Team:Washington/Magnetosomes/Parts

From 2011.igem.org

(Difference between revisions)
 
(14 intermediate revisions not shown)
Line 4: Line 4:
<center><big><big><big><big>'''iGEM Toolkits: Parts Submitted'''</big></big></big></big></center><br><br>
<center><big><big><big><big>'''iGEM Toolkits: Parts Submitted'''</big></big></big></big></center><br><br>
-
iGem Toolkits: submitted a total twenty-two parts to the registry:  
+
The iGEM toolkits group submitted a total twenty-two parts to the registry:  
-
*10 magnetosome gene-groups,
+
* 10 magnetosome gene groups from <i>mamAB</i> operon
-
*2 mam gene-sfGFP fusions,
+
* 3 superassemblies of the <i>mamAB</i> operon from the set of 10 gene groups
-
*3 parts of the essential magnetosome gene- assembly, and  
+
* 2 <i>sfGFP-mamK</i> and <i>sfGFP-mamI</i> gene fusions
-
*5 pGA vectors.
+
* 5 Gibson Assembly (pGA) vectors
-
 
+
<br/>
-
==Magnetosome Toolkit Favorite Parts==
+
=='''Magnetosome Toolkit Favorite Parts'''==
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015 '''sfGFP_mamK_pGA1C3''']
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015 '''sfGFP_mamK_pGA1C3''']
-
This part consists of mamK gene from Magnetospirillum magneticum strain AMB-1, sfGFP in the backbone of pGA1C3. mamK was previously reported for its importance proper magnetosome chain organization in magnetic bacteria; it is bacterial actin-like cytoskeleton protein required for proper alignment of the magnetosomes in a chain.
+
This part consists of the <i>mamK</i> gene from <i>Magnetospirillum magneticum</i> strain AMB-1, fused to superfolder <i>gfp</i> on pGA1C3. MamK has been reported to be essential for proper magnetosome formation in magnetotactic bacteria; its bacterial actin-like cytoskeleton protein is required for proper alignment of the magnetosomes in a chain. Beyond magnetosome alignment, the MamK filament could act as a scaffold for protein localization or to alter cell morphology.
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3''']
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3''']
-
This part consists of mamI gene from Magnetospirillum magneticum strain AMB-1, sfGFP in the backbone of pGA1C3. MamI is a membrane-localized protein that localizes magnetic vesicles to the surface of cells, thus forming characteristic magnetosome chains.
+
This part consists of the <i>mamI</i> gene from <i>Magnetospirillum magneticum</i> strain AMB-1, fused to  superfolder <i>gfp</i> on pGA1C3. MamI is a membrane-localized protein that is essential for magnetosome vesicle formation, and is also known to bind the MamK filament. Since it localizes to the membrane, MamI may be useful in maximizing the flux of biosynthetic pathways as a membrane-linker protein.
 +
 
 +
 
 +
=='''The Gibson Assembly Toolkit'''==
 +
 
 +
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010 '''pGA1A3_pLacGFP''']
 +
 
 +
This is a high copy plasmid backbone (replication origin pMB1) that confers ampicillin resistance. It has an insert with a LacI-repressible promoter driving GFP expression. It is identical to pSB1A3 except for its bglBrick prefix and suffix, and is optimized for Gibson Assembly.
 +
 
 +
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011 '''pGA1C3_pLacGFP''']
 +
 
 +
This is a high copy plasmid backbone (replication origin pMB1) that confers chloramphenicol resistance. It has an insert with a LacI-repressible promoter driving GFP expression. It is identical to pSB1C3 except for its bglBrick prefix and suffix, and is optimized for Gibson Assembly.
 +
 
