SymE-SymR toxin-antitoxin system

Last updated
SymR
SymR SScons.png
Conserved secondary structure of SymR RNA.
Identifiers
SymbolSymR
Rfam RF01809
Other data
RNA type Antisense RNA
Domain(s) E. coli
PDB structures PDBe
SymE Toxin of Type I toxin-antitoxin system
SymE Toxin SymE Toxin.png
SymE Toxin
SymE Toxin of Type I toxin-antitoxin system
Identifiers
SymbolSymE_toxin
Pfam PF13957
InterPro IPR020883
PROSITE PS51740
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary
https://swissmodel.expasy.org/repository/uniprot/P39394

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. [1] SymE-SymR is a type I toxin-antitoxin system, and is under regulation by the antitoxin, SymR. [2] The SymE-SymR complex is believed to play an important role in recycling damaged RNA and DNA. [1] The relationship and corresponding structures of SymE and SymR provide insight into the mechanism of toxicity and overall role in prokaryotic systems.

Contents

Discovery

SymR was originally labelled RyjC and is a 77 nucleotide (nt) RNA with a σ70 promoter. RyjC was found to overlap the yjiW open reading frame on the opposite strand by 6 nt, and was characterized as an antisense RNA which bound the 5' untranslated region of yjiW. [3] Further study led to the renaming of both yjiW and RyjC to SymE (SOS-induced yjiW gene with similarity to MazE) and SymR, respectively. [1] Despite similarities to the AbrB superfamily, the SymE family has been exclusively found in proteobacteria. [1]

Relationship between SymE and SymR

The SymR antisense RNA is transcribed 3 nt behind the SymE start codon which is why the SymR promoter is considered embedded within the SymE codon. [2] As a result, SymR blocks RNA translation of SymE by antisense binding, suggesting that this ultimately leads to SymR mRNA degradation. [4] Amino acid analysis has concluded that SymE may have evolved into an RNA cleavage protein that exhibits toxin-like behavior due to transcription factors or antitoxins. [2] In contrast to other common toxin-antitoxin systems, the SymR antitoxin is more stable than the SymE toxin. [1]

Following DNA damage, the SOS response represses transcription of SymR RNA, allowing SymE toxin to degrade potentially damaged mRNA until DNA has been repaired. [1] Conversely, SymE is tightly repressed by LexA repressor binding sites, SymR, and the Lon protease. [2] These three factors are present at multiple levels where LexA is involved in transcription downregulation, SymR RNA is involved in translation downregulation, and Lon protease is involved in protein degradation. [1] [2] The extent of repression on SymE is dependent on the additive power of LexA, SymR, and Lon protease. [2] Overall, SymE synthesis is slow since its activity is highly dependent on DNA repair proteins. [2] In the cellular environment, mitomycin C damages DNA which leads to an overexpression of SymE mRNA to initiate DNA repair. [5]

Toxicity

The overexpression of SymE demonstrated negative effects on the growth of colony-forming cells when tested in vitro . [1] SymE exhibits its toxicity by repressing global translation within the cell, cleaving mRNA in a similar manner to MazF, another toxin. [6] Quantitative Northern blot experiments showed that SymR RNA is present in cells at 10 times the concentration of SymE mRNA (0.02 fmol μg −1 and 0.2 fmol μg−1). [1]

Structure

SymE

The SymE toxin consists of 113 amino acids. [5] When evaluating the amino acid sequence and tertiary structure of SymE, strong similarities were found which resemble the AbrB superfamily. [1] This superfamily mainly functions as transcription factors or antitoxins; however, the similarity of SymE to the primary sequence and tertiary structure of the AbrB superfamily suggests that SymE proteins experienced an evolutionary shift from a transcription factor or antitoxin to a RNA-associating protein that exhibits toxin behavior. [1] Between the AbrB superfamily protein structure and the SymE protein structure, there are several key hydrophobic residues that are highly conserved in the -helix at the center of the protein as well as the strand-1. [1] Despite these key similarities, SymE exhibits polar residues not found in the general structure of the AbrB superfamily, indicating that these residues may have a role in the SymE RNA cleavage ability. [1]

SWISS-MODEL contains more than several experimental structures and theoretical homology models that define certain aspects of the SymE primary sequence and tertiary structure. The UniProtKB accession number P39394 indicates the general structure of the SymE toxin in Escherichia coli (strain K12). [1] [7] In the SWISS-MODEL SymE theoretical model, the -helix contains amino acids G44, Q45, W46, L47, E48, A49, and A50. [8] [9] [10] [11] [12] The strand-1 contains amino acids G55, T56, A57, V58, D59, V60, K61, V62, I67, V68, L69, T70, A71, Q72, P73, and P74 with the -turn containing M63, E64, G65, and C66. [8] [9] [10] [11] [12]

SymR

SymR is an antisense RNA meaning its secondary structure has characteristic stem-and-loop elements as well as unpaired regions flanking the structure. [13] The predicted secondary structure of SymR showcases a loop containing the nucleotide sequence CCAG. [4] This characteristic loop is shared with the lstR-1 and OhsC RNA proteins and is predicted to be a binding site for other proteins. [4] Currently, there are no known files on the RCSB protein data bank or SWISS-MODEL repository that indicate a predicted tertiary structure of SymR.

