Latest revision as of 18:24, 21 September 2011

Overview

The cold resistance BioBricks - or CryoBricks - we've developed for our project are classified as basic or composite parts. Composite parts are further grouped into finalized parts, containing a promoter, RBS and coding region, and construction intermediates, containing either a promoter and RBS, or an RBS and coding region. Note that some of the parts listed below were submitted to the registry by other teams. Our own parts are coded K538###. Some of them are submitted as physical DNA, where others are theoretical submissions that never got past the planning stage.

Basic Parts

We use 3 different types of basic parts in the construction of our CryoBricks: promoters, RBSes, and protein coding regions. More detailed information about their purpose can be found on the basic parts page.

Promoters

Based on literature study and safety considerations, we had planned to incorporate four different promoters in our project. The selection comprised the lac operon's promoter (pLacI, [http://partsregistry.org/Part:BBa_R0010 BBa_R0010]), two arabinose-induced promoters (pBAD derivatives - strong, [http://partsregistry.org/Part:BBa_K206000 BBA_K206000], and weak, [http://partsregistry.org/Part:BBa_K206001 BBa_K206001]) and the hydrogenase II operon's promoter (hybB, [http://partsregistry.org/Part:BBa_J45503 BBa_J45503]). While the selected promoters are relatively well characterized, little to no information is available about the effect of low temperature on their activity. For our project, investigating this effect would have been of great value to fine-tune protein expression at different temperatures. Unfortunately, due to facing many difficulties with assembly, we weren't able to characterize the promoter activities, and we ended up working with only two of the selected promoters: pLacI and the strong pBAD promoter.

RBSes

Many iGEM teams before us have characterised the strength of one or several ribosome binding sites, and this information is valuable for the same reasons as characterising promoter activities: fine-tuning protein expression. Again, no information was available of RBS activity at different temperatures. We would have liked to carry out characterisation experiments, but failing assemblies and constraints on time prevented this. In the end, we simply decided to work with one of the strongest RBSes in the Community Collection: [http://partsregistry.org/Part:BBa_B0034 BBa_B0034].

Coding Regions

Our project aims to enhance E. coli's growth rate at low temperatures, by heterologously expressing chaperones from cryophillic bacteria. Their effect may possible be further exacerbated by adding genes encoding anti-freeze proteins (AFPs). Three different AFPs we'd hoped to use for this were generously provided by the team that represents Yale this year. Unfortunately, we received their shipment too late to incorporate their parts in our project.

Selection of chaperones suitable for our project was done based on literature study. We have selected five, the first two of which depending on eachother to function. The selected chaperones are: Cpn10 and Cpn60, forming Oleispira antarctica 's Cpn60/10 system ([http://partsregistry.org/Part:BBa_K538000 BBa_K538000] and [http://partsregistry.org/Part:BBa_K538001 BBa_K538001]); SheDnaK, from Shewanella sp. AC10 ([http://partsregistry.org/Part:BBa_K538002 BBa_K538002]); CspA, from Polaribacter irgensii ([http://partsregistry.org/Part:BBa_K538003 BBa_K538003]); and CspC, also from Polaribacter irgensii ([http://partsregistry.org/Part:BBa_K538004 BBa_K538004]). GeneArt synthesized these parts for us de novo, from sequences that were taken from online repositories and recoded for compatibility with assembly standards.

Composite Parts

The composite parts we submitted to the registry are either construction intermediates or finalized parts. The construction intermediates consist of all possible combinations of our selected promoters ([http://partsregistry.org/Part:BBa_R0010 BBa_R0010] and [http://partsregistry.org/Part:BBa_K206000 BBa_K206000]) and RBS ([http://partsregistry.org/Part:BBa_B0034 BBa_B0034]), and all combinations of that same RBS with our coding regions ([http://partsregistry.org/Part:BBa_K538000 BBa_K538000] through [http://partsregistry.org/Part:BBa_K538004 BBa_K538004]). Note that the promoter + RBS parts contain no bricks that weren't already in the registry.

