Molecular biology

SOS Repair – SOS Response in Bacteria

What is SOS Response or SOS Repair? The SOS response is a worldwide gene regulation mechanism that bacteria such as Escherichia coli...

MN Editors avatar
MN Editors
This article writter by MN Editors on September 16, 2022

Microbiology Notes is an educational niche blog related to microbiology (bacteriology, virology, parasitology, mycology, immunology, molecular biology, biochemistry, etc.) and different branches of biology.

Follow
X

Follow

E-mail :*
* Your personal data will be used to support your experience throughout this website and for other purposes described in our Privacy Policy. I hereby agree and consent to the privacy policy.
· 10 min read >
SOS Repair - SOS Response in Bacteria
SOS Repair - SOS Response in Bacteria

What is SOS Response or SOS Repair?

The SOS response is a worldwide gene regulation mechanism that bacteria such as Escherichia coli employ to respond to treatments that damage DNA or limit DNA replication.

  • Miroslav Radman discovered and named the SOS reaction in 1975.
  • When bacteria are exposed to harsh conditions that result in extensive DNA damage, the typical repair processes are incapable of mending the damage. A prolonged exposure to ultraviolet light can cause significant damage to the DNA of bacteria. However, bacteria have one more trump card, appropriately named the SOS reaction.
  • This response activates at least 15 proteins, including the mysterious DNA polymerase II.
  • recA is an additional essential protein. It derives its name from its participation in a recombination event.
  • Homologous DNA can recombine through a number of different ways. It suffices to mention that DNA sequences exist that can be utilised to replace one strand by crossing it over another.
  • Part (a) of the diagram demonstrates how this may function. If a lesion is too complicated for the regular repair enzymes to work, DNA polymerases are unable to synthesis new DNA over the lesion, leaving a gap during replication.
  • However, the other replicating strand (shown in blue) should include the correct complement.
  • This DNA segment is recombined to the lower strand by RecA and a large number of other proteins.
  • This leaves the upper strand devoid of DNA, but it has its right complement (in red), allowing DNA polymerases to duplicate it.
  • DNA polymerase becomes involved in error-prone repair if the damaged strand has too many lesions. In this instance, DNA polymerase continues to replicate across the damaged region, despite its inability to directly match bases over the lesions.
  • Consequently, it inserts bases without a template, essentially guessing. This contradicts the principle of replication fidelity, but it is better than nothing for the damaged cells.
  • Several replication attempts result in fatal mutations, leading to the demise of numerous cells. Nonetheless, some survivors are preferable to the alternative.
  • Approximately twenty genes are expressed at elevated rates during this reaction.
  • These genes are called SOS genes individually and the SOS regulon collectively.
  • Their expression is regulated by the interaction of two regulatory proteins: the LexA repressor, which limits SOS gene expression during normal cell growth, and the RecA protein, which is activated by therapies that activate the SOS response.
  • The activation of RecA results in the specific proteolytic inactivation of LexA.
  • It is believed that production of the SOS genes helps the cell combat DNA damage, resulting in DNA repair and the return of normal cell growth.
  • A bacterial cell does not need to activate DNA repair genes in the presence of normal DNA. Therefore, there must be a regulator that controls the expression of these genes. LexA is a repressor protein that binds to certain DNA sites or SOS boxes. The binding will inhibit SOS gene expression.
  • In altered DNA, however, the deactivation of the LexA repressor is required to stimulate the production of SOS genes. RecA functions as an activator of SOS genes in the SOS system, causing proteolysis of the repressor protein and allowing the SOS genes to be expressed as various DNA repair inducing proteins.

Elements of SOS Response or SOS Repair System

A SOS system consisting of the following elements:

  • Regulator protein: It is expressed by the “RecA” gene and its role is to activate the repressed SOS system by preventing LexA from binding to the SOS operator.
  • Repressor protein: The “LexA” gene encodes this protein, which deactivates inducer proteins. The repressor attaches to the operator and renders the SOS system inactive or repressed.
  • Inducer proteins: They are encoded by SOS-box genes that, depending on the type of DNA damage, can activate the inducer proteins.

