2009-07-29

Ampicillin inhibits cell wall biosynthesis. Cleavage of the B-lactam ring by B-lactamase (bla gene) is the mode of resistence.

Chloramphenicol inhibits translation of the 50S ribosomal subunit at the peptidyltransferase step (elongation inhibition). Acetylation by chloramphenicol acetylgtransferase (cat gne) is the mode of resistence.

Kanamycin binds to 70S ribosomal subunit, inhibits translocation and elicits miscoding. Aminoglycoside modifying enzymes (acetyltransferase, phophotransferase and nucleotidyltransferase) alter the antibiotic, preventing its interaction with ribosomes and inactivation it.

Streptomycin inhibits protein synthesis. It binds to the S12 protein of the 30S ribosomal subunit, causing misreading or inhibiting initiation. Mutation in the rpsL (gene for S12 ribosomal protein) prevents binding of streptomycin to the ribosome. Aminoglycoside phosphotransferase also inactiviates this antibiotic.

Tetracycline inhibits protein synthesis (elongation) by preventing binding of aminoacyl-tRNA to the ribosome. Loss of cell wall permeability is the mode of resistance.

2009-07-21

10# Cole et al. 2009 Mol Cell-(nonfunctional rRNA decay)

Quality control of eukaryotic transcripts begins in the nucleus. Nuclear RNA surveillance has been most extensively studied in S. cerevisiae and relies heavily on the exosome, the cell’s major 3′-5′ exonuclease. The nuclear and cytoplasmic exosomes share ten core subuntis, one of which, Rrp44p, is responsbile for its exonucleolytic activity. However, nuclear and cytoplasmic exosomes differ by the presence of the exoribonuclease Rrp6p and nucleic acid binding protein Rrp47p in the nucleus versus the GTPase Ski7p in the cytoplasm. Within the nucleus, the exosome has been shown to degrade aberrant pre-mRNAs, pre-tRNAs, pre-rRNAs and pre-snoRNAs. Prior to their decay, many nuclear exosome substrates undergo polyadenylation by the Trf4/5o/Air/Mtr4p polyadenylation (TRAMP) complex, which stimulates decay via exosome recruitment. Decay of such polyadenylated RNAs is thought to occur within a region of the nucleolus known as the No-body. Come polyadenylated pre-RNAs are also thought to be decayed by the nculear 5′-3′ exonuclease Rat1p, although where this occurs within the nucleus is unknown.

In the cytoplasm, several pathways have been described for mRNA quality control. all of these pathways are translation dependent, initiating when a ribosome stalls during translation in a context that impedes efficient elongation or termination. Nonstop mRNA decay (NSD) eliminates mRNAs lacking any in frame stop codon, such as trancated or prematurely polyadenylated transcripts. This pathway is dependent on Ski7p, which recruits the cytoplasmic exosome. A second quality control system, nonsense-mediated mRNA decay (NMD), eliminates mRNAs containing a stop codon in a poor context for translation termination, often a nonsense or premature termination codon. Following recruitment of th eUpf proteins (Upf1p, Upf2p and Upf3p) to the stalled translation complex, the mRNA is decapped and then degraded by the major cytoplasmic 5′-3′ exoribonculease Xrn1p. Nonsense transcripts are also subject to 3′-5′ degradation by the cytoplasmic exosome via interaction between Upf1p and Ski7p. Finnaly, no-go mRNA decay (NGD) eliminates mRNAs containing a structural barrier within the open reading frame that induces ribosome stalling. Such stalling stimulates endonucleolytic cleavage of the mRNA immediately upstream of the structural barrier, followed by Xrn1p- and Ski7p- mediated decay of the 3′ and 5′ halves, respectively. Within the cytoplasm, both general mRNA turnover and NMD are thought to occur in discrete structures known as processing or P-bodies. P-bodies are gegions in eukaryotic cells that contain translationally repressed mRNPs and proteins involved in mRNA decay. These proteins include the decapping cimplex Dcp1p/Dcp2p, decapping activator Dhh1p, and exoribonuclease Xrn1p. Where in the cytoplasm NSD and NGD occur, however, has not been previously examined.

Mature tRNAs undergo rapid tRNa decay (RTD) by a process involving Rat1p and Xrn1p. rRNAs containg deleterious mutations in either the peptidyl tansferase center of 25S rRNA or the decoding site of 18S rRNA are subject to a late-acting quality control system dubbed nonfunctional rRNA decay (NRD).
Cycloheximide is an antibiotic that inhibits the peptidyl transferase activity of ribosomes engaged in translation elongation, effectively locking them onto mRNA via an interaction with  the large subunit.

18S NRD is a cytoplasmic porcess. P-bodies also function in aberrant rRNA elimination.

25S NRD appears unrelated to any of the knwon ranslation-dependent mRNA decay pathways. Unlike NMD, NSD, NGD and 18S NRD, 25S NRD still occurs in the presence of translation elongation inhibitors. Further, 25S NRD substrates accumulate around the nuclear envelope as opposed to the dispersed cytoplasmic localization observed for 18S NRD substrates in WT cells. Finnaly, 25S NRD is independent of all mRNA decay factors tested, with teh exception of the core exosome exonculease Rrp44p. 25S NRD must recruit the exosme independent of Ski7p.