Hok/sok system

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The hok/sok system is a postsegregational killing mechanism employed by the R1 plasmid in Escherichia coli . It was the first type I toxin-antitoxin pair to be identified through characterisation of a plasmid-stabilising locus. [1] It is a type I system because the toxin is neutralised by a complementary RNA, rather than a partnered protein (type II toxin-antitoxin). [2]

Contents

The conserved secondary structure of sok non-coding RNA transcript which binds with hok mRNA. Sok RNA.png
The conserved secondary structure of sok non-coding RNA transcript which binds with hok mRNA.

Genes involved

The hok/sok system involves three genes: [3]

HOK
Identifiers
SymbolHOK_GEF
Pfam PF01848
InterPro IPR000021
PROSITE PDOC00481
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary

Killing mechanism

When E. coli undergoes cell division, the two daughter cells inherit the long-lived hok toxin from the parent cell. Due to the short half-life of the sok antitoxin, daughter cells inherit only small amounts and it quickly degrades. [3]

If a daughter cell has inherited the R1 plasmid, it has inherited the sok gene and a strong promoter which brings about high levels of transcription. So much so that in an R1-positive cell, Sok transcript exists in considerable molar excess over Hok mRNA. [5] Sok RNA then indirectly inhibits the translation of hok by inhibiting mok translation. There is a complementary region where sok transcript binds hok mRNA directly (pictured), but it does not occlude the Shine-Dalgarno sequence. Instead, sok RNA regulates the translation of the mok open reading frame, which nearly entirely overlaps that of hok. It is this translation-coupling which effectively allows sok RNA to repress the translation of hok mRNA. [6]

The sok transcript forms a duplex with the leader region of hok mRNA and this is recognized by RNase III and degraded. The cleavage products are very unstable and soon decay. [7]

Hok sok system R1 plasmid present.gif Hok sok system R1 plasmid absent.gif

Daughter cells without a copy of the R1 plasmid die because they do not have the means to produce more sok antitoxin transcript to inhibit translation of the inherited hok mRNA. The killing system is said to be postsegregational (PSK), [8] since cell death occurs after segregation of the plasmid. [9] [10]

Hok toxin

The hok gene codes for a 52 amino acid toxic protein which causes cell death by depolarization of the cell membrane. [11] [12] It works in a similar way to holin proteins which are produced by bacteriophages before cell lysis. [2] [13]

Homologous systems

Other plasmids

hok/sok homologues denoted flmA/B (FlmA is the protein toxin and FlmB RNA the antisense regulator) [14] are carried on the F plasmid which operate in the same way to maintain the stability of the plasmid. [15] The F plasmid contains another homologous toxin-antitoxin system called srnB. [11]

The first type I toxin-antitoxin system to be found in gram-positive bacteria is the RNAI-RNAII system of the pAD1 plasmid in Enterococcus faecalis . Here, RNAI encodes a toxic protein Fst while RNAII is the regulatory sRNA. [16]

Chromosomal toxin-antitoxin systems

In E. coli strain K-12 there are four long direct repeats (ldr) which encode short open reading frames of 35 codons organised in a homologous manner to the hok/sok system. One of the repeats encodes LdrD, a toxic protein which causes cell death. An unstable antisense RNA regulator (Rd1D) blocks the translation of the LdrD transcript. [17] A mok homologue which overlaps each ldr loci has also been found. [3]

IstR RNA works in a similar system in conjunction with the toxic TisB protein. [18]

See also

Related Research Articles

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<span class="mw-page-title-main">Sib RNA</span>

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<span class="mw-page-title-main">Hfq protein</span>

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<span class="mw-page-title-main">R1 plasmid</span>

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<span class="mw-page-title-main">PtaRNA1</span> Family of non-coding RNAs

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<span class="mw-page-title-main">TisB-IstR toxin-antitoxin system</span>

The TisB-IstR toxin-antitoxin system is the first known toxin-antitoxin system which is induced by the SOS response in response to DNA damage.

<span class="mw-page-title-main">Toxin-antitoxin system</span> Biological process

A toxin-antitoxin system is a set of two or more closely linked genes that together encode both a "toxin" protein and a corresponding "antitoxin". Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in multiple copies. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable antitoxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK).

<span class="mw-page-title-main">LdrD-RdlD toxin-antitoxin system</span>

RdlD RNA is a family of small non-coding RNAs which repress the protein LdrD in a type I toxin-antitoxin system. It was discovered in Escherichia coli strain K-12 in a long direct repeat (LDR) named LDR-D. This locus encodes two products: a 35 amino acid peptide toxin (ldrD) and a 60 nucleotide RNA antitoxin. The 374nt toxin mRNA has a half-life of around 30 minutes while rdlD RNA has a half-life of only 2 minutes. This is in keeping with other type I toxin-antitoxin systems.

