Difference between revisions of "Part:BBa K4192021"
 
(5 intermediate revisions by 2 users not shown)
Line 3: Line 3:
 
<partinfo>BBa_K4192021 short</partinfo>
 
<partinfo>BBa_K4192021 short</partinfo>
  
−
It is one of the genes required for oxalic acid synthesis in Burkholderia glumae, which can act together with ObcB to catalyze oxaloacetic acid (OAA) and citric acid to form oxalic acid (OA). When there is only ObcB, it cannot form oxalic acid.
+
It is one of the genes required for oxalic acid synthesis in <i>Burkholderia glumae</i>, which can act together with ObcB to catalyze oxaloacetic acid (OAA) and citric acid to form oxalic acid (OA). When there is only ObcB, it cannot form oxalic acid.
  
 
===Biology===
 
===Biology===
−
<p>CAU_China 2022 plan to use the CDS sequence of _obcB_ in this composite part and the expression product of _obcB_ is one of the main enzyme in in the oxalate secretion circuit<sup>[1]</sup>. It can act together with ObcA to catalyze oxaloacetic acid (OAA) and citric acid to form oxalic acid (OA). When there is only ObcB, it cannot form oxalic acid<sup>[2]</sup>.</p>
+
<p>CAU_China 2022 used this part in their oxalate secretion circuit and the expression product of <i>obcB</i> is one of the main enzyme in in the oxalate secretion circuit<sup>[1]</sup>. It can act together with ObcA to catalyze oxaloacetic acid (OAA) and citric acid to form oxalic acid (OA). When there is only ObcB, it cannot form oxalic acid<sup>[2]</sup>.</p>
 
[[File:CAU-obcAB-pic.jpeg|600px|thumb|center|]]
 
[[File:CAU-obcAB-pic.jpeg|600px|thumb|center|]]
 
<p style="text-align: center;"><b>Fig.1 Effects of <i>obcA</i> and <i>obcB</i>, the shade of purple reflects the concentration of oxalic acid<sup>[1]</sup>.</b></p>
 
<p style="text-align: center;"><b>Fig.1 Effects of <i>obcA</i> and <i>obcB</i>, the shade of purple reflects the concentration of oxalic acid<sup>[1]</sup>.</b></p>
Line 16: Line 16:
 
<p style="text-align: center;"><b>Fig.2 Mechanism of <i>obcA</i> and <i>obcB</i><sup>[2]</sup>.</b></p >
 
<p style="text-align: center;"><b>Fig.2 Mechanism of <i>obcA</i> and <i>obcB</i><sup>[2]</sup>.</b></p >
  
−
<p>Considering the importance of _obcA_ and _obcB_ occur togrther in the biosynthesis of oxalic acid, the CDS of them are in close proximity to each other, even encoded on a single polycistronic message. The implication of this for our project is that we can make these two genes share the same promoter<sup>[2]</sup>.</p>
+
<p>Considering the importance of <i>obcA</i> and <i>obcB</i> occur togrther in the biosynthesis of oxalic acid, the CDS of them are in close proximity to each other, even encoded on a single polycistronic message. The implication of this for our project is that we can make these two genes share the same promoter<sup>[2]</sup>.</p>
 
<br>
 
<br>
 
[[File:CAU-obcAB-gene.jpeg|600px|thumb|center|]]
 
[[File:CAU-obcAB-gene.jpeg|600px|thumb|center|]]
−
<p style="text-align: center;"><b>Fig.3 Distribution of <i>obcA</i> and <i>obcB</i><sup>[1]</sup>.</b></p >
+
<p style="text-align: center;"><b>Fig.3 Distribution of <i>obcA</i> and <i>obcB</i><sup>[1]</sup>.</b></p>
  
 +
We constructed a separate pET-<i>obcB</i> plasmid, and determined that the ObcB protein can be successfully expressed in <i>E.coli</i> BL21 (DE3) through SDS-PAGE, the results are as follows:
 +
 +
[[File:Sdsobcbpic.png|600px|thumb|center|]]
 +
<p style="text-align: center;"><b>Fig.4 Obc protein in SDS-PAGE.</b></p>
 +
 +
<!-- Add more about the biology of this part here
 +
===Usage and Biology===
 +
 +
<!-- -->
 