The finalized parts all comprise a promoter, an RBS and a coding region. They are made either by appending a coding region to the construction intermediates containing a promoter and RBS, or by prepending a promoter to the construction intermediates containing an RBS and a coding region. An additional four final constructs are designed as 'operons' comprising Cpn10 and Cpn60. They are made by appending either the RBS + Cpn10 or the RBS + Cpn60 construction intermediates to the finalized parts that contain the other.

None of these bricks contain a terminator sequence; we have considered appending [http://partsregistry.org/Part:BBa_KB0014 BBa_B0014] to them, but the tightly constrained time we had for our project, and what little of it remained after sorting out (part of) the problems with assembling BioBricks, caused us to decide against this and relying instead on the terminator sequence in the standard plasmid backbones.

Registry Submissions

All parts we submitted to the registry are listed in the table below. The BBa_* links will take you to their respective pages on the parts registry. To view their information on this wiki, refer to our basic and composite part pages instead. Our newly synthesized chaperone genes (basic parts) are labelled K5380##. Construction intermediates are labelled K5381##. Finalized CryoBricks are labelled K5382## or K5383## depending on their promoter: 2## for parts containing pLacI, 3## for parts containing pBAD.

<groupparts>iGEM011 Amsterdam</groupparts>

@@ Line 1: / Line 1: @@
 {{:Team:Amsterdam/Header}}
 __NOTOC__
-=BioBricks=
+=Overview=
-The cold resistance BioBricks - or CryoBricks - we've develpped for our project are classified as [[Team:Amsterdam/BioBricks/Basic_Parts | basic]] or [[Team:Amsterdam/BioBricks/Composite_Parts | composite]] parts. Composite parts are further grouped into finalized parts, containing a promoter, RBS and coding region, and construction intermediates, containing either a promoter and RBS, or an RBS and coding region. Note that some of the parts listed below were submitted to the registry by other teams. Our own parts are coded K538###. Some of them are submitted as physical DNA, where others are theoretical submissions that never got past the planning stage.
+The cold resistance BioBricks - or CryoBricks - we've developed for our project are classified as [[Team:Amsterdam/Biobricks/Basic_Parts|basic]] or [[Team:Amsterdam/Biobricks/Composite_Parts|composite]] parts. Composite parts are further grouped into finalized parts, containing a promoter, RBS and coding region, and construction intermediates, containing either a promoter and RBS, or an RBS and coding region. Note that some of the parts listed below were submitted to the registry by other teams. Our own parts are coded K538###. Some of them are submitted as physical DNA, where others are theoretical submissions that never got past the planning stage.
 ==Basic Parts==
-We use 3 different types of basic parts in the construction of our CryoBricks: promoters, RBSs, and protein coding regions. More detailed information about their selection, biological function and design can be found on the [[Team:Amsterdam/BioBricks/Basic_Parts | basic parts]] page.
+We use 3 different types of basic parts in the construction of our CryoBricks: promoters, RBSes, and protein coding regions. More detailed information about their purpose can be found on the [[Team:Amsterdam/Biobricks/Basic_Parts | basic parts]] page.
 ===Promoters===
 Based on literature study and safety considerations, we had planned to incorporate four different promoters in our project. The selection comprised the lac operon's promoter (pLacI, [http://partsregistry.org/Part:BBa_R0010 BBa_R0010]), two arabinose-induced promoters (pBAD derivatives - strong, [http://partsregistry.org/Part:BBa_K206000 BBA_K206000], and weak, [http://partsregistry.org/Part:BBa_K206001 BBa_K206001]) and the hydrogenase II operon's promoter (hybB, [http://partsregistry.org/Part:BBa_J45503 BBa_J45503]). While the selected promoters are relatively well characterized, little to no information is available about the effect of low temperature on their activity. For our project, investigating this effect would have been of great value to fine-tune protein expression at different temperatures. Unfortunately, due to facing many difficulties with assembly, we weren't able to characterize the promoter activities, and we ended up working with only two of the selected promoters: pLacI and the strong pBAD promoter.