Functions of SOS Gene Products

  • Numerous SOS gene products have a direct role in DNA repair. These include the excision repair proteins UvrA and UvrB and the daughter-strand gap repair proteins RuvA, RuvB, and RecA.
  • Other SOS gene products have indirect DNA repair functions.
  • The SulA protein inhibits cell division. While the SOS response is active, cell division is prevented. It is believed that this facilitates daughter-strand gap repair by maintaining multiple copies of the chromosome inside the same cell, thereby serving as templates for damaged molecules.
  • UmuD and UmuC, which are encoded by the SOS gene, perform key roles in SOS mutagenesis. This method is regarded to be a “court of last resort” in which irreparable harm is transformed into a readable sequence, which typically results in errors.
  • After synthesis, the UmuD protein is converted to its active form, designated UmuD’.
  • This processing step is, once again, a particular proteolytic cleavage reaction that is entirely parallel to those that deactivate LexA and l repressor. The difference, however, is that the cleavage product is activated rather than deactivated.
  • UmuD’ and UmuC collaborate with RecA to perform yet another function in DNA metabolism. It is hypothesised that these proteins limit the DNA polymerase III proofreading activity.
  • Other SOS genes encode activities that are not well understood. This could be due to the fact that E. coli is often not investigated in its natural environment.
  • Laboratory conditions (exponential growth in rich medium) are chosen for their repeatability and convenience, although in nature the organism is typically found in the digestive tract or in diluted aquatic habitats, such as streams.
  • It is probable that several processes that enhance cell survival following DNA damage in these environments differ from laboratory conditions and from each other.

SOS Repair Mechanism 

SOS Repair Mechanism
SOS Repair Mechanism
  1. During normal growth, LexA repressor protein dimers negatively control the SOS genes.
  2. LexA binds to a 20-bp consensus sequence (the SOS box) in the operator region of these genes under normal conditions.
  3. Depending on the affinity of LexA for their SOS box, a subset of these SOS genes express at a certain level even in the repressed condition.
  4. After DNA damage caused by the accumulation of single-stranded DNA (ssDNA) regions at replication forks, where DNA polymerase is inhibited, the SOS genes are activated.
  5. RecA is activated by forming a filament around these ssDNA sequences in an ATP-dependent manner. The activated version of RecA interacts with the LexA repressor to allow its separation from the operon. [o3r]
  6. According to the amount of LexA affinity for SOS boxes, suppression of the SOS genes diminishes as the pool of Lex declines.
  7. Operators that weakly bind LexA are the first to be completely expressed.
  8. Thus, LexA can successively activate various repair mechanisms.
  9. Genes (such as lexA, recA, UVrA, uvrB, and uvrD) with a weak SOS box are fully triggered in response to even weak SOS-inducing stimuli.
  10. The first SOS repair mechanism to be activated is ucleotide excision repair (NER), whose purpose is to repair DNA damage without committing to a full-fledged SOS response. cell.
  11. Nonetheless, if NER is insufficient to repair the damage, the LexA concentration is reduced further, inducing the production of genes with stronger Lex boxes (such as sulA, umuD, and umuC, which are expressed late).
  12. By attaching to FtsZ, the starting protein of cell division, SulA inhibits cell division. This produces filamentation and induces mutagenesis repair dependent on UmuDC.
  13. Some genes may be partially triggered in response to even endogenous amounts of DNA damage, whilst other genes appear to be induced only when substantial or chronic DNA damage is present in the cell.
SOS Repair Mechanism
SOS Repair Mechanism

Near promoters in Escherichia coli, SOS boxes are 20-nucleotide sequences with a palindromic structure and a high level of sequence conservation. The sequence of SOS boxes in various classes and phyla varies widely in length and composition, but it is always highly conserved and one of the most potent short genomic signals. The large information richness of SOS boxes enables differential binding of LexA to various promoters and permits timing of the SOS response.

