Difference between revisions of "Part:BBa K3552021"

 
(→‎Characterization)
 
(2 intermediate revisions by the same user not shown)
Line 5: Line 5:
 
HofN is a DNA utilization protein which is required for the use of extracellular DNA as a nutrient. Its functions include the carbon utilization, DNA catabolic process, type IV pilus biogenesis and type IV pilus-dependent motility.This part is in the part collection where we have 12 genes that code for the base generator of pilA.  
 
HofN is a DNA utilization protein which is required for the use of extracellular DNA as a nutrient. Its functions include the carbon utilization, DNA catabolic process, type IV pilus biogenesis and type IV pilus-dependent motility.This part is in the part collection where we have 12 genes that code for the base generator of pilA.  
  
−
The part collection includes: Parts that are different kinds of type 4 pilus: BBa_K3552000 BBa_K3552001 BBa_K3552002. Parts that are the generator of the type 4 pilus: BBa_K3552003 BBa_K3552004 BBa_K3552005 BBa_K3552006 BBa_K3552007 BBa_K3552008 BBa_K3552018 BBa_K3552019 BBa_K3552020 BBa_K3552021 BBa_K3552022 BBa_K3552023 BBa_K3552024 BBa_K3552025 BBa_K3552026 BBa_K3552027 BBa_K3552028 BBa_K3552029. Parts that are a complete circuit: BBa_K3552009 BBa_K3552010 BBa_K3552011 BBa_K3552012.
+
The part collection includes:
 +
Parts that are different kinds of type 4 pilus:
 +
<partinfo>BBa_K3552000</partinfo> 
 +
<partinfo>BBa_K3552001</partinfo> 
 +
<partinfo>BBa_K3552002</partinfo>.
 +
Parts that are the generator of the type 4 pilus:
 +
<partinfo>BBa_K3552003</partinfo> 
 +
<partinfo>BBa_K3552004</partinfo>
 +
<partinfo>BBa_K3552005</partinfo>
 +
<partinfo>BBa_K3552006</partinfo>
 +
<partinfo>BBa_K3552007</partinfo>
 +
<partinfo>BBa_K3552008</partinfo>
 +
<partinfo>BBa_K3552018</partinfo> 
 +
<partinfo>BBa_K3552019</partinfo> 
 +
<partinfo>BBa_K3552020</partinfo> 
 +
<partinfo>BBa_K3552021</partinfo> 
 +
<partinfo>BBa_K3552022</partinfo> 
 +
<partinfo>BBa_K3552023</partinfo> 
 +
<partinfo>BBa_K3552024</partinfo> 
 +
<partinfo>BBa_K3552025</partinfo> 
 +
<partinfo>BBa_K3552026</partinfo> 
 +
<partinfo>BBa_K3552027</partinfo> 
 +
<partinfo>BBa_K3552028</partinfo> 
 +
<partinfo>BBa_K3552029</partinfo>.
 +
Parts that are a complete circuit:
 +
<partinfo>BBa_K3552009</partinfo> 
 +
<partinfo>BBa_K3552010</partinfo> 
 +
<partinfo>BBa_K3552011</partinfo> 
 +
<partinfo>BBa_K3552012</partinfo>.
  
 
Our part collection can instruct other teams to designed new rechargeable pilus and substitution of different major pilin.
 
Our part collection can instruct other teams to designed new rechargeable pilus and substitution of different major pilin.
  
−
Usage and Biology:
+
<span class='h3bb'>'''Sequence and Features'''</span>
−
HofN is a component in the transmembrane protein that connected to the outer membrane secretin channel formed by the hofQ. The HofB gene is a ATPase motor which localized at the base of the pilin generator system in the inner membrane, propel the assembly of pilus and it interacts with the platform protein HofC and HofM component of the inner membrane anchored assembly platform complex that also includes HofN and HofO. The  hofMNOPQ operon encodes the assembly platform complex connecting HofB ATPase with the secretin hofQ. The hofMNOPQ is the generation pathway of pilA from the inner membrane to the surface of outer membrane.
+
<partinfo>BBa_K3552021 SequenceAndFeatures</partinfo>
  
−
Characterization:
+
==Reference==
−
We tried to uncoupled all the genes into single ones and we already separated them. We mutated the sequence and codon optimization of the repeated sequence from two genes to prevent recombination. In the future we are going to link all single genes to the same promotor and reconstructed all genes into a complete circuit to see any difference comparing to the initial combined genes.
+
Luna Rico, Areli et al. “Functional reconstitution of the type IVa pilus assembly system from enterohaemorrhagic Escherichia coli.” Molecular microbiology vol. 111,3 (2019): 732-749. doi:10.1111/mmi.14188
  
−
<!-- Add more about the biology of this part here
+
==Usage and Biology==
−
===Usage and Biology===
+
HofN is a component in the transmembrane protein that connected to the outer membrane secretin channel formed by the hofQ. The HofB gene is a ATPase motor which localized at the base of the pilin generator system in the inner membrane, propel the assembly of pilus and it interacts with the platform protein HofC and HofM component of the inner membrane anchored assembly platform complex that also includes HofN and HofO. The  hofMNOPQ operon encodes the assembly platform complex connecting HofB ATPase with the secretin hofQ. The hofMNOPQ is the generation pathway of pilA from the inner membrane to the surface of outer membrane.
  
