Difference between revisions of "Part:BBa K2463000"

Latest revision as of 20:24, 22 October 2017

Biofilm and Motility Regulation Device
The Biofilm and Motility Regulation Device is a single part capable of regulating motility of bacteria and dictyostelium. By overriding standard cellular processes via overexpression of enzymes, the system alters the biochemistry of the cell, specifically the expression of the signalling molecule responsible for regulating motility.

Background

Cyclic di-GMP is a secondary signalling molecule used to control motility in bacteria and dictyostelium: concentration of c-di-GMP alters motility.
c-di-GMP can be formed from two GTP molecules with the catalytic activity of a GGDEF domain found in diguanylate cyclases - in the case of the biofilm and motility control device, the diguanylate cyclase enzyme in question is PLeD.
c-di-GMP can be degraded into 5'-phosphoguanylyl(3'->5')guanosine (PGPG) with a water molecule and the catalytic activity of an EAL domain found in cyclic di-GMP phosphodiesterases - the c di-GMP phosphodiesterase in question is yhjH gene.

Function

The device contains an inverter function between the PLeD and yhjH genes. The inverter (example with tetR) uses an Mnt repressor followed by a terminator and finally an Mnt repressible promoter. When the device is not being transcribed the protein from the yhjH gene is produced, causing c-di-GMP within the cell to be degraded. When the device is transcribed the yhjH gene is silenced and the PLeD protein is produced, causing the synthesis of c-di-gmp. The yhjH gene lacks a degrading tag thus the cells take a longer time to respond to the device being activated.

Diagram

Usage

The device was designed to provide a simplified system of biofilm and motility manipulation. Insert a promoter downstream of the device: the rate of transcription of the device defines the function. For motility do not transcribe the device, for biofilm formation upregulate transcription of the device. Place the device in a circuit in order to override cellular responses regarding motility and biofilm formation.

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 1806
Illegal BamHI site found at 32
Illegal BamHI site found at 1190
Illegal XhoI site found at 1768
23
COMPATIBLE WITH RFC[23]
25
INCOMPATIBLE WITH RFC[25]
Illegal NgoMIV site found at 448
Illegal NgoMIV site found at 595
Illegal AgeI site found at 931
1000
INCOMPATIBLE WITH RFC[1000]
Illegal BsaI site found at 105

@@ Line 2: / Line 2: @@
 __NOTOC__
 <partinfo>BBa_K2463000 short</partinfo>
+<br>The Biofilm and Motility Regulation Device is a single part capable of regulating motility of bacteria and dictyostelium. By overriding standard cellular processes via overexpression of enzymes, the system alters the biochemistry of the cell, specifically the expression of the signalling molecule responsible for regulating motility.
-Summary
+==Background==
-The Biofilm Regulation Device is a single part capable of regulating motility of bacteria and dictyostelium. By overriding standard cellular processes via overexpression of enzymes, the system alters the biochemistry of the cell, specifically the expression of the signalling molecule responsible for regulating motility.
+*Cyclic di-GMP is a secondary signalling molecule used to control motility in bacteria and dictyostelium: concentration of c-di-GMP alters motility.
+*c-di-GMP can be formed from two GTP molecules with the catalytic activity of a GGDEF domain found in diguanylate cyclases - in the case of the biofilm and motility control device, the diguanylate cyclase enzyme in question is PLeD.
+*c-di-GMP can be degraded into 5'-phosphoguanylyl(3'->5')guanosine (PGPG) with a water molecule and the catalytic activity of an EAL domain found in cyclic di-GMP phosphodiesterases - the c di-GMP phosphodiesterase in question is yhjH gene.
-Background
+==Function==
-Cyclic di-GMP is a secondary signalling molecule used to control motility in bacteria and dictyostelium.
+The device contains an inverter function between the [https://parts.igem.org/Part:BBa_K2012002 PLeD] and [https://parts.igem.org/Part:BBa_K861090 yhjH] genes. The inverter <i>[https://parts.igem.org/Part:BBa_K173005 (example with tetR)]</i> uses an [https://parts.igem.org/Part:BBa_C0072 Mnt repressor] followed by a terminator and finally an [https://parts.igem.org/Part:BBa_R0073 Mnt repressible promoter]. When the device is not being transcribed the protein from the yhjH gene is produced, causing c-di-GMP within the cell to be degraded. When the device is transcribed the yhjH gene is silenced and the PLeD protein is produced, causing the synthesis of c-di-gmp. The yhjH gene lacks a degrading tag thus the cells take a longer time to respond to the device being activated.
-c-di-GMP can be formed from two GTP molecules with the catalytic activity of a GGDEF domain found in diguanylate cyclases - in the case of the biofilm control device, the diguanylate cyclase enzyme in question is PLeD.
+==Diagram==
+[[Image:Warwick-Biofilm-Control-Device.png|center]]
-c-di-GMP can be degraded into 5'-phosphoguanylyl(3'->5')guanosine (PGPG) with a water molecule and the catalytic activity of an EAL domain found in cyclic di-GMP phosphodiesterases - the c di-GMP phosphodiesterase in question is yhjH gene.
+==Usage==
-Function
-The device contains a not-gate function between the PLeD and yhjH genes (Mnt repressor -> terminator -> repressible promoter). When the device is not being transcribed the yhjH gene is upregulated, causing c-di-GMP within the cell to be degraded. When the device is transcribed the yhjH gene is silenced and the PLeD protein is produced, causing the synthesis of c-di-gmp. The yhjH gene lacks a degrading tag thus the cells take a longer time to respond to the device being activated (exact details are unknown).
-Usage
 The device was designed to provide a simplified system of biofilm and motility manipulation. Insert a promoter downstream of the device: the rate of transcription of the device defines the function. For motility do not transcribe the device, for biofilm formation upregulate transcription of the device. Place the device in a circuit in order to override cellular responses regarding motility and biofilm formation.