Difference between revisions of "Team:Jilin China/Basic Part"

 
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<div class="banner"><div class="menu">Basic Parts</div><img src="https://static.igem.org/mediawiki/2017/b/b1/T--Jilin_China--_sec_bg_t.jpg"></div>
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    <strong style="color: #229d73;">1.wt-Pr</strong> <br />
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<p>wt-Pr is a constitutive promoter which is in the upstream of DmpR, a transcriptional factor of dmp operon from <i>Pseudomonas</i> sp. Strain CF600 encoded by <i>dmp</i>R gene[1]. </p>
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<strong style="color: #229d73;">2.cphA-1</strong> <br />
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<p>CphA-1, a catechol 1,2-dioxygenase from <i>Arthrobacter chlorophenolicus</i> A6, is responsible for ring cleavage in aromatic compounds degrading process [2].</p>
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<div class="pic_box center">
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<img src="https://static.igem.org/mediawiki/2017/3/3e/T--Jilin_China--basic_parts01.png"  /><br />
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Figure 2. Reaction of cphA-1
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</div>
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<br />
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<strong style="color: #229d73;">3.CaO19</strong> <br />
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<p>CaO19, a hydroxyquinol 1,2-dioxygenase from <i>Candida albicans</i> TL3, is responsible for ring cleavage in aromatic compounds degrading process[3].</p>
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<div class="pic_box center">
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<img src="https://static.igem.org/mediawiki/2017/5/52/T--Jilin_China--basic_parts02.png"  /><br />
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Figure 3. Reaction of CaO19
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</div>
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<br />
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<strong style="color: #229d73;">4.CbtA (toxin)</strong> <br />
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<p>CbtA is a protein found in crytic prophage CP4-44 in <i>Escherichia coli</i> K-12. CbtA could inhibit cell division and cell elongation via direct and independent interactions with FtsZ and MreB[4], so it is defined as a kind of toxin.</p>
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<br />
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<strong style="color: #229d73;">5.CbeA (antitoxin)</strong> <br />
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<p>CbeA is a protein found in crytic prophage CP4-44 in <i>Escherichia coli</i> K-12 which could suppress the effect of CbtA, so it is defined as a kind of antitoxin. Instead of interacting with CbtA, CbeA directly binds MreB and FtsZ and promotes the assembly of FtsZ and MreB filaments[4].</p>
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    <div class="pic_box center">
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<img src="https://static.igem.org/mediawiki/2017/9/91/T--Jilin_China--basic_parts03.png"  /><br />
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Figure 4. TA system
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</div>
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<p>
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This year we use CbtA and CbeA to build the Geneguard system in our project. For detailed information about toxin/antitoxin (TA) system, <a href="https://2017.igem.org/Team:Jilin_China/Description">please visit ...</a>
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</p>
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                <strong style="color: #229d73;">6.DmpR</strong> <br />
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                <p>DmpR is a σ54-dependent transcriptional factor of <i>dmp</i> operon from <i>Pseudomonas</i> sp. Strain CF600.[5] Transcription of Po, promoter of <i>dmp</i> operon, is activated when DmpR detects the presence of certain phenol compounds.[5-6] DmpR directly interacts with proper inducers at its effector-sensing domain, and the effector-sensor compound then binds to Po promoter and downstream transcription is initiated. The DmpR we use is based on the wild type DmpR used by 2013 Peking (<a href="http://parts.igem.org/Part:BBa_K1031211">BBa_K1031211</a>) but has 5 sites of nucleotides mutation[7] of which two are nonsense mutation and others lead to two amino acids change. The mutant type shows <a
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href="https://2017.igem.org/Team:Jilin_China/Application">high efficiency of transcription initiation</a>.
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                </p>
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                <div class="pic_box center">         
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<img src="https://static.igem.org/mediawiki/2017/e/e4/T--Jilin_China--design002.png" width="80%" /><br />
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Figure 5. The mechanism of DmpR sensor.
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</div>
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                <strong style="color: #229d73;">7.TfdB-JLU</strong> <br />
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                <p>TfdB-JLU is a novel 2,4-dichlorophenol hydroxylase whose amino acid sequence exhibits less than 48% homology with other known TfdBs. The rate-limited step of phenolic degradation is the ortho hydroxylation[8]. Compared to wild-type TfdB, TfdB-JLU has a wilder substrate range and higher catalysis activity. Thus, the enzyme has advantages in efficient disposing of phenolic effluents[8].
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                </p>
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                <div class="pic_box center">
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<img src="https://static.igem.org/mediawiki/2017/9/9a/T--Jilin_China--composite_parts05.png" width="60%" /><br />
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Figure 6. Reaction of TfdB-JLU 
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                </div>
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<strong>Reference：</strong>
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<p>[1] Shingler, V., M. Bartilson, and T. Moore. Cloning and nucleotide sequence of the gene encoding the positive regulator (DmpR) of the phenol catabolic pathway encoded by pVI150 and identification of DmpR as a member of the NtrC family of transcriptional activators. J. Bacteriol. ( 1993) 175: 1596–1604.</p>
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<p>[2] Seok H. Lee. Effective biochemical decomposition of chlorinated aromatic hydrocarbons with a biocatalyst immobilized on a natural enzyme support. Bioresource Technology. (2013) 141:89–96.</p>
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<p>[3] Purification and characterization of a catechol 1,2-dioxygenase from a phenol degrading Candida albicans TL3. San-Chin Tsai · Yaw-Kuen Li Arch Microbiol. (2007) 187:199–206.</p>
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<p>[4] Masuda, Tan. YeeU enhances the bundling of cytoskeletal polymers of MreB and FtsZ, antagonizing the CbtA (YeeV) toxicity in Escherichia coli. Molecular Microbiology. (2012) 84(5), 979–989.</p>
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                <p>[5] V. L. Campos. Detection of Chlorinated Phenols in Kraft Pulp Bleaching Effluents Using DmpR Mutant Strains Bull. Environ. Contam. Toxicol. (2004) 73:666–673</p>
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                <p>[6] V. L. Campos,1 Monitoring Phenolic Compounds During Biological Treatment of Kraft Pulp Mill Effluent Using Bacterial Biosensors Bull. Environ. Contam. Toxicol. (2006) 77:383–390</p>
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                <p>[7] ARLENE A. WISE AND CHERYL R. KUSKE*. Generation of Novel Bacterial Regulatory Proteins That Detect Priority Pollutant Phenols. APPLIED AND ENVIRONMENTAL MICROBIOLOGY,0099-2240/00/$04.0010 Jan. 2000, p. 163-169.</p>
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                <p>[8] Yang Lu • Ying Yu • Rui Zhou, Cloning and characterisation of a novel 2,4 dichlorophenol hydroxylase from a metagenomic library derived from polychlorinated biphenyl-contaminated soil. Biotechnol Lett 2011, 33:1159–1167</p>
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<h1>Basic Parts</h1>
 
