Difference between revisions of "Part:BBa K3552004"

Latest revision as of 13:41, 27 October 2020

hofM-hofN-hofO-hofP-hofQ(gene from DH5a)

HofM is a DNA utilization protein which is required for the use of extracellular DNA as a nutrient. Its functions include the carbon utilization and DNA catabolic process. 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. HofO is a DNA utilization protein which is required for the use of extracellular DNA as a nutrient. Its functions include the carbon utilization and DNA catabolic process. HofP is a DNA utilization protein which is required for the use of extracellular DNA as a nutrient. Its functions include the carbon utilization and DNA catabolic process. HofQ is a DNA utilization protein which is required for the use of extracellular DNA as a nutrient. Could be the porin responsible for transport of DNA across the outer membrane. Its functions include the carbon utilization, DNA binding, protein secretion and DNA catabolic process.This part is in the part collection where we have 13 genes that code for the proteins.

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
INCOMPATIBLE WITH RFC[21]
Illegal BglII site found at 11
Illegal BglII site found at 1813
Illegal BamHI site found at 336
23
COMPATIBLE WITH RFC[23]
25
INCOMPATIBLE WITH RFC[25]
Illegal AgeI site found at 1781
1000
INCOMPATIBLE WITH RFC[1000]
Illegal SapI.rc site found at 1417

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

HofM is a component of the IM complex that is connected to the outer membrane secretin channel formed by the hofQ and allows pilus exposure on the bacterial surface. HofN is a component in the transmembrane protein that connected to the outer membrane secretin channel formed by the hofQ. HofO is a component in the transmembrane protein that connected to the outer membrane secretin channel formed by the hofQ. The inner membrane anchored assembly platform complex is connected via hofP to the outer membrane secretin channel formed by hofQ that allows pilus to expose on the bacterial surface. 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

Construction

We amplified each gene cluster of pili generator (BBa_K3552003, BBa_K3552004 and BBa_K3552005) from E.coli DH5a. Then, due to the long length of each gene cluster, we initially assembled all segments we obtained separately on pSB1CJ vector by Gibson Assembly to form three sub-plasmid: 1)BBa_K3552000 and BBa_K3552003 , 2)BBa_K3552004 , and 3)BBa_K3552005. Additionally, we constructed another sub-plasmid with pET28a vector for the backbone of our major plasmid. Finally, four sub-plasmids were assembled through Golden Gate Assembly to form the final major plasmid of Gs pilA with pili generator, BBa_K3552009.

Since using the pili generator from the strain Enterohaemorrhagic Escherichia Coli (EHEC) will give a better production of T4P, we conducted point mutation on three the sub-plasmids we constructed before (BBa_K3552003, BBa_K3552004 and BBa_K3552005) for further construction, deriving the original gene sequence into that of EDL933, obtaining three new sub-plasmids: BBa_K3552006, BBa_K3552007 and BBa_K3552008. We then conducted the same assembling method to assemble three new sub-plasmids on pET28a vector into a new major plasmid possesses Gs pilA with EHEC pili generator, BBa_K3552010.

Pili production

In order to compare the function of two types of generator, generator similar to EHEC genes and generator from DH5a genes, we carried out a pili production analysis. In this analysis, we determined the yield of three types of pili production and measured the effects of two variables on pili production: cultivation time and mobile oxygen presence. We did two repeated experiments under the same environmental conditions for cultivation except for the variables. To further prove that the use of the EDL933 pili generator could result in a better yield of pili, we designed a new plasmid of Gs pili with a DH5a generator, and compare the pili yield of two plasmids.

For the first experiment, We prepared 32 plates, 8 plates for each group; half of the plates were sealed with laboratory films to limit the mobility of oxygen and cultured at 30-celsius degrees. We added 8 plates in the second group for an additional measurement in 72h growth. In the first experiment, we set two groups of time variables: 24h vs 48h cultivation time. We took two plates for each sample group for every 24h. The results showed that all four samples had a better yield of pili after 48h cultivation comparing to 24h. Furthermore, we wanted to discover whether the pili production will increase as the time of cultivation increases beyond 48h. In the second experiment, we did a repeat experiment with an additional group of 72h cultivation time. The results were similar to that of the first experiment, showing the same trend of better yield in 48h than 24h cultivation, and that 24h cultured plates basically have no pili produced. The 72h cultivation might not have the highest yield and parts of the sample have high pili production after 48h period. For Gs and Pa pilA, 48h cultivation will be better than 72h in pili production while the trend of Gm pilA and Gs pilA with DH5a generator goes the opposite. But these results would have a certain degree of uncertainty.

