Toxin-Antitoxin Modules May Regulate Synthesis of Macromolecules during Nutritional Stress

Abstract

The recent enormous expansion of the microbial DNA databases has made it profitable to search for homologues and paralogues (homologues within species) of interesting genes. In combination with genetic, biochemical, and physiological investigations, such analyses may yield new, valuable information with impact on entire research fields. Here I present one such example, the combined description and database analyses of toxin-antitoxin (TA) loci from prokaryotes.Naturally occurring plasmids are genetically stable. In most cases, stable plasmid inheritance is due to the presence of gene cassettes that actively prevent plasmid loss at cell division. These cassettes can be divided into three classes: (i) centromere-like systems that actively secure ordered segregation of replicons prior to cell division (31,39,40,97), (ii) site-specific recombination systems that actively resolve tandem plasmid multimers into monomers (81, 85), and (iii) cassettes that mediate killing of newborn, plasmid-free cells resulting from failure of the first two systems to secure plasmid maintenance. This latter, paradoxical type of cell differentiation has been termed postsegregational killing (PSK) (24). Two types of PSK mechanisms have been described in detail at the molecular level. In both cases, the killing of plasmid-free progeny relies on stable toxins whose action or expression is counteracted by metabolically unstable regulators. The instability of the regulators results in activation of the toxins in cells that have lost the toxin-encoding plasmid. In one type of PSK mechanism, the regulators are unstable antisense RNAs that inhibit the translation of stable, toxin-encoding mRNAs (i.e., the hok mRNAs). The instability of the antisense RNAs leads to activation of translation of the toxin-encoding mRNAs specifically in plasmid-free cells, thereby leading to their elimination. The complex posttranscriptional regulation of the hok genes has been reviewed previously (26) and will not be discussed further here.The other type of PSK mechanism relies on stable toxins whose action is prevented by cognate protein antitoxins (reviewed previously in references 35, 38, and 42). Again, the indigenous instability of the antitoxins (also called antidotes by some researchers) leads to activation of the toxins in plasmidfree cells. The PSK phenotype results in increased plasmid maintenance, since plasmid-free progeny have a much lower chance of survival than the plasmid-bearing cells. Accordingly, the plasmid-encoded TA loci have also been called plasmid addiction modules and proteic plasmid stabilization systems, terms that should be used exclusively for the plasmid-encoded loci. Here I present an overview combined with a database analysis of prokaryotic TA loci, with emphasis on recent findings. The ubiquity of the TA loci in prokaryotic chromosomes indicates that they have function(s) unrelated to plasmid maintenance. Two such potential alternative functions are discussed here. The general phenomenon of programmed cell death in bacteria has been...

Amino Acid Starvation and Colicin D Treatment Induce A-site mRNA Cleavage in Escherichia coli

“…1c). These downstream cleavages were not detected in cells overexpressing tRNA 4 Arg or tRNA 5 Arg suggesting that they are produced in response to ribosome pausing (Fig. 1c).…”

“…2a). The accumulation of truncated mRNA was inhibited in cells overproducing tRNA 5 Arg , indicating that translational pausing at the tandem AGG codons was required for cleavage (Fig. 2a).…”

“…The following DNA oligonucleotides were 5′-radiolabeled with 32 P and used for Northern blot hybridizations: RBS for pET-derived mRNA ribosome binding site, (5′-GTA TAT CTC CTT CTT AAA GTT AAA C); argQ for tRNA 2 Arg , (5′ -GCT GAG CTA CGG ATG C); argW for tRNA 5 Arg , (5′-CCT GCA ATT AGC CCT TAG G); argU for tRNA 4 Arg , (5′-CCT GCG GCC CAC GAC TTA G); argX for tRNA 3 Arg , (5′-CCT GAG ACC TCT GCC TCC GGA); hisR for tRNA His , (5′ -CAC GAC AAC TGG AAT CAC); and trpT for tRNA Trp , (5′ -CCC AAC ACC CGG TTT TGG). The following DNA oligonucleotides were 3′-radiolabeled using terminal deoxynucleotide transferase and α-[ 32 P]-3′-deoxyadenosine triphosphate, and used as probes for S1 nuclease protection analyses: PPRR CGU S1 probe, (5′-CCT TTC GGG CTT TGT TAG CAG CCG GAT CCT TAA CGA CGC GGA GGG TTA GCG TCG AGG AAC TCT TTC AAC TGA CCT TTA G); KKRR AGG S1 probe, (5′-CCT TTC GGG CTT TGT TAG CAG CCG GAT CCT TAC CTC CTC TTC TTG TTA GCG TCG AGG AAC TCT TTC AAC TGA CCT TTA G); PPRR AGG S1 probe, (5′-CCT TTC GGG CTT TGT TAG CAG CCG GAT CCT TAC CTC CTC GGA GGG TTA GCG TCG AGG AAC TCT TTC AAC TGA CCT TTA G); and PPWWLA S1 probe, (5′ -CCT TTC GGG CTT TGT TAG CAG CCG GAT CCT TAC GCC AGC CAC CAC GGA GGG TTA GCG TCG AGG AAC TCT TTC AAC TGA CCT TTA G).…”

Lon protease promotes survival of Escherichia coli during anaerobic glucose starvation

“…It also degrades certain regulatory proteins, including the SulA cell division regulator (Mizusawa and Gottesman, 1983;Schoemaker et al, 1984;Higashitani et al, 1997), the positive regulator of capsule synthesis, RcsA (Torres-Cabassa and Gottesman, 1987), and possibly TER components involved in blocking septation sites during the SOS response (Dopazo et al, 1987). Lon is also involved in the turnover of several antitoxin proteins in toxin-antitoxin systems (Gerdes, 2000). For example, Lon degrades RelB, leading to the accumulation of RelE toxin and to global inhibition of translation (Christensen et al, 2001).…”

The C-Terminal Portion of an Archaeal Toxin, aRelE, Plays a Crucial Role in Protein Synthesis Inhibition

“…2) The TA systems are composed of two genes organized in an operon that encodes a stable toxin and a labile cognate antitoxin. 3) In the steady state, antitoxins neutralize the effects of toxins by direct protein-protein interactions. 4) Upon induction by environmental stresses, such as amino acid and carbon source limitation, labile antitoxins are degraded by a specific protease such as Lon, ClpXP, or ClpAP, leading to rapid growth arrest and cell death by the cellular effects of the toxins.…”