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A <b>basic part</b> is a functional unit of DNA that cannot be subdivided into smaller component parts. <a href="http://parts.igem.org/wiki/index.php/Part:BBa_R0051">BBa_R0051</a> is an example of a basic part, a promoter regulated by lambda cl.
 
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<p>Most genetically-encoded functions have not yet been converted to BioBrick parts. Thus, there are <b>many</b> opportunities to find new, cool, and important genetically encoded functions, and refine and convert the DNA encoding these functions into BioBrick standard biological parts. </p>
 
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<h3>Best Basic Part Special Prize</h3>
 
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<p>Most genetically-encoded functions have not yet been converted to BioBrick parts. Thus, there are *many* opportunities to find new, cool, and important genetically encoded functions, and refine and convert the DNA encoding these functions into BioBrick standard biological parts. To be eligible for this award, this part must adhere to <a href="http://parts.igem.org/DNA_Submission">Registry sample submission guidelines</a> and have been sent to the Registry of Standard Biological Parts. If you have a part you wish to nominate your team for this <a href="https://2017.igem.org/Judging/Awards">special prize</a>, make sure you add your part number to your <a href="https://2017.igem.org/Judging/Judging_Form">judging form</a> and delete the box at the top of this page.
 
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<b>Please note:</b> Judges will only look at the first part number you list, so please only enter ONE (1) part number in the judging form for this prize. </p>
 
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<h4>Note</h4>
 
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<p>This page should list all the basic parts your team has made during your project. You must add all characterization information for your parts on the Registry. You should not put characterization information on this page. Remember judges will only look at the first part in the list for the Best Basic Part award, so put your best part first!</p>
 
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{{Jilin_footer}}

Latest revision as of 10:57, 1 November 2017

1.wt-Pr

wt-Pr is a constitutive promoter which is in the upstream of DmpR, a transcriptional factor of dmp operon from Pseudomonas sp. Strain CF600 encoded by dmpR gene[1].