−
<!-- -->
+
==Characterization==
−
<span class='h3bb'>Sequence and Features</span>
+
One of the possibilities that limit the pili yield could be the coupling of the genetic sequence of pili generator (<partinfo>BBa_K3552006</partinfo> <partinfo>BBa_K3552007</partinfo> and <partinfo>BBa_K3552008</partinfo>). When the genes in the clusters overlap each other and share a same sequence, it could be extremely inconvenient for us to modify the gene sequence such as RBSs (ribosomal binding sites) and conduct codon optimization for biosynthetic engineering purpose. In order to improve the yield of pili production, we designed and carried out experiments to decouple these gene clusters into singular genes with optimization of RBS in front of each gene. We suggest that the reassembled pili generator of decoupled gene segments would not decrease or might increase the pili productivity.
−
<partinfo>BBa_K3552021 SequenceAndFeatures</partinfo>
+
  
 +
There are two steps in decoupling: 1) amplification of each genes; 2) codon optimization and point mutation. We first amplified all the 12 genes from the gene clusters. Then, we designed codon optimization to alter the RBS with a similar strength as the original one and carried out point mutations to eliminate the same sequence of two genes according to the design and therefore avoid the recombination of the genes back to the original form. In the design, we kept the beginning sequence of the later gene unchanged but altered the ending of the former gene. After every portions of the gene of generator was decoupled with targeting molecular masses, we reassembled all parts together directly to form a new plasmid with decoupled pili generator by using Gibson Assembly due to the time limitation. But the result of our Gibson Assembly is basically all negative.
 +
[[File:T--LINKS_China--Fig decoupling.jpeg|800px]]
  
 
<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  

Latest revision as of 07:48, 27 October 2020


hofN

HofN is a DNA utilization protein which is required for the use of extracellular DNA as a nutrient. Its functions include the carbon utilization, DNA catabolic process, type IV pilus biogenesis and type IV pilus-dependent motility.This part is in the part collection where we have 12 genes that code for the base generator of pilA.

The part collection includes: Parts that are different kinds of type 4 pilus: BBa_K3552000 BBa_K3552001 BBa_K3552002. Parts that are the generator of the type 4 pilus: BBa_K3552003 BBa_K3552004 BBa_K3552005 BBa_K3552006 BBa_K3552007 BBa_K3552008 BBa_K3552018 BBa_K3552019 BBa_K3552020 BBa_K3552021 BBa_K3552022 BBa_K3552023 BBa_K3552024 BBa_K3552025 BBa_K3552026 BBa_K3552027 BBa_K3552028 BBa_K3552029. Parts that are a complete circuit: BBa_K3552009 BBa_K3552010 BBa_K3552011 BBa_K3552012.

Our part collection can instruct other teams to designed new rechargeable pilus and substitution of different major pilin.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]

Reference

Luna Rico, Areli et al. “Functional reconstitution of the type IVa pilus assembly system from enterohaemorrhagic Escherichia coli.” Molecular microbiology vol. 111,3 (2019): 732-749. doi:10.1111/mmi.14188

Usage and Biology

HofN is a component in the transmembrane protein that connected to the outer membrane secretin channel formed by the hofQ. The HofB gene is a ATPase motor which localized at the base of the pilin generator system in the inner membrane, propel the assembly of pilus and it interacts with the platform protein HofC and HofM component of the inner membrane anchored assembly platform complex that also includes HofN and HofO. The hofMNOPQ operon encodes the assembly platform complex connecting HofB ATPase with the secretin hofQ. The hofMNOPQ is the generation pathway of pilA from the inner membrane to the surface of outer membrane.

Characterization

One of the possibilities that limit the pili yield could be the coupling of the genetic sequence of pili generator (BBa_K3552006 BBa_K3552007 and BBa_K3552008). When the genes in the clusters overlap each other and share a same sequence, it could be extremely inconvenient for us to modify the gene sequence such as RBSs (ribosomal binding sites) and conduct codon optimization for biosynthetic engineering purpose. In order to improve the yield of pili production, we designed and carried out experiments to decouple these gene clusters into singular genes with optimization of RBS in front of each gene. We suggest that the reassembled pili generator of decoupled gene segments would not decrease or might increase the pili productivity.

There are two steps in decoupling: 1) amplification of each genes; 2) codon optimization and point mutation. We first amplified all the 12 genes from the gene clusters. Then, we designed codon optimization to alter the RBS with a similar strength as the original one and carried out point mutations to eliminate the same sequence of two genes according to the design and therefore avoid the recombination of the genes back to the original form. In the design, we kept the beginning sequence of the later gene unchanged but altered the ending of the former gene. After every portions of the gene of generator was decoupled with targeting molecular masses, we reassembled all parts together directly to form a new plasmid with decoupled pili generator by using Gibson Assembly due to the time limitation. But the result of our Gibson Assembly is basically all negative. T--LINKS China--Fig decoupling.jpeg