-===RBSs===
+===RBSes===
-Many iGEM teams before us have characterized the strength of one or several ribosome binding sites, and this information is valuable for the same purpose as characterizing promoter activities: fine-tuning protein expression. Again, no information was available of RBS activity at different temperatures. We would have liked to carry out characterisation experiments, but failing assemblies and constraints on time prevented this. In the end, we simply decided to work with the strongest RBS in the registry: [http://partsregistry.org/Part:BBa_B0034 BBa_B0034].
+Many iGEM teams before us have characterised the strength of one or several ribosome binding sites, and this information is valuable for the same reasons as characterising promoter activities: fine-tuning protein expression. Again, no information was available of RBS activity at different temperatures. We would have liked to carry out characterisation experiments, but failing assemblies and constraints on time prevented this. In the end, we simply decided to work with one of the strongest RBSes in the Community Collection: [http://partsregistry.org/Part:BBa_B0034 BBa_B0034].
 ===Coding Regions===
-Our project aims to enhance ''E. coli'''s growth rate at low temperatures, by heterologously expressing chaperones from cryophillic bacteria, and possibly exacerbating their effect by adding genes encoding anti-freeze proteins (AFPs). Three different AFPs we'd hoped to use for this were generously provided by the team that represents [https://2011.igem.org/Team:Yale Yale] this year. Unfortunately, we received their shipment too late to incorporate their parts in our project.
+Our project aims to enhance ''E. coli'''s growth rate at low temperatures, by heterologously expressing chaperones from cryophillic bacteria. Their effect may possible be further exacerbated by adding genes encoding anti-freeze proteins (AFPs). Three different AFPs we'd hoped to use for this were generously provided by the team that represents [https://2011.igem.org/Team:Yale Yale] this year. Unfortunately, we received their shipment too late to incorporate their parts in our project.
+<br><br>
-Selection of chaperones suitable for our project was done based on literature study. We have selected five, the first two of which depending on eachother to function. The selected chaperones are: Cpn10 and Cpn60, forming ''Oleispira antarctica'''s Cpn60/10 system ([http://partsregistry.org/Part:BBa_K538000 BBa_K538000] and [http://partsregistry.org/Part:BBa_K538001 BBa_K538001]); SheDnaK, from ''Shewanella'' sp. AC10 ([http://partsregistry.org/Part:BBa_K538002 BBa_K538002]); CspA, from ''Polaribacter irgensii'' ([http://partsregistry.org/Part:BBa_K538003 BBa_K538003]); and CspC, also from ''Polaribacter irgensii'' ([http://partsregistry.org/Part:BBa_K538004 BBa_K538004]). GeneArt synthesized these parts for us ''de novo'', from sequences that were taken from online repositories and recoded for compatibility with assembly standards.
+Selection of chaperones suitable for our project was done based on literature study. We have selected five, the first two of which depending on eachother to function. The selected chaperones are: ''Cpn10'' and ''Cpn60'', forming ''Oleispira antarctica'' 's ''Cpn60/10'' system ([http://partsregistry.org/Part:BBa_K538000 BBa_K538000] and [http://partsregistry.org/Part:BBa_K538001 BBa_K538001]); ''SheDnaK'', from ''Shewanella'' sp. AC10 ([http://partsregistry.org/Part:BBa_K538002 BBa_K538002]); ''CspA'', from ''Polaribacter irgensii'' ([http://partsregistry.org/Part:BBa_K538003 BBa_K538003]); and ''CspC'', also from ''Polaribacter irgensii'' ([http://partsregistry.org/Part:BBa_K538004 BBa_K538004]). GeneArt synthesized these parts for us ''de novo'', from sequences that were taken from online repositories and recoded for compatibility with assembly standards.
 ==Composite Parts==