2.cphA-1

CphA-1, a catechol 1,2-dioxygenase from Arthrobacter chlorophenolicus A6, is responsible for ring cleavage in aromatic compounds degrading process [2].


Figure 2. Reaction of cphA-1

3.CaO19

CaO19, a hydroxyquinol 1,2-dioxygenase from Candida albicans TL3, is responsible for ring cleavage in aromatic compounds degrading process[3].


Figure 3. Reaction of CaO19

4.CbtA (toxin)

CbtA is a protein found in crytic prophage CP4-44 in Escherichia coli K-12. CbtA could inhibit cell division and cell elongation via direct and independent interactions with FtsZ and MreB[4], so it is defined as a kind of toxin.


5.CbeA (antitoxin)

CbeA is a protein found in crytic prophage CP4-44 in Escherichia coli K-12 which could suppress the effect of CbtA, so it is defined as a kind of antitoxin. Instead of interacting with CbtA, CbeA directly binds MreB and FtsZ and promotes the assembly of FtsZ and MreB filaments[4].


Figure 4. TA system

This year we use CbtA and CbeA to build the Geneguard system in our project. For detailed information about toxin/antitoxin (TA) system, please visit ...

6.DmpR

DmpR is a σ54-dependent transcriptional factor of dmp operon from Pseudomonas sp. Strain CF600.[5] Transcription of Po, promoter of dmp operon, is activated when DmpR detects the presence of certain phenol compounds.[5-6] DmpR directly interacts with proper inducers at its effector-sensing domain, and the effector-sensor compound then binds to Po promoter and downstream transcription is initiated. The DmpR we use is based on the wild type DmpR used by 2013 Peking (BBa_K1031211) but has 5 sites of nucleotides mutation[7] of which two are nonsense mutation and others lead to two amino acids change. The mutant type shows high efficiency of transcription initiation.


Figure 5. The mechanism of DmpR sensor.
7.TfdB-JLU

TfdB-JLU is a novel 2,4-dichlorophenol hydroxylase whose amino acid sequence exhibits less than 48% homology with other known TfdBs. The rate-limited step of phenolic degradation is the ortho hydroxylation[8]. Compared to wild-type TfdB, TfdB-JLU has a wilder substrate range and higher catalysis activity. Thus, the enzyme has advantages in efficient disposing of phenolic effluents[8].


Figure 6. Reaction of TfdB-JLU
Reference：

[1] Shingler, V., M. Bartilson, and T. Moore. Cloning and nucleotide sequence of the gene encoding the positive regulator (DmpR) of the phenol catabolic pathway encoded by pVI150 and identification of DmpR as a member of the NtrC family of transcriptional activators. J. Bacteriol. ( 1993) 175: 1596–1604.

[2] Seok H. Lee. Effective biochemical decomposition of chlorinated aromatic hydrocarbons with a biocatalyst immobilized on a natural enzyme support. Bioresource Technology. (2013) 141:89–96.

[3] Purification and characterization of a catechol 1,2-dioxygenase from a phenol degrading Candida albicans TL3. San-Chin Tsai · Yaw-Kuen Li Arch Microbiol. (2007) 187:199–206.

[4] Masuda, Tan. YeeU enhances the bundling of cytoskeletal polymers of MreB and FtsZ, antagonizing the CbtA (YeeV) toxicity in Escherichia coli. Molecular Microbiology. (2012) 84(5), 979–989.

[5] V. L. Campos. Detection of Chlorinated Phenols in Kraft Pulp Bleaching Effluents Using DmpR Mutant Strains Bull. Environ. Contam. Toxicol. (2004) 73:666–673

[6] V. L. Campos,1 Monitoring Phenolic Compounds During Biological Treatment of Kraft Pulp Mill Effluent Using Bacterial Biosensors Bull. Environ. Contam. Toxicol. (2006) 77:383–390

[7] ARLENE A. WISE AND CHERYL R. KUSKE*. Generation of Novel Bacterial Regulatory Proteins That Detect Priority Pollutant Phenols. APPLIED AND ENVIRONMENTAL MICROBIOLOGY,0099-2240/00/$04.0010 Jan. 2000, p. 163-169.

[8] Yang Lu • Ying Yu • Rui Zhou, Cloning and characterisation of a novel 2,4 dichlorophenol hydroxylase from a metagenomic library derived from polychlorinated biphenyl-contaminated soil. Biotechnol Lett 2011, 33:1159–1167