The genes for lesion repair are activated at the onset of the SOS response. UmuCD’2 (also known as DNA polymerase V) and other error-prone translesion polymerases are activated as a last resort. Reducing the number of RecA filaments limits the cleavage activity of LexA homodimer, which binds to the SOS boxes near promoters to restore normal gene expression.

SOS Response Inactivation and Activation

Inactivation

  • A SOS system is always deactivated while DNA is healthy.
  • The LexA promoter results in the production of LexA repressor protein.
  • The interaction of LexA repressor with the consensus sequence (consisting of 20 SOS-box base pairs) inhibits the operation of the SOS system.
  • Thus, LexA inhibits the SOS box, halting the action of SOS genes involved in the repair of damaged DNA.

SOS Activation

  • When DNA is aberrant and all other repair systems fail, the SOS repair system is activated.
  • In reaction to damage from UV radiation or other conditions, the organisms activate the SOS mechanism automatically.
  • The SOS system is only activated in the event of severe DNA damage resulting in single-strand breakage at the replication fork.
  • This DNA damage activates RecA, a regulatory protein that interacts with single-stranded DNA through ATP.
  • Attachment of RecA to ssDNA produces a right-handed nucleoprotein complex or “RecA + ssDNA filament.”
  • Upon interaction between LexA repressor and a nucleoprotein complex, LexA dimer is proteolytically cleaved.
  • The conversion of RecA protein to protease results in proteolytic cleavage, which limits the activity of LexA protein.
  • The SOS box genes will now be expressed as diverse DNA-repair inducer proteins.
  • According to the type of DNA damage, inducer protein expression will not occur simultaneously but will vary.
  • Therefore, in the presence and absence of the activator protein RecA, the SOS system is activated and deactivated correspondingly.

Regulatory Proteins of SOS Response

  • RecA is a complex protein that, in addition to its regulatory function, performs crucial roles in genetic recombination and DNA repair.
  • It is hypothesised, based on in vitro research, that the activated form of RecA is a helical filament composed of several RecA molecules polymerized on single-stranded DNA and carrying ATP or dATP. Additionally, this filament is essential for recombination and repair.
  • Similar to phage l repressor, LexA is a repressor. It possesses an N-terminal DNA-binding domain and a C-terminal dimerization domain.
  • The protein binds to dyad-symmetric DNA locations, and the bound form is a dimer.
  • The unique proteolytic cleavage site is located between the two protein domains.
  • Consequently, cleavage separates the DNA-binding function from the dimerization function, and DNA binding is reduced due to the protein’s inability to dimerize.
  • Biochemically speaking, the proteolytic reaction is remarkable in that the cleavage is a self-processing event carried out by groups in LexA and not RecA.
  • RecA serves as a “co-protease” to stimulate this reaction when it is activated (see LExA Repressor).
  • If the cell has a prophage for phage l or a comparable bacterial virus (see Lambda Phage), the prophage’s CI repressor can undergo a similar cleavage process driven by active RecA.
  • This reaction is referred to as prophage induction. The normally inhibited viral lytic genes are then depressed, and the virus grows lytically, generating a burst of offspring virus.
  • It is assumed that the responsiveness of the CI repressor to active p53 is responsible for its function. RecA is the virus’s response to a signal indicating that the cell is in peril and may not survive. According to this theory, the cell has not evolved a regulatory system for the virus’s benefit.
  • Instead, the virus exploits a preexisting cellular process. The rate of cleavage of the l repressor is significantly slower than that of LexA.
  • Therefore, if the DNA damage is not substantial, cleavage of CI does not occur before the DNA damage is repaired (see Figure 1), and prophage induction does not occur.
  • This variance in sensitivity between LexA and phage repressors is a result of their distinct regulatory habitats. LexA has evolved to respond quickly to even minor inducers, whereas l has evolved to respond slowly and only to degrees of damage that jeopardise cell viability.
  • In fact, prophage induction becomes effective only at DNA damage levels that initiate cell death.
  • SOS induction is reversible, allowing cells to return to their normal growth state, which is another difference between the two systems.
  • In contrast, prophage induction is irreversible due to the fact that the complex regulatory circuitry of the l genetic switch inhibits continued CI expression, even if cleavage pauses.
Regulation of SOS Response
Regulation of SOS Response