<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>
 
<partinfo>BBa_K1529151 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K1529151 SequenceAndFeatures</partinfo>
Line 29: Line 38:
 
<p>[1]Nakata, Paul A, and Cixin He. “Oxalic acid biosynthesis is encoded by an operon in Burkholderia glumae.” FEMS microbiology letters vol. 304,2 (2010): 177-82. doi:10.1111/j.1574-6968.2010.01895.x</p>
 
<p>[1]Nakata, Paul A, and Cixin He. “Oxalic acid biosynthesis is encoded by an operon in Burkholderia glumae.” FEMS microbiology letters vol. 304,2 (2010): 177-82. doi:10.1111/j.1574-6968.2010.01895.x</p>
 
<p>[2]Oh, Juntaek et al. “Structural basis for bacterial quorum sensing-mediated oxalogenesis.” The Journal of biological chemistry vol. 289,16 (2014): 11465-11475. doi:10.1074/jbc.M113.543462</p>
 
<p>[2]Oh, Juntaek et al. “Structural basis for bacterial quorum sensing-mediated oxalogenesis.” The Journal of biological chemistry vol. 289,16 (2014): 11465-11475. doi:10.1074/jbc.M113.543462</p>
−
 
−
<!-- Add more about the biology of this part here
 
−
===Usage and Biology===
 
−
 
−
<!-- -->
 
−
<span class='h3bb'>Sequence and Features</span>
 
−
<partinfo>BBa_K4192021 SequenceAndFeatures</partinfo>
 
  
  

Latest revision as of 15:08, 12 October 2022


obcB, one of the genes required for oxalic acid synthesis

It is one of the genes required for oxalic acid synthesis in Burkholderia glumae, which can act together with ObcB to catalyze oxaloacetic acid (OAA) and citric acid to form oxalic acid (OA). When there is only ObcB, it cannot form oxalic acid.

Biology

CAU_China 2022 used this part in their oxalate secretion circuit and the expression product of obcB is one of the main enzyme in in the oxalate secretion circuit[1]. It can act together with ObcA to catalyze oxaloacetic acid (OAA) and citric acid to form oxalic acid (OA). When there is only ObcB, it cannot form oxalic acid[2].

CAU-obcAB-pic.jpeg

Fig.1 Effects of obcA and obcB, the shade of purple reflects the concentration of oxalic acid[1].


When producing oxalic acid, obcB turns C6-CoA adduct into CoA, acetoacetate,and oxalic acid


CAU-obcAB-work.jpeg

Fig.2 Mechanism of obcA and obcB[2].

Considering the importance of obcA and obcB occur togrther in the biosynthesis of oxalic acid, the CDS of them are in close proximity to each other, even encoded on a single polycistronic message. The implication of this for our project is that we can make these two genes share the same promoter[2].


CAU-obcAB-gene.jpeg

Fig.3 Distribution of obcA and obcB[1].

We constructed a separate pET-obcB plasmid, and determined that the ObcB protein can be successfully expressed in E.coli BL21 (DE3) through SDS-PAGE, the results are as follows:

Sdsobcbpic.png

Fig.4 Obc protein in SDS-PAGE.

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 669
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal PstI site found at 669
    Illegal NotI site found at 582
    Illegal NotI site found at 687
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 650
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal PstI site found at 669
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 669
    Illegal NgoMIV site found at 460
    Illegal NgoMIV site found at 501
    Illegal NgoMIV site found at 625
  • 1000
    COMPATIBLE WITH RFC[1000]



References

[1]Nakata, Paul A, and Cixin He. “Oxalic acid biosynthesis is encoded by an operon in Burkholderia glumae.” FEMS microbiology letters vol. 304,2 (2010): 177-82. doi:10.1111/j.1574-6968.2010.01895.x

[2]Oh, Juntaek et al. “Structural basis for bacterial quorum sensing-mediated oxalogenesis.” The Journal of biological chemistry vol. 289,16 (2014): 11465-11475. doi:10.1074/jbc.M113.543462