Team:Osaka/Project

From 2011.igem.org

(Difference between revisions)
(Factors)
(2. Detection of DNA damage)
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=== 2. Detection of DNA damage===
=== 2. Detection of DNA damage===
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==== SOS response ====
[[File:SOS response.png|left|sos responce|300px]]
[[File:SOS response.png|left|sos responce|300px]]
<p>If DNA is significantly damaged (eg by exposure to UV radiation or chemicals), synthesis of several DNA damage-related proteins occurs quickly.
<p>If DNA is significantly damaged (eg by exposure to UV radiation or chemicals), synthesis of several DNA damage-related proteins occurs quickly.
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In addition, our Bio-dosimeter must have some sort of visible output to alert users to radioactivity (detected as DNA damage). Therefore we decided to employ lycopene biosynthesis as a reporter.</p>
In addition, our Bio-dosimeter must have some sort of visible output to alert users to radioactivity (detected as DNA damage). Therefore we decided to employ lycopene biosynthesis as a reporter.</p>
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==== Pigment Biosynthesis ====
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==== Lycopene biosynthesis ====
[[File:Pigment.jpg‎|280px|right]]
[[File:Pigment.jpg‎|280px|right]]
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<p>In our previous project, "colrcoli", we intended to use <I>E.coli</I> as a paint tool. We studied pigment synthesis.</p>
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<p>In a previous iGEM project, "colrcoli", we attempted to use <I>E.coli</I> as a paint tool. To that end, we examined biosynthesis of carotenoid pigments as a way of producing color. Here, we attempted to use biosynthesis of the carotenoid lycopene as a reporter for DNA damage.</p>
<p>Carotenoid is a family of natural pigments. Many plants such as fruits and vegetables contain these pigments. For example, tomato has lycopene(red), carrot has carotene(orange). Xanthophyll(yellow) is found in almost all plants.
<p>Carotenoid is a family of natural pigments. Many plants such as fruits and vegetables contain these pigments. For example, tomato has lycopene(red), carrot has carotene(orange). Xanthophyll(yellow) is found in almost all plants.
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Biosynthesis of carotenoid pigments starts from FPP(FARNESYL DIPHOSPHATE). FPP is formed from isopentenylpyrophosphate(IPP) and dimethylallylpyrophosphate(DMAPP). IPP and DMAPP are formed in mevalonate pathway or nonmevalonate pathway. Mevalonate pathway is an important cellular metabolic pathway present in all higher eukaryotes and many bacteria. And nonmevalone pathway is to produce isoprenoids in plants and apicomplexan protozoa.(starting with pyruvate and glyceradehyde-3-phosphate). While the Mevalonate Pathway is present in all higher eukaryotes, the Non-mevalonate Pathway is present in <I>E.coli</I>. </p>
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Biosynthesis of carotenoid pigments starts from FPP(FARNESYL DIPHOSPHATE). FPP is formed from isopentenylpyrophosphate(IPP) and dimethylallylpyrophosphate(DMAPP). IPP and DMAPP are formed through two distinct pathways, the mevalonate and non-mevalonate pathways. In <i>E.coli</i>, FPP is formed through the non-mevalonate pathway. By the introduction of heterologous enzymatic genes colorless FPP is then converted to orange-red lycopene, which has a peak absorbance at 407nm that is easily measured. </p>
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<p>After IPP and DMAPP go on to form FPP, a series of enzymatic reactions convert the colourless FPP to a coloured compound: red lycopene.</p>
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<p>In this study, we used genes coding enzymes constructed by [http://2009.igem.org/Team:Cambridge CAMBRIDGE]. Please refer to part details and [http://2009.igem.org/Team:Osaka our previous wiki]</p>
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Revision as of 19:32, 28 October 2011

Project Details

1. Damage tolerance

D.radiodurans

The bacterium Deinococcus radiodurans shows remarkable resistance to a range of damage caused by ionizing radiation, desiccation, UV radiation, oxidizing agents, and electrophilic mutagens.It is an aerobic bacterium that is most famous for its extreme resistance to ionizing radiation; it not only can survive acute exposures to gamma radiation that exceed 15,000 Gy, but it can also grow continuously in the presence of chronic radiation (60 Gy/hour) without any effect on its growth rate or ability to express cloned genes. For comparison, an acute exposure of just 5-10 Gy is lethal to the average human.