About Above Image: The regulating system SOS. (a) The system’s condition during normal cell proliferation. LexA is an active protein that inhibits the synthesis of RecA (left) and SOS proteins (right). (b). DNA damage induces induction and transition to the induced state. The activated RecA protein causes the LexA repressor protein to self-cleave, rendering it inactive as a repressor. (c). Induced SOS condition In the absence of an active LexA, the recA and SOS genes are highly expressed. Prophage induction occurs if the cell harbours a l prophage and remains in this state for an extended period of time. (c) Transition to the state of normal growth. RecA activation is reversible, hence DNA repair results in deactivation of RecA. The degree of RecA coprotease activity regulates the system’s state and its transitions between two states.

Note: The LexA repressor limits SOS gene expression during normal cell growth. The RecA protein is activated by therapies that induce the SOS response.

Gene NameProtien encoded/roel in DNA repair
Pol B (din A) Encoded polymerisation subunit of DNA polymerase II, required for replication
restrat in recombinational repair
uvrA , uvrBEncode ABC excinuclease subunit UvrA and UvrB
umuC, umuDEncode DNA polymerase V
sulAEncode protien that iinhibit cell division,possibly to allow time for DNA repair
dinBEncodes DNA polymerase IV
uvrDEncodes DNA helicase II (DNA unwinding protien)
recAEncodes RecA protien rwequired for error-prone repair and recombinational repair
ssbEncodes ssDNA binding protien (SSB)
recNRequired for recombinational repair.
himAEncodes subunit of integration host factor,involved in site specific recombination, replication, transposition,regulation of gene expression.
dinFGene of unknown function
dinDGene of unknown function

E. coli SOS System Mechanism

  • Cross-linking compounds, UV irradiation, alkylating chemicals, etc., can damage DNA.
  • RecA, a LexA protease, detects broken DNA and becomes active by removing its repressor once it is compromised.
  • Once the LexA dimer repressor is eliminated, the LexA operon is capable of autoregulation.
  • In addition to being a LexA protease, the RecA protein catalyses several unique DNA processes, including annealing of single-stranded DNA and strand transfer.
  • The SOS system has increased DNA-repair capabilities, which include excision and post-replication repair, enhanced mutagenesis, and prophage induction.
  • Additionally, the mechanism can impede cell division and respiration.
E. coli SOS System Mechanism
E. coli SOS System Mechanism | Source: Skowro28, CC BY-SA 4.0, via Wikimedia Commons

Important Note

  • Changes in gene expression in E. coli and other bacteria in response to significant DNA damage are referred to as the SOS response. Lex A and Rec A are the two principal proteins that govern the bacterial SOS system.
  • Despite the existence of various DNA repair systems, the DNA of some organisms is occasionally so severely damaged that the regular repair mechanisms cannot fix all of the damage. Consequently, DNA synthesis ceases entirely. In such instances, the SOS response worldwide control network is triggered.
  • It is known that the SOS response is prevalent in the Bacteria domain, yet it is largely lacking in certain bacterial phyla, such as the Spirochetes.
  • Similar to recombination repair, the SOS response is dependent on the activities of the RecA and Lex A proteins.
  • The most prevalent cellular signals that activate the SOS response are sections of single-stranded DNA (ssDNA) resulting from stalled replication forks or double-strand breaks, which are separated by DNA helicase. RecA protein binds to ssDNA in an ATP hydrolysis-driven process during the initiation step, forming RecA–ssDNA filaments.
  • RecA attaches to single- or double-stranded DNA breaks and gaps produced when DNA synthesis ceases. RecA binding initiates DNA repair through recombination.
  • RecA–ssDNA filaments stimulate LexA autoprotease activity, which ultimately results in the cleavage of LexA dimer and subsequent destruction of LexA.
  • The absence of LexA repressor increases transcription of the SOS genes and permits additional signal induction, inhibition of cell division, and an increase in the levels of proteins involved in damage processing.
  • The LexA homodimer is a transcriptional repressor that binds to SOS boxes, also known as operator sequences. Lex A is known to regulate transcription of around 48 genes in E. coli, including the LexA and RecA genes.
  • Numerous genes involved in DNA synthesis and repair are negatively controlled by lexA. Destruction of LexA stimulates transcription of genes for excision repair, while MutS identifies base mismatches and glides along the DNA. MutL binds to MutS and connects MutS to MutH. Looping DNA is required for this interaction to occur.
  • MutH is responsible for identifying the methylated DNA strand, which is the nonmutated parental strand.

