View source for Bacillus subtilis

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|valign='top' align='center' width=50px | {{Click || image=Part icon plasmid backbone.png | link={{PAGENAME}}#Plasmid backbones |width=30px | height=30px}} 
|valign='top' |'''[[{{PAGENAME}}#Plasmid backbones|Plasmid backbones]] [[Help:Plasmid backbones|(?)]]'''
|valign='top' align='center' width=50px | {{Click || image=Part icon regulatory.png | link={{PAGENAME}}#Constitutive promoters |width=30px | height=30px}} 
|valign='top'|'''[[{{PAGENAME}}#Constitutive promoters|Promoters]] [[Help:Promoters|(?)]]'''
|valign='top' align='center' width=50px | {{Click || image=Part icon rbs.png | link={{PAGENAME}}#Ribosome binding sites |width=30px | height=30px}} 
|valign='top' |'''[[{{PAGENAME}}#Ribosome binding sites|Ribosome binding sites]] [[Help:Ribosome Binding Sites|(?)]]'''
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|valign='top' align='center' width=50px | {{Click || image=Part icon cds.png | link={{PAGENAME}}#Protein coding sequences |width=30px | height=30px}} 
|valign='top' |'''[[{{PAGENAME}}#Protein coding sequences|Protein coding sequences]] [[Help:Protein coding sequences|(?)]]'''
|valign='top' align='center' width=50px | {{Click || image=Part icon dna.png | link={{PAGENAME}}#DNA parts |width=30px | height=30px}} 
|valign='top'|'''[[{{PAGENAME}}#DNA parts|DNA parts]] [[Help:DNA|(?)]]'''
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{{:{{PAGENAME}}/Help}}

==Plasmid backbone==

{{:Plasmid_backbones/Overview}}



The plasmids for ''B. Subtilis'' you can find in the registry are usually not built as standard registry plasmid so far. They come from third parties sources, that have been biobricked. Hence, these plasmid are often not silent.  Cloning inside often works in different conditions than with standard E. coli plasmids. You may need to optimize again your ligation conditions.

As a particular drawback we noticed using replicative plasmids, is that they are often subject to recombination. We invite you to read in detail the experiment done and the peer review page before choosing a plasmid and a strategy.

There are 2 main kind of plasmids for B. Subtilis:

* Replicative or also called episomal plasmids, are the same kind of plasmid with a replication origin and a resistance gene we are used to work with in E. Coli. These plasmids are often made to be multihost, so that they can be cloned using E. Coli and then the miniprep can be transformed into ''B. subtilis'' by starvation or electroporation. (Note that some replicative plasmids requires to be transformed into RecA+ E. Coli strains first before incorporating by starvation)

* Integration plasmids is the most used technique by specialist in B. subtilis. They are E. Coli plasmids with two homologous sequence with two fragments of a chromosomal gene of B. Subtilis, and a resistance cassette inserted in between. If your brick is cloned in between these two homologous region, the vector act as a shuttle that integrate your construct into the chromosome.


Note that you should check your backbone and biobrick part sequence whether more than one side can be cut by same enzyme.You should not use if it has more than one same restriction enzyme site. 

If you always see same bands in every gel images as different bp length from part page, you can try to transform your plasmid. Make sure that antibiotic you will use matches with which the backbone has..

And also if you see another band too, always at the same place and since first run. You can try transform your plasmid and check the viability when you exclude the possibility of contamination or any other things which can cause this problem in your lab. Another possibility could be that the part itself has already additional contaminated DNAs.


<parttable>bsubtilis_plasmid_backbone</parttable>

==Constitutive promoters==

{{:Promoters/Catalog/B._subtilis/Constitutive}}

==Positively regulated promoters==

{{:Promoters/Catalog/B._subtilis/Positive}}

==Repressible promoters==

{{:Promoters/Catalog/B._subtilis/Repressible}}

==Ribosome binding sites==

''B. subtilis'' have the same system of RBS than E. coli to drive its transcription. Hoever, the RBS sequences are not always compatible since ''B. subtilis'' ribsomomal RNA (rRNA) is slightly different in sequence compare to ''E. coli''.

In this list, you can find the most common RBSs usually use in B. subtilis. They are classified by strengh in a qualitative manner, since no strengh reference ranking have been established for ''B. subtilis'' yet. It is not obvious to transport directly the system for ''E. coli'' since we need to have a promoter that is exactly the same strengh as an E. coli one to make both scales comparable between the organism.

We can also notice that ''E. coli'' RBSs usually doesn't works for ''B. subtilis'', but it is not rare to find ''B. subtilis'' RBSs that works fine in ''E. coli'' (the SpoVg RBS for instance).

Please go in the description of each parts for more information.

<parttable>bsubtilis_rbs</parttable>

==Protein coding sequences==

{{:Protein coding sequences/Overview}}

<br />

'''Note of the codon availability in B. subtilis:''' B. subtilis is more codon tolerent than ''E. coli'', which means that you can generally express any protein from ''E. coli'' into ''B. subtilis'' without any problem. However, some proteins are said to be for subtilis for two reasons: One is because they comes from B. subtilis genome, (which means that you may have trouble in expressing them in ''E. coli'') or because they are made to trigger a certain effect in ''B. subtilis'' (for instance kill it).


<parttable>bsubtilis_protein_coding_sequence</parttable>

<!-- To include a part in this table, include the categories "//chassis/prokaryote/bsubtilis" set the part type to Coding under the Hard Information tab of the part. -->

==DNA parts for building integration vector==

Any ''E. coli'' plasmid can be converted into an integration vector if one add two pieces of a a gene sequence that is homologous to a gene into ''B. subtilis'' genes, and an antibiotic resistance cassette or other screening method.
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{{:DNA/Chromosomal_integration/{{PAGENAME}}/Overview}}

<parttable>bsubtilis_DNA</parttable>

==References==

{{:{{PAGENAME}}/References}}

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