Team:Washington/Magnetosomes/Parts

From 2011.igem.org

(Difference between revisions)

Revision as of 00:52, 28 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, its 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.

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

@@ Line 14: / Line 14: @@
 [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015 '''sfGFP_mamK_pGA1C3''']
-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 was previously reported to be essential for proper magnetosome chain alignment in magnetotactic bacteria; its bacterial actin-like cytoskeleton protein is required for proper alignment of the magnetosomes in a chain. Beyond magnetosome alignment, its filament could act as a scaffold for protein localization or to alter cell morphology.
+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, its 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 <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 known to also bind the MamK filament.
+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'''==