See also

Related Research Articles

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<span class="mw-page-title-main">Tryptophan repressor</span> Transcription factor

Tryptophan repressor is a transcription factor involved in controlling amino acid metabolism. It has been best studied in Escherichia coli, where it is a dimeric protein that regulates transcription of the 5 genes in the tryptophan operon. When the amino acid tryptophan is plentiful in the cell, it binds to the protein, which causes a conformational change in the protein. The repressor complex then binds to its operator sequence in the genes it regulates, shutting off the genes.

<span class="mw-page-title-main">Helix-turn-helix</span> Structural motif capable of binding DNA

Helix-turn-helix is a DNA-binding protein (DBP). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.

<i>trp</i> operon Operon that codes for the components for production of tryptophan

The trp operon is a group of genes that are transcribed together, encoding the enzymes that produce the amino acid tryptophan in bacteria. The trp operon was first characterized in Escherichia coli, and it has since been discovered in many other bacteria. The operon is regulated so that, when tryptophan is present in the environment, the genes for tryptophan synthesis are repressed.

The gene rpoS encodes the sigma factor sigma-38, a 37.8 kD protein in Escherichia coli. Sigma factors are proteins that regulate transcription in bacteria. Sigma factors can be activated in response to different environmental conditions. rpoS is transcribed in late exponential phase, and RpoS is the primary regulator of stationary phase genes. RpoS is a central regulator of the general stress response and operates in both a retroactive and a proactive manner: it not only allows the cell to survive environmental challenges, but it also prepares the cell for subsequent stresses (cross-protection). The transcriptional regulator CsgD is central to biofilm formation, controlling the expression of the curli structural and export proteins, and the diguanylate cyclase, adrA, which indirectly activates cellulose production. The rpoS gene most likely originated in the gammaproteobacteria.

fis E. coli gene

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

OxyS RNA is a small non-coding RNA which is induced in response to oxidative stress in Escherichia coli. This RNA acts as a global regulator to activate or repress the expression of as many as 40 genes, by an antisense mechanism, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages. Binding to Hfq alters the conformation of OxyS. The 109 nucleotide RNA is thought to be composed of three stem-loops.

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

Sib RNA refers to a group of related non-coding RNA. They were originally named QUAD RNA after they were discovered as four repeat elements in Escherichia coli intergenic regions. The family was later renamed Sib when it was discovered that the number of repeats is variable in other species and in other E. coli strains.

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

The MicA RNA is a small non-coding RNA that was discovered in E. coli during a large scale screen. Expression of SraD is highly abundant in stationary phase, but low levels could be detected in exponentially growing cells as well.

<span class="mw-page-title-main">Hok/sok system</span>

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. It is a type I system because the toxin is neutralised by a complementary RNA, rather than a partnered protein.

<span class="mw-page-title-main">Guanosine pentaphosphate</span> Chemical compound

(p)ppGpp, guanosine pentaphosphate and tetraphosphate, also known as the "magic spot" nucleotides, are alarmones involved in the stringent response in bacteria that cause the inhibition of RNA synthesis when there is a shortage of amino acids. This inhibition by (p)ppGpp decreases translation in the cell, conserving amino acids present. Furthermore, ppGpp and pppGpp cause the up-regulation of many other genes involved in stress response such as the genes for amino acid uptake and biosynthesis.

In a screen of the Bacillus subtilis genome for genes encoding ncRNAs, Saito et al. focused on 123 intergenic regions (IGRs) over 500 base pairs in length, the authors analyzed expression from these regions. Seven IGRs termed bsrC, bsrD, bsrE, bsrF, bsrG, bsrH and bsrI expressed RNAs smaller than 380 nt. All the small RNAs except BsrD RNA were expressed in transformed Escherichia coli cells harboring a plasmid with PCR-amplified IGRs of B. subtilis, indicating that their own promoters independently express small RNAs. Under non-stressed condition, depletion of the genes for the small RNAs did not affect growth. Although their functions are unknown, gene expression profiles at several time points showed that most of the genes except for bsrD were expressed during the vegetative phase, but undetectable during the stationary phase. Mapping the 5' ends of the 6 small RNAs revealed that the genes for BsrE, BsrF, BsrG, BsrH, and BsrI RNAs are preceded by a recognition site for RNA polymerase sigma factor σA.