 +
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014 '''pGA3K3_pLacGFP''']
-
==The Gibson Assembly Toolkit==
+
This is a medium copy plasmid backbone (replication origin p15A) that confers kanamycin resistance. It has an insert with a LacI-repressible promoter driving GFP expression. pGA3K3 is identical to pSB3K3 except for its bglBrick prefix and suffix, and is optimized for Gibson Assembly.
 +
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012 '''pGA4C5_pLacGFP''']
 +
This is a low copy plasmid backbone (replication origin pSC101) that confers chloramphenicol resistance. It has an insert with a LacI-repressible promoter driving GFP expression. It is identical to pSB4C5 except for its bglBrick prefix and suffix, and is optimized for Gibson Assembly.
 +
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013 '''pGA4A5_pLacGFP''']
-
{| class="wikitable"
+
This is a low copy plasmid backbone (replication origin pSC101) that confers ampicillin resistance. It has an insert with a LacI-repressible promoter driving GFP expression. It is identical to pSB4A5 except for its bglBrick prefix and suffix, and is optimized for Gibson Assembly. It is also notable that though we searched in multiple BioBrick distributions from different years, we could not find any that could be sequence-verified as pSB4A5 (the Vf2 sequence reads all suggested pSB1A2). We then generated pGA4A5 from pGA4C5 using the ampicillin cassette from pSB1A3.
-
|-
+
-
! Gene
+
-
! AMB Number
+
-
! Cluster Membership
+
-
! Member of 28 genes list? (specific*/related**)
+
-
! Function Summary (Vesicle chain formation, and/or biomineralization)
+
-
! Gene Function
+
-
|-
+
-
| mamH
+
-
| amb0961
+
-
| mamAB
+
-
| Related
+
-
|
+
-
|
+
-
|-
+
-
| mamI
+
-
| amb0962
+
-
| mamAB
+
-
| Specific
+
-
| Vesicle, (Chain Formation?)
+
-
| >berkeley 2010: Loss causes no membrane formation, is localized onto chains
+
-
|-
+
-
| mamE
+
-
| amb0963
+
-
| mamAB; mam Islet
+
-
| Related
+
-
|
+
-
| >Membrane-bound serine protease required for magnetite formation; might control the localization of other magnetosome proteins
+
-
|-
+
-
| mamJ
+
-
| amb0964
+
-
| mamAB; mam Islet
+
-
| Specific
+
-
| Chain Formation
+
-
| >Proper magnetosome chain organization/assembly
+
-
|-
+
-
| mamK
+
-
| amb0965
+
-
| mamAB; mam Islet
+
-
| Related
+
-
| Chain Formation
+
-
| >required for proper magnetosome chain organization; *bacterial actin-like cytoskeleton protein required for proper alignment of the magnetosomes in a chain, shown to localize the mamI
+
-
|-
+
-
| mamL
+
-
| amb0966
+
-
| mamAB; mam Islet
+
-
| Specific
+
-
| Vesicle, biomineralization
+
-
| >berkely 2010: Crucial to mangneosome membrane creation, shown to be spread across the cell membrane and sometimes forms lines
+
-
|-
+
-
| mamM
+
-
| amb0967
+
-
| mamAB
+
-
| Related
+
-
|
+
-
| >biomineralization, involved in iron transport, magnetite nucleation, or establishement of the proper chemical enviornment for magnetite synthesis in the magnetosome
+
-
|-
+
-
| mamN
+
-
| amb0968
+
-
| mamAB
+
-
| Related
+
-
|
+
-
| >biomineralization, involved in iron transport, magnetite nucleation, or establishement of the proper chemical enviornment for magnetite synthesis in the magnetosome
+
-
|-
+
-
| mamO
+
-
| amb0969
+
-
| mamAB
+
-
| Related
+
-
|
+
-
| >biomineralization, involved in iron transport, magnetite nucleation, or establishement of the proper chemical enviornment for magnetite synthesis in the magnetosome
+
-
|- 
+
-
| mamP
+
-
| amb0970
+
-
| mamAB
+
-
| Related
+
-
| Biomineralization
+
-
| >berkeley 2010: loss causes weak magnetic response, with large but fewer crystals
+
-
|-
+
-
| mamA
+
-
| amb0971
+
-
| mamAB
+
-
| Related
+
-
|
+
-
| >Required for magnetosome activation; activation of vessicles
+
-
|-
+
-
| mamQ
+
-
| amb0972
+
-
| mamAB; mam Islet
+
-
| Related
+
-
|
+
-
| >ORF; formation/maintenance of magnetosome membranes
+
-
|-
+
-
| mamR
+
-
| amb0973
+
-
| mamAB
+
-
| Specific
+
-
| Chain formation, Biomineralization
+
-
| >ORF; plays a role in controlling both particle number and size of magnetite cyrstals
+
-
|-
+
-
| mamB
+
-
| amb0974
+
-
| mamAB
+
-
| Related
+
-
| Vesicle, Biomineralization
+
-
| >indirect role in magnetosome membrane invagination and biomineralization; magnetosome compartment formation
+
-
|-
+
-
| mamS
+
-
| amb0975
+
-
| mamAB
+
-
| Specific
+
-
|
+
-
|
+
-
|-
+
-
| mamT
+
-
| amb0976
+
-
| mamAB
+
-
| Specific
+
-
| Biomineralization
+
-
| >magnetite crystal growth; participates in different steps during magnetite synthesis
+
-
|-
+
-
| mamU
+
-
| amb0977
+
-
| mamAB
+
-
| Related
+
-
|
+
-
|
+
-
|-
+
-
| mamV
+
-
| amb0978
+
-
| mamAB
+
-
| N/A
+
-
|
+
-
|
+
-
|-
+
-
|}
+