-The composite parts we submitted to the registry are either construction intermediates or finalized parts. The construction intermediates consist of all possible combinations of our selected promoters ([http://partsregistry.org/Part:BBa_R0010 BBa_R0010] and [http://partsregistry.org/Part:BBa_K206000 BBa_K206000]) and RBS ([http://partsregistry.org/Part:BBa_B0034 BBa_B0034]), and all combinations of that same RBS with our coding regions ([http://partsregistry.org/Part:BBa_K538000 BBa_K538000] through [http://partsregistry.org/Part:BBa_K538004 BBa_K538004]). Note that the promoter + RBS parts contain no bricks that weren't already in the registry. The finalized parts all comprise a promoter, an RBS and a coding region. They are made either by appending a coding region to the construction intermediates containing a promoter and RBS, or by prepending a promoter to the construction intermediates containing an RBS and a coding region. Note that none of them contain a terminator; we have considered appending [http://partsregistry.org/Part:BBa_KB0014 BBa_B0014] to them, but the tightly constrained time we had for our project, and what little of it remained after sorting out (part of) the problems with assembling BioBricks, caused us to decide against this and relying instead on the terminator sequence in the standard plasmid backbones.
+The composite parts we submitted to the registry are either construction intermediates or finalized parts. The construction intermediates consist of all possible combinations of our selected promoters ([http://partsregistry.org/Part:BBa_R0010 BBa_R0010] and [http://partsregistry.org/Part:BBa_K206000 BBa_K206000]) and RBS ([http://partsregistry.org/Part:BBa_B0034 BBa_B0034]), and all combinations of that same RBS with our coding regions ([http://partsregistry.org/Part:BBa_K538000 BBa_K538000] through [http://partsregistry.org/Part:BBa_K538004 BBa_K538004]). Note that the promoter + RBS parts contain no bricks that weren't already in the registry.
+<br><br>
+The finalized parts all comprise a promoter, an RBS and a coding region. They are made either by appending a coding region to the construction intermediates containing a promoter and RBS, or by prepending a promoter to the construction intermediates containing an RBS and a coding region. An additional four final constructs are designed as 'operons' comprising Cpn10 and Cpn60. They are made by appending either the RBS + Cpn10 or the RBS + Cpn60 construction intermediates to the finalized parts that contain the other.
+<br><br>
+None of these bricks contain a terminator sequence; we have considered appending [http://partsregistry.org/Part:BBa_KB0014 BBa_B0014] to them, but the tightly constrained time we had for our project, and what little of it remained after sorting out (part of) the problems with assembling BioBricks, caused us to decide against this and relying instead on the terminator sequence in the standard plasmid backbones.
 ==Registry Submissions==
-All parts we submitted to the registry are listed in the table below. The links BBa_* links will take you to their respective pages on the parts registry. To view their information on this wiki, refer to our [[Team:Amsterdam/BioBricks/Basic_Parts | basic]] and [[Team:Amsterdam/BioBricks/Composite_Parts | composite]] part pages instead. Our newly synthesized chaperone genes (basic parts) are labelled K5380##. Finalized parts are labelled K5381## or K5382## depending on their promoter: 1## for parts containing pLacI, 2## for parts containing pBAD. Construction intermediates are labelled S######, their number being assigned automatically by the registry.
+All parts we submitted to the registry are listed in the table below. The BBa_* links will take you to their respective pages on the parts registry. To view their information on this wiki, refer to our [[Team:Amsterdam/Biobricks/Basic_Parts | basic]] and [[Team:Amsterdam/Biobricks/Composite_Parts | composite]] part pages instead. Our newly synthesized chaperone genes (basic parts) are labelled K5380##. Construction intermediates are labelled K5381##. Finalized CryoBricks are labelled K5382## or K5383## depending on their promoter: 2## for parts containing pLacI, 3## for parts containing pBAD.
+<br><br>
 <groupparts>iGEM011 Amsterdam</groupparts>
+<br><br>
 {{:Team:Amsterdam/Footer}}

Team:Amsterdam/Biobricks/Overview

From 2011.igem.org