@@ Line 47: / Line 47: @@
 ==Characterization==
-We amplified each gene cluster of pili generator (<partinfo>BBa_K3552003</partinfo>, <partinfo>BBa_K3552004</partinfo> and <partinfo>BBa_K3552005</partinfo>) from E.coli DH5a. Then, due to the long length of each gene cluster, we initially assembled all segments we obtained separately on pSB1CJ vector by Gibson Assembly to form three sub-plasmid: 1)<partinfo>BBa_K3552000</partinfo> and <partinfo>BBa_K3552003</partinfo> ,  2)<partinfo>BBa_K3552004</partinfo> , and 3)<partinfo>BBa_K3552005</partinfo>. Additionally, we constructed another sub-plasmid with pET28a vector for the backbone of our major plasmid. Finally, four sub-plasmids were assembled through Golden Gate Assembly to form the final major plasmid of Gs pilA with pili generator, <partinfo>BBa_K3552009</partinfo> .
+===Construction===
+We amplified each gene cluster of pili generator (<partinfo>BBa_K3552003</partinfo>, <partinfo>BBa_K3552004</partinfo> and <partinfo>BBa_K3552005</partinfo>) from E.coli DH5a. Then, due to the long length of each gene cluster, we initially assembled all segments we obtained separately on pSB1CJ vector by Gibson Assembly to form three sub-plasmid: 1)<partinfo>BBa_K3552000</partinfo> and <partinfo>BBa_K3552003</partinfo> ,  2)<partinfo>BBa_K3552004</partinfo> , and 3)<partinfo>BBa_K3552005</partinfo>. Additionally, we constructed another sub-plasmid with pET28a vector for the backbone of our major plasmid. Finally, four sub-plasmids were assembled through Golden Gate Assembly to form the final major plasmid of Gs pilA with pili generator, <partinfo>BBa_K3552009</partinfo>.
+                [[File:T--LINKS_China--Figure construction of DH5a.jpeg|600px]]
 Since using the pili generator from the strain Enterohaemorrhagic Escherichia Coli (EHEC) will give a better production of T4P, we conducted point mutation on three the sub-plasmids we constructed before (<partinfo>BBa_K3552003</partinfo>, <partinfo>BBa_K3552004</partinfo> and <partinfo>BBa_K3552005</partinfo>) for further construction, deriving the original gene sequence into that of EDL933, obtaining three new sub-plasmids: <partinfo>BBa_K3552006</partinfo>, <partinfo>BBa_K3552007</partinfo> and <partinfo>BBa_K3552008</partinfo>. We then conducted the same assembling method to assemble three new sub-plasmids on pET28a vector into a new major plasmid possesses Gs pilA with EHEC pili generator, <partinfo>BBa_K3552010</partinfo>.
-In order to compare the function of two types of generator, generator similar to EHEC genes and generator from DH5a genes, we carried out a pili production analysis. In this analysis, we determined the yield of three type of pili production, and measured the effects of two variables on pili production: cultivation time and mobile oxygen presence. We did two repeated experiments under same environmental conditions for cultivation except the variables. To further prove that the use of EDL933 pili generator could result in a better yield of pili, we designed a new plasmid of Gs pili with DH5a generator, and compare the pili yield of two plasmids.
+                [[File:T--LINKS_China--Figure construction of EHEC.jpeg|600px]]
+===Pili production===
+In order to compare the function of two types of generator, generator similar to EHEC genes and generator from DH5a genes, we carried out a pili production analysis. In this analysis, we determined the yield of three types of pili production and measured the effects of two variables on pili production: cultivation time and mobile oxygen presence. We did two repeated experiments under the same environmental conditions for cultivation except for the variables. To further prove that the use of the EDL933 pili generator could result in a better yield of pili, we designed a new plasmid of Gs pili with a DH5a generator, and compare the pili yield of two plasmids.
+For the first experiment, We prepared 32 plates, 8 plates for each group; half of the plates were sealed with laboratory films to limit the mobility of oxygen and cultured at 30-celsius degrees. We added 8 plates in the second group for an additional measurement in 72h growth. In the first experiment, we set two groups of time variables: 24h vs 48h cultivation time. We took two plates for each sample group for every 24h. The results showed that all four samples had a better yield of pili after 48h cultivation comparing to 24h.
+Furthermore, we wanted to discover whether the pili production will increase as the time of cultivation increases beyond 48h. In the second experiment, we did a repeat experiment with an additional group of 72h cultivation time. The results were similar to that of the first experiment, showing the same trend of better yield in 48h than 24h cultivation, and that 24h cultured plates basically have no pili produced. The 72h cultivation might not have the highest yield and parts of the sample have high pili production after 48h period. For Gs and Pa pilA, 48h cultivation will be better than 72h in pili production while the trend of Gm pilA and Gs pilA with DH5a generator goes the opposite. But these results would have a certain degree of uncertainty.
-For the first experiment, We prepared 32 plates, 8 plates for each group; half of the plates was sealed with laboratory films to limit the mobility of oxygen and cultured in 30 celsius degrees. We added 8 plates in the second group for an additional measurement in 72h growth. In the first experiment, we set two groups of time variables: 24h vs 48h cultivation time. We took two plates each sample group for every 24h. The results showed that all four samples had a better yield of pili after 48h cultivation comparing to 24h.
+                [[File:T--LINKS_China--Figure results of concentration of bacteria.jpeg|600px]]
-Furthermore, we wanted to discover whether the pili production will increase as the time of cultivation increases beyond 48h. In the second experiment, we did a repeat experiment with an additional group of 72h cultivation time. The results were similar as that of the first experiment, showing the same trend of better yield in 48h than 24h cultivation, and that 24h cultured plates basically have no pili produced. The 72h cultivation might not have the highest yield and parts of the sample have high pili production after 48h period. For Gs and Pa pilA, 48h cultivation will be better than 72h in pili production while the trend of Gm pilA and Gs pilA with DH5a generator goes opposite. But these results would have a certain degrees of uncertainty.
 <partinfo>BBa_K3552004 parameters</partinfo>
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