<span class="mw-page-title-main">SymE-SymR toxin-antitoxin system</span>

The SymE-SymR toxin-antitoxin system consists of a small symbiotic endonuclease toxin, SymE, and a non-coding RNA symbiotic RNA antitoxin, SymR, which inhibits SymE translation. SymE-SymR is a type I toxin-antitoxin system, and is under regulation by the antitoxin, SymR. The SymE-SymR complex is believed to play an important role in recycling damaged RNA and DNA. The relationship and corresponding structures of SymE and SymR provide insight into the mechanism of toxicity and overall role in prokaryotic systems.

<span class="mw-page-title-main">FlmA-FlmB toxin-antitoxin system</span>

The FlmA-FlmB toxin-antitoxin system consists of FlmB RNA, a family of non-coding RNAs and the protein toxin FlmA. The FlmB RNA transcript is 100 nucleotides in length and is homologous to sok RNA from the hok/sok system and fulfills the identical function as a post-segregational killing (PSK) mechanism.

<span class="mw-page-title-main">TxpA-RatA toxin-antitoxin system</span>

The TxpA/RatA toxin-antitoxin system was first identified in Bacillus subtilis. It consists of a non-coding 222nt sRNA called RatA and a protein toxin named TxpA.

par stability determinant

The par stability determinant is a 400 bp locus of the pAD1 plasmid which encodes a type I toxin-antitoxin system in Enterococcus faecalis. It was the first such plasmid addiction module to be found in gram-positive bacteria.

vapBC

VapBC is the largest family of type II toxin-antitoxin system genetic loci in prokaryotes. VapBC operons consist of two genes: VapC encodes a toxic PilT N-terminus (PIN) domain, and VapB encodes a matching antitoxin. The toxins in this family are thought to perform RNA cleavage, which is inhibited by the co-expression of the antitoxin, in a manner analogous to a poison and antidote.

The SrnB-SrnC toxin-antitoxin system of the F plasmid is homologous to the hok/sok system of R1. Like the hok/sok system, it performs a post-segregational killing function, ensuring that all surviving daughter cells inherit the F plasmid. The system consists of srnB' mRNA, which is relatively stable and codes for the toxic protein SrnB, srnB mRNA, a regulatory element and srnC mRNA, an antitoxin with complementarity to srnB.

<span class="mw-page-title-main">CcdA/CcdB Type II Toxin-antitoxin system</span>

The CcdA/CcdB Type II Toxin-antitoxin system is one example of the bacterial toxin-antitoxin (TA) systems that encode two proteins, one a potent inhibitor of cell proliferation (toxin) and the other its specific antidote (antitoxin). These systems preferentially guarantee growth of plasmid-carrying daughter cells in a bacterial population by killing newborn bacteria that have not inherited a plasmid copy at cell division.

<span class="mw-page-title-main">ParDE type II toxin-antitoxin system</span>

The parDE type II toxin-antitoxin system is one example of the bacterial toxin-antitoxin (TA) systems that encode two proteins, one a potent inhibitor of cell proliferation (toxin) and the other its specific antidote (antitoxin). These systems preferentially guarantee growth of plasmid-carrying daughter cells in a bacterial population by killing newborn bacteria that have not inherited a plasmid copy at cell division.