References

  • Maslowska KH, Makiela-Dzbenska K, Fijalkowska IJ. The SOS system: A complex and tightly regulated response to DNA damage. Environ Mol Mutagen. 2019 May;60(4):368-384. doi: 10.1002/em.22267. Epub 2019 Jan 7. PMID: 30447030; PMCID: PMC6590174.
  • Whitney, A.K., Weir, T.L. Interaction of caffeine with the SOS response pathway in Escherichia coli . Gut Pathog 7, 21 (2015). https://doi.org/10.1186/s13099-015-0069-x
  • Leonard Schärfen, Miloš Tišma, Andreas Hartmann, Michael Schlierf bioRxiv 2020.07.14.201889; doi: https://doi.org/10.1101/2020.07.14.201889
  • Harshad GhodkeBishnu P PaudelJacob S LewisSlobodan JergicKamya GopalZachary J RomeroElizabeth A WoodRoger WoodgateMichael M CoxAntoine M van Oijen (2019) Spatial and temporal organization of RecA in the Escherichia coli DNA-damage response eLife 8:e42761.
  • Hostetler, Zachary. (2018). A Genetically Encoded Fluorescent Amino Acid Reveals Protein Dynamics Regulating the Bacterial DNA Damage Response. 
  • Podlesek, Z., & Bertok, D. Ž.  (2021). The <em>Escherichia coli</em> SOS Response: Much More than DNA Damage Repair. In  (Ed.), Escherichia coli [Working Title]. IntechOpen. https://doi.org/10.5772/intechopen.100353
  • https://www.sciencedirect.com/topics/neuroscience/sos-response
  • https://biologyreader.com/sos-repair.html
  • https://www.brainkart.com/article/The-SOS-Response-in-E–coli_27555/
  • http://genesdev.cshlp.org/content/15/4/415/F9.expansion.html
  • https://www.cleanpng.com/png-sos-response-dna-repair-repressor-lexa-reca-3322583/
  • http://what-when-how.com/molecular-biology/sos-response-molecular-biology/
  • https://favpng.com/png_view/sos-response-dna-repair-reca-biology-e-coli-png/Ksssdfzn
  • https://blogs.scientificamerican.com/lab-rat/the-sos-response-how-bacteria-deal-with-damaged-dna/
microbiology note app
microbiology note app qr code Scane to download
Download Microbiology Note App Download this app for free from google play store and read ads free notes
Need a Note? Request us
Request
Sourav Bio
0

Leave a Reply

Your email address will not be published.

Sourav Bio
0
Follow
X

Follow

E-mail :*
* Your personal data will be used to support your experience throughout this website and for other purposes described in our Privacy Policy. I hereby agree and consent to the privacy policy.

Microbiology Notes is an educational niche blog related to microbiology (bacteriology, virology, parasitology, mycology, immunology, molecular biology, biochemistry, etc.) and different branches of biology.

More From Microbiology

Ads Blocker Image Powered by Code Help Pro

Ads Blocker Detected!!!

We have detected that you are using extensions to block ads. Please support us by disabling these ads blocker.