Bacterial small RNAs (bsRNA) are small RNAs produced by bacteria; they are 50- to 500-nucleotide non-coding RNA molecules, highly structured and containing several stem-loops. Numerous sRNAs have been identified using both computational analysis and laboratory-based techniques such as Northern blotting, microarrays and RNA-Seq in a number of bacterial species including Escherichia coli, the model pathogen Salmonella, the nitrogen-fixing alphaproteobacterium Sinorhizobium meliloti, marine cyanobacteria, Francisella tularensis, Streptococcus pyogenes, the pathogen Staphylococcus aureus, and the plant pathogen Xanthomonas oryzae pathovar oryzae. Bacterial sRNAs affect how genes are expressed within bacterial cells via interaction with mRNA or protein, and thus can affect a variety of bacterial functions like metabolism, virulence, environmental stress response, and structure.

<span class="mw-page-title-main">TisB-IstR toxin-antitoxin system</span> Biochemical process related to DNA damage

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 consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. The toxin is usually a protein while the antitoxin can be a protein or an RNA. 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">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.

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.

<i>Escherichia coli</i> sRNA

Escherichia coli contains a number of small RNAs located in intergenic regions of its genome. The presence of at least 55 of these has been verified experimentally. 275 potential sRNA-encoding loci were identified computationally using the QRNA program. These loci will include false positives, so the number of sRNA genes in E. coli is likely to be less than 275. A computational screen based on promoter sequences recognised by the sigma factor sigma 70 and on Rho-independent terminators predicted 24 putative sRNA genes, 14 of these were verified experimentally by northern blotting. The experimentally verified sRNAs included the well characterised sRNAs RprA and RyhB. Many of the sRNAs identified in this screen, including RprA, RyhB, SraB and SraL, are only expressed in the stationary phase of bacterial cell growth. A screen for sRNA genes based on homology to Salmonella and Klebsiella identified 59 candidate sRNA genes. From this set of candidate genes, microarray analysis and northern blotting confirmed the existence of 17 previously undescribed sRNAs, many of which bind to the chaperone protein Hfq and regulate the translation of RpoS. UptR sRNA transcribed from the uptR gene is implicated in suppressing extracytoplasmic toxicity by reducing the amount of membrane-bound toxic hybrid protein.

The dinQ-agrB type I toxin-antitoxin (TA) system was initially identified in Escherichia coli. This type I TA system is induced by the bacterial DNA damage response system known as the SOS response system.

References

  1. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Kawano M, Aravind L, Storz G (May 2007). "An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin". Molecular Microbiology. 64 (3): 738–54. doi:10.1111/j.1365-2958.2007.05688.x. PMC   1891008 . PMID   17462020.
  2. 1 2 3 4 5 6 7 Kawano M (December 2012). "Divergently overlapping cis-encoded antisense RNA regulating toxin-antitoxin systems from E. coli: hok/sok, ldr/rdl, symE/symR" (PDF). RNA Biology. 9 (12): 1520–7. doi: 10.4161/rna.22757 . PMID   23131729.
  3. ↑ Kawano M, Reynolds AA, Miranda-Rios J, Storz G (2005). "Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli". Nucleic Acids Research. 33 (3): 1040–50. doi:10.1093/nar/gki256. PMC   549416 . PMID   15718303.
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  5. 1 2 Brielle R, Pinel-Marie ML, Felden B (April 2016). "Linking bacterial type I toxins with their actions" (PDF). Current Opinion in Microbiology. Cell regulation. 30: 114–121. doi:10.1016/j.mib.2016.01.009. PMID   26874964.
  6. ↑ Gerdes K, Wagner EG (April 2007). "RNA antitoxins". Current Opinion in Microbiology. 10 (2): 117–24. doi:10.1016/j.mib.2007.03.003. PMID   17376733.
  7. ↑ The UniProt Consortium (2020). "UniProtKB - P39394 (SYME_ECOLI)". uniprot.org. Archived from the original on 10 July 2007. Retrieved 4 May 2020.
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  11. 1 2 Studer G, Rempfer C, Waterhouse AM, Gumienny R, Haas J, Schwede T (April 2020). "QMEANDisCo-distance constraints applied on model quality estimation". Bioinformatics. 36 (8): 2647. doi:10.1093/bioinformatics/btaa058. PMC   7178391 . PMID   32048708.
  12. 1 2 Bertoni M, Kiefer F, Biasini M, Bordoli L, Schwede T (September 2017). "Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology". Scientific Reports. 7 (1): 10480. Bibcode:2017NatSR...710480B. doi:10.1038/s41598-017-09654-8. PMC   5585393 . PMID   28874689.
  13. ↑ Brenner SX, Miller JH. Encyclopedia of genetics. San Diego. ISBN   0-12-227080-0. OCLC   48655705.

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