript from its enclosure within the enzyme as an RNA/DNA hybrid. We show that blocking downstream translocation of RNAP and preventing downstream DNA unwinding both inhibit transcript release. We argue that translocation of RNA polymerase is essential and that translocation of the bubble stimulates, but is not required, for RNA release; we conclude that forward translocation is the natural pathway of RNA release at an intrinsic terminator.

Bacterial Proteins↗
PubMed1999

Characterization of transient RNA-RNA interactions important for the facilitated structure formation of bacterial ribosomal 16S RNA.

The co-transcribed leader sequences of bacterial rRNA are known to affect the structure and function of the small ribosomal subunits. Base changes in the leader nut -like sequence elements have been shown to cause misfolded but correctly processed 16S rRNA structures at low growth temperature. Transient interactions of leader sequences with the nascent 16S rRNA are considered to guide rRNA folding and to facilitate correct structure formation. In order to understand this chaperone-like activity of the leader RNA we have analyzed the thermodynamic stabilities of wild-type and mutant leader transcripts. We show here that base changes cause subtle differences in the melting profiles of the corresponding leader transcripts. Furthermore, we show that direct interaction between leader transcripts and the 16S rRNA is limited to the 5'-domain of the 16S rRNA for both wild-type and mutant leaders. Binding studies of mutant and wild-type leader transcripts to 16S rRNA revealed small changes in the affinities and the thermal stabilities as a consequence of the base changes. Different complex stabilities as a function of the Mg(2+) ion concentration indicated that mutant and wild-type leader transcripts interact differently with the 16S rRNA, consistent with a less stable and tightly folded structure of the mutant leader. Employing time-resolved oligonucleotide hybridization assays we could show different folding kinetics for 16S rRNA molecules when linked to wild-type leader, mutant leader or in the absence of leader RNA. The studies help to understand how bacterial rRNA leader transcripts may affect the folding of the small subunit rRNA.

5' Untranslated Regions↗
PubMed1996

Analysis of the shut-off of ribosomal RNA promoters in Escherichia coli upon entering the stationary phase of growth.

Most bacterial RNA consists of stable RNA which is composed of rRNA and tRNA. We have followed by primer extension analysis the level of ribosomal RNA synthesis along the growth phases of a cell culture. A sharp drop in rRNA synthesis was observed upon the transition from the exponential to the stationary phase of growth. Our results demonstrate that an effective shut-off of rRNA synthesis occurs also in the absence of ppGpp. Mutations in the host factors Fis and H-NS, which are known to regulate rrn P1 promoters, did not affect the shut-off process of ribosomal RNA promoters. We also tested the effect of RpoS, the sigma factor known to induce a number of genes in the stationary phase. It was shown that the host factors Fis, H-NS and RpoS do not play a major role in the regulation of the shut-off process of rRNA synthesis. The results presented demonstrate that the rate of rRNA synthesis provides a sensitive measure of the growth phase of the bacterial culture.

Bacterial Proteins↗
PubMed1963

The fate of bacteria within phagocytic cells. I. The degradation of isotopically labeled bacteria by polymorphonuclear leucocytes and macrophages.

The intraleucocytic fate of a variety of P(32)- and C(14)-labeled bacteria has been studied in both polymorphonuclear leucocytes and macrophages. Both cell types brought about extensive degradation of bacterial lipids, nucleic acids, and proteins. Intracellular breakdown was primarily dependant upon the composition of the ingested particle rather than on the type or source of the phagocyte. Evidence is presented for the reincorporation of bacterial constituents into leucocyte lipid. More than 50 per cent of the acid-soluble degradation products of P(32)-labeled bacteria appear as inorganic phosphate. Bacterial RNA is degraded more readily than DNA. Following phagocytosis, labeled bacteria lose their pool of small molecular weight intermediates. This is followed by the degradation of acid-insoluble constituents. The majority of bacterial breakdown products are then excreted by the leucocyte and appear in the medium. Heat-killed bacteria were more readily broken down than viable organisms. Only small amounts of C(14)-labeled bacteria were completely oxidized by leucocytic enzymes to C(14)O(2). Acid extracts of polymorphonuclear leucocyte granules, which were highly bactericidal, liberated the acid-soluble constituents of labeled bacteria but did not significantly degrade bacterial macromolecules.

Bacteria↗
PubMedDate not supplied

MALDI-TOF mass spectrometry of bacteria.

The development of MALDI-TOF mass spectrometry methods for the characterization of bacteria is reviewed and discussed. The general use of MALDI for the characterization of large biomolecules led directly to obvious applications involving the analysis of isolated bacterial proteins. More surprising was the observation that MALDI-TOF mass spectrometry could be applied directly to crude cellular fractions or cellular suspensions and that the resulting data from such complex mixtures could provide evidence for chemotaxonomic classification. Versatility and the rapidity of analysis led to the rapid development of a number of MALDI-TOF methods involving bacteria. Examples of some of the applications covered in this review are the analysis of bacterial RNA and DNA, the detection of recombinant proteins, the characterization of targeted or unknown proteins, bacterial proteomics, the detection of virulence markers, and the very rapid characterization of bacteria at the genus, species, and strain level. The demonstrated capability of taxonomic classification at the strain level, using unprocessed cells, opens the possibility that MALDI-TOF and similar mass spectrometry approaches may contribute significantly to fulfilling emerging needs for the development of near real-time methods for the characterization of bacteria.

Bacteria↗