Factors

  • recA
    The D. radiodurans RecA protein has been characterized and its gene has been sequenced; it shows greater than 50% identity to the E. coli RecA protein. D. radiodurans recA mutants are highly sensitive to UV and ionizing radiation. In this context, early work by Carroll et al (1996) reported that E. coli RecA did not complement an IR-sensitive D. radiodurans recA point-mutant (rec30) and that expression of D. radiodurans RecA in E. coli was lethal. More recently, however, it has been reported that E. coli recA can provide partial complementation to a D. radiodurans recA null mutant (Schlesinger, 2007).
  • pprI
    PprI, which is unique to D. radiodurans, is invoked by present data as the most important protein for radiation response mechanism. PprI can significantly and specifically induce the gene expression of recA and pprA and enhance the enzyme activities of catalases. These results strongly suggest that PprI plays a crucial role in regulating multiple DNA repair and protection pathways in response to radiation stress.
  • pprA
    A pleiotropic protein promoting DNA repair, role in radiation resistance of Deinococcus radiodurans was demonstrated. PprA preferentially bound to double-stranded DNA carrying strand breaks, inhibited E. coli exonuclease III activity, and stimulated the DNA end-joining reaction catalysed by ATPdependent and NAD-dependent DNA ligases. These results suggest that D. radiodurans has a radiationinduced non-homologous end-joining repair mechanism in which PprA plays a critical role.
  • pprM
    PprM (a modulator of the PprI-dependent DNA damage response) is a homolog of cold shock protein (Csp)PprM regulates the induction of PprA but not that of RecA. PprM belongs in a distinct clade of a subfamily together with Csp homologs from D. geothermalis and Thermus thermophilus. PprM plays an important role in the induction of RecA and PprA and is involved in the unique radiation response mechanism controlled by PprI in D. radiodurans.

2. Detection of DNA damage

SOS response

sos responce

If DNA is significantly damaged (eg by exposure to UV radiation or chemicals), synthesis of several DNA damage-related proteins occurs quickly. This reaction to DNA damage is the SOS response.

RecA is a 38 kilodalton Escherichia coli protein essential for the repair and maintenance of DNA. RecA has multiple activities, all related to DNA repair. In the bacterial SOS response, it has a co-protease function in the autocatalytic cleavage of the LexA repressor and the λ repressor. LexA is expressed constitutively and prevents expression of damage-related proteins by binding to SOS box as a repressor. RecA is activated by binding to single-stranded DNA, and the activated RecA then turns on LexA protease activity. Self-cleavage of LexA derepresses the expression of damage-related proteins enabling a response to be mounted.

We decided to employ the RecA promoter(BBa J22106) to detect DNA damage. Expression of genes downstream of this promoter is induced by DNA damage. In addition, our Bio-dosimeter must have some sort of visible output to alert users to radioactivity (detected as DNA damage). Therefore we decided to employ lycopene biosynthesis as a reporter.

Lycopene biosynthesis

Pigment.jpg

In a previous iGEM project, "colrcoli", we attempted to use E.coli as a paint tool. To that end, we examined biosynthesis of carotenoid pigments as a way of producing color. Here, we attempted to use biosynthesis of the carotenoid lycopene as a reporter for DNA damage.

Carotenoid is a family of natural pigments. Many plants such as fruits and vegetables contain these pigments. For example, tomato has lycopene(red), carrot has carotene(orange). Xanthophyll(yellow) is found in almost all plants. Biosynthesis of carotenoid pigments starts from FPP(FARNESYL DIPHOSPHATE). FPP is formed from isopentenylpyrophosphate(IPP) and dimethylallylpyrophosphate(DMAPP). IPP and DMAPP are formed through two distinct pathways, the mevalonate and non-mevalonate pathways. In E.coli, FPP is formed through the non-mevalonate pathway. By the introduction of heterologous enzymatic genes colorless FPP is then converted to orange-red lycopene, which has a peak absorbance at 407nm that is easily measured.






References

  1. [1] Y. Hua et al., “PprI: a general switch responsible for extreme radioresistance of Deinococcus radiodurans,” Biochemical and Biophysical Research Communications, vol. 306, no. 2, pp. 354-360, Jun. 2003.
  2. G. Gao, B. Tian, L. Liu, D. Sheng, B. Shen, and Y. Hua, “Expression of Deinococcus radiodurans PprI enhances the radioresistance of Escherichia coli,” DNA Repair, vol. 2, no. 12, pp. 1419-1427, Dec. 2003.
  3. I. Narumi, K. Satoh, S. Cui, T. Funayama, S. Kitayama, and H. Watanabe, “PprA: a novel protein from Deinococcus radiodurans that stimulates DNA ligation,” Molecular Microbiology, vol. 54, no. 1, pp. 278-285, Oct. 2004.
  4. S. Kota and H. S. Misra, “PprA: A protein implicated in radioresistance of Deinococcus radiodurans stimulates catalase activity in Escherichia coli,” Applied Microbiology and Biotechnology, vol. 72, no. 4, pp. 790-796, Oct. 2006.
  5. H. Lu et al., “Deinococcus radiodurans PprI switches on DNA damage response and cellular survival networks after radiation damage,” Molecular & Cellular Proteomics: MCP, vol. 8, no. 3, pp. 481-494, Mar. 2009.
  6. H. Ohba, K. Satoh, H. Sghaier, T. Yanagisawa, and I. Narumi, “Identification of PprM: a modulator of the PprI-dependent DNA damage response in Deinococcus radiodurans,” Extremophiles: Life Under Extreme Conditions, vol. 13, no. 3, pp. 471-479, May 2009.