Latest revision as of 00:11, 29 September 2011


iGEM Toolkits: Parts Submitted


The iGEM toolkits group submitted a total twenty-two parts to the registry:

  • 10 magnetosome gene groups from mamAB operon
  • 3 superassemblies of the mamAB operon from the set of 10 gene groups
  • 2 sfGFP-mamK and sfGFP-mamI gene fusions
  • 5 Gibson Assembly (pGA) vectors


Magnetosome Toolkit Favorite Parts

[http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015 sfGFP_mamK_pGA1C3]

This part consists of the mamK gene from Magnetospirillum magneticum strain AMB-1, fused to superfolder gfp on pGA1C3. MamK has been reported to be essential for proper magnetosome formation in magnetotactic bacteria; its bacterial actin-like cytoskeleton protein is required for proper alignment of the magnetosomes in a chain. Beyond magnetosome alignment, the MamK filament could act as a scaffold for protein localization or to alter cell morphology.

[http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 sfGFP_mamI_pGA1C3]

This part consists of the mamI gene from Magnetospirillum magneticum strain AMB-1, fused to superfolder gfp on pGA1C3. MamI is a membrane-localized protein that is essential for magnetosome vesicle formation, and is also known to bind the MamK filament. Since it localizes to the membrane, MamI may be useful in maximizing the flux of biosynthetic pathways as a membrane-linker protein.


The Gibson Assembly Toolkit

[http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010 pGA1A3_pLacGFP]

This is a high copy plasmid backbone (replication origin pMB1) that confers ampicillin resistance. It has an insert with a LacI-repressible promoter driving GFP expression. It is identical to pSB1A3 except for its bglBrick prefix and suffix, and is optimized for Gibson Assembly.

[http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011 pGA1C3_pLacGFP]

This is a high copy plasmid backbone (replication origin pMB1) that confers chloramphenicol resistance. It has an insert with a LacI-repressible promoter driving GFP expression. It is identical to pSB1C3 except for its bglBrick prefix and suffix, and is optimized for Gibson Assembly.

[http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014 pGA3K3_pLacGFP]

This is a medium copy plasmid backbone (replication origin p15A) that confers kanamycin resistance. It has an insert with a LacI-repressible promoter driving GFP expression. pGA3K3 is identical to pSB3K3 except for its bglBrick prefix and suffix, and is optimized for Gibson Assembly.

[http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012 pGA4C5_pLacGFP]

This is a low copy plasmid backbone (replication origin pSC101) that confers chloramphenicol resistance. It has an insert with a LacI-repressible promoter driving GFP expression. It is identical to pSB4C5 except for its bglBrick prefix and suffix, and is optimized for Gibson Assembly.

[http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013 pGA4A5_pLacGFP]

This is a low copy plasmid backbone (replication origin pSC101) that confers ampicillin resistance. It has an insert with a LacI-repressible promoter driving GFP expression. It is identical to pSB4A5 except for its bglBrick prefix and suffix, and is optimized for Gibson Assembly. It is also notable that though we searched in multiple BioBrick distributions from different years, we could not find any that could be sequence-verified as pSB4A5 (the Vf2 sequence reads all suggested pSB1A2). We then generated pGA4A5 from pGA4C5 using the ampicillin cassette from pSB1A3.

Retrieved from "http://2011.igem.org/Team:Washington/Magnetosomes/Parts"