To the Editor: Preservation of RNA integrity is important in microarray techniques for identifying differentially expressed genes so that results reflect true biological differences and not differences in RNA degradation (1 ). RNA degradation is usually low in RNA isolated from cultured cells (2 ). When samples isolated from RNaserich tissues are used, however, RNA degradation may introduce bia...

The effect of chloramphenicol on the synthesis and accumulation of ribonucleic acid (RNA) in Bacillus subtilis was studied. In the presence of chloramphenicol, transfer RNA and ribosomal RNA were synthesized as rapidly 2 to 3 hr after challenge as they were just prior to the addition of the antibiotic. However, under the same conditions, net RNA accumulation ceased after only 30 to 45 min. The ...

The nuclear exosome is involved in numerous RNA metabolic processes. Exosome degradation of rRNA, snoRNA, snRNA and tRNA in Saccharomyces cerevisiae is activated by TRAMP complexes, containing either the Trf4p or Trf5p poly(A) polymerase. These enzymes are presumed to facilitate exosome access by appending oligo(A)-tails onto structured substrates. Another role of the nuclear exosome is that of...

The disappearance of ribosomes in Escherichia coli cells starved for a carbon source was studied. We used a series of mutants, some of them lacking in ribonuclease I(RNase I, EC 2.7.7.17), and other containing various combinations of modified polynucleotide phosphorylase (PNPase, EC 2.7.7.8) and modified ribonuclease II (RNase II, EC 3.1.4.1). RNA was prepared from the starved mutant cells and ...

During nitrogen starvation, a nonselective bulk degradation of cytosolic proteins and organelles including ribosomes, termed macro‐autophagy (hereafter termed autophagy), is induced. The precise mechanism of RNA degradation by this pathway has not been yet elucidated. In this issue of the The EMBO Journal, Huang et al characterize an autophagy‐dependent RNA catabolism in yeast and identify the ...

Polyadenylation of RNAs plays a critical role in modulating rates of RNA turnover and ultimately in controlling gene expression in all systems examined to date. In mitochondria, the precise mechanisms by which RNAs are degraded, including the role of polyadenylation, are not well understood. Our previous in organello pulsechase experiments suggest that poly(A) tails stimulate degradation of mRN...

Only few small, regulatory RNAs encoded opposite another gene have been identified in bacteria. Here, we report the characterization of a locus where a small RNA (SymR) is encoded in cis to an SOS-induced gene whose product shows homology to the antitoxin MazE (SymE). Synthesis of the SymE protein is tightly repressed at multiple levels by the LexA repressor, the SymR RNA and the Lon protease. ...

Affymetrix 3' expression arrays employ a specific experimental protocol and a specific probe design that allows assessment of RNA integrity based on probe signal data. Problems of RNA integrity are primarily governed to the degradation of the target transcripts. We have shown in Fasold and Binder (2012) that (i) degradation leads to a probe positional bias that needs to be corrected in order to...

In all domains of life, the catalysed degradation of RNA facilitates rapid adaptation to changing environmental conditions, while destruction of foreign RNA is an important mechanism to prevent host infection. We have identified a virus-encoded protein termed gp37/Dip, which directly binds and inhibits the RNA degradation machinery of its bacterial host. Encoded by giant phage фKZ, this protein...