References

  1. ↑ Gerdes K, Larsen JE, Molin S (January 1985). "Stable inheritance of plasmid R1 requires two different loci". J. Bacteriol. 161 (1): 292–8. doi:10.1128/JB.161.1.292-298.1985. PMC   214870 . PMID   2981804.
  2. 1 2 Hayes F (September 2003). "Toxins-antitoxins: plasmid maintenance, programmed cell death, and cell cycle arrest". Science. 301 (5639): 1496–9. doi:10.1126/science.1088157. PMID   12970556. S2CID   10028255.
  3. 1 2 3 Gerdes K, Wagner EG (April 2007). "RNA antitoxins". Curr. Opin. Microbiol. 10 (2): 117–24. doi:10.1016/j.mib.2007.03.003. PMID   17376733.
  4. ↑ Faridani OR, Nikravesh A, Pandey DP, Gerdes K, Good L (2006). "Competitive inhibition of natural antisense Sok-RNA interactions activates Hok-mediated cell killing in Escherichia coli". Nucleic Acids Res. 34 (20): 5915–22. doi:10.1093/nar/gkl750. PMC   1635323 . PMID   17065468.
  5. ↑ Gerdes K, Thisted T, Martinussen J (November 1990). "Mechanism of post-segregational killing by the hok/sok system of plasmid R1: sok antisense RNA regulates formation of a hok mRNA species correlated with killing of plasmid-free cells". Mol. Microbiol. 4 (11): 1807–18. doi:10.1111/j.1365-2958.1990.tb02029.x. PMID   1707122. S2CID   45453320.
  6. ↑ Thisted T, Gerdes K (January 1992). "Mechanism of post-segregational killing by the hok/sok system of plasmid R1. Sok antisense RNA regulates hok gene expression indirectly through the overlapping mok gene". J. Mol. Biol. 223 (1): 41–54. doi:10.1016/0022-2836(92)90714-U. PMID   1370544.
  7. ↑ Gerdes K, Nielsen A, Thorsted P, Wagner EG (August 1992). "Mechanism of killer gene activation. Antisense RNA-dependent RNase III cleavage ensures rapid turn-over of the stable hok, srnB and pndA effector messenger RNAs". J. Mol. Biol. 226 (3): 637–49. doi:10.1016/0022-2836(92)90621-P. PMID   1380562.
  8. ↑ Gerdes K, Rasmussen PB, Molin S (May 1986). "Unique type of plasmid maintenance function: postsegregational killing of plasmid-free cells". Proc. Natl. Acad. Sci. U.S.A. 83 (10): 3116–20. doi: 10.1073/pnas.83.10.3116 . PMC   323463 . PMID   3517851.
  9. ↑ Thisted T, Sørensen NS, Gerdes K (1995). "Mechanism of post-segregational killing: secondary structure analysis of the entire Hok mRNA from plasmid R1 suggests a fold-back structure that prevents translation and antisense RNA binding". J. Mol. Biol. 247 (5): 859–73. doi:10.1006/jmbi.1995.0186. PMID   7536849.
  10. ↑ Gerdes K, Bech FW, Jørgensen ST, et al. (August 1986). "Mechanism of postsegregational killing by the hok gene product of the parB system of plasmid R1 and its homology with the relF gene product of the E. coli relB operon". EMBO J. 5 (8): 2023–9. doi:10.1002/j.1460-2075.1986.tb04459.x. PMC   1167073 . PMID   3019679.
  11. 1 2 Gerdes K, Poulsen LK, Thisted T, Nielsen AK, Martinussen J, Andreasen PH (November 1990). "The hok killer gene family in gram-negative bacteria". New Biol. 2 (11): 946–56. PMID   2101633.
  12. ↑ Pecota DC, Osapay G, Selsted ME, Wood TK (2003). "Antimicrobial properties of the Escherichia coli R1 plasmid host killing peptide". J. Biotechnol. 100 (1): 1–12. doi:10.1016/S0168-1656(02)00240-7. PMID   12413781.
  13. ↑ Wang IN, Smith DL, Young R (2000). "Holins: the protein clocks of bacteriophage infections". Annu. Rev. Microbiol. 54: 799–825. doi:10.1146/annurev.micro.54.1.799. PMID   11018145.
  14. ↑ Loh SM, Cram DS, Skurray RA (June 1988). "Nucleotide sequence and transcriptional analysis of a third function (Flm) involved in F-plasmid maintenance". Gene. 66 (2): 259–68. doi:10.1016/0378-1119(88)90362-9. PMID   3049248.
  15. ↑ Pedersen K, Gerdes K (June 1999). "Multiple hok genes on the chromosome of Escherichia coli". Mol. Microbiol. 32 (5): 1090–102. doi: 10.1046/j.1365-2958.1999.01431.x . PMID   10361310.
  16. ↑ Greenfield TJ, Ehli E, Kirshenmann T, Franch T, Gerdes K, Weaver KE (August 2000). "The antisense RNA of the par locus of pAD1 regulates the expression of a 33-amino-acid toxic peptide by an unusual mechanism". Mol. Microbiol. 37 (3): 652–60. doi: 10.1046/j.1365-2958.2000.02035.x . PMID   10931358.[ dead link ]
  17. ↑ Kawano M, Oshima T, Kasai H, Mori H (July 2002). "Molecular characterization of long direct repeat (LDR) sequences expressing a stable mRNA encoding for a 35-amino-acid cell-killing peptide and a cis-encoded small antisense RNA in Escherichia coli". Mol. Microbiol. 45 (2): 333–49. doi: 10.1046/j.1365-2958.2002.03042.x . PMID   12123448.[ dead link ]
  18. ↑ Darfeuille F, Unoson C, Vogel J, Wagner EG (May 2007). "An antisense RNA inhibits translation by competing with standby ribosomes". Mol. Cell. 26 (3): 381–92. doi: 10.1016/j.molcel.2007.04.003 . PMID   17499044.

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