Difference between revisions of "Methods"
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Here you can find a list of methods for working with ''Bacillus subtilis'': | Here you can find a list of methods for working with ''Bacillus subtilis'': | ||
| + | |||
| + | == Media == | ||
| + | * [[C minimal medium]] | ||
| + | * [[M9 minimal medium]] | ||
| + | * [[Spizizen minimal medium]] | ||
| + | |||
| + | == A collection of mutant strains == | ||
| + | * the complete mutant strain collection from the [http://www.sciencedirect.com/science/article/pii/S2405471216304471?via%3Dihub Koo et al.] paper is now available: get access [https://www.addgene.org/kits/grosslab-bsubtilis-collections/ here] | ||
| + | |||
| + | == Toolboxes for the work with ''B. subtilis'' == | ||
| + | * the biobrick box {{PubMed|24295448}} | ||
| + | * the biobrick box 2.0 {{PubMed|29118374}} | ||
| + | * a part toolbox to tune genetic expression {{PubMed|27402159}} | ||
==Analysis of protein-protein interactions== | ==Analysis of protein-protein interactions== | ||
| Line 7: | Line 20: | ||
* ''in vivo'' detection of [[protein-protein interactions]] using [[DivIVA]] and GFP {{PubMed|19698693}} | * ''in vivo'' detection of [[protein-protein interactions]] using [[DivIVA]] and GFP {{PubMed|19698693}} | ||
| + | |||
| + | ==Analysis of membrane proteins== | ||
| + | * application of a split green fluorescent protein reporter {{PubMed|22285978}} | ||
| + | |||
| + | == Antibodies == | ||
| + | * List of available [[Antibodies]] | ||
| + | |||
| + | == Protein expression == | ||
| + | * the LIKE system {{PubMed|23110498}} | ||
==Strain construction== | ==Strain construction== | ||
| − | * introduction of markerfree deletions: {{PubMed|20057169}} | + | * introduction of markerfree deletions: {{PubMed|26238998,24140578,23916947,23911571,22422839,20057169}} |
| − | + | * generation of markerfree mutations: {{PubMed|20134232,21542786,24282588}} | |
| − | * generation of markerfree mutations: {{PubMed|20134232}} | + | * an improved method for transformation: {{PubMed|24838881}} |
==RNA analysis== | ==RNA analysis== | ||
* Mechanical cell disruption and extraction of RNA from ''B. subtilis'': [[Media:SOP-RNA.pdf]] | * Mechanical cell disruption and extraction of RNA from ''B. subtilis'': [[Media:SOP-RNA.pdf]] | ||
| − | == | + | ==Genetic work with non-standard strains== |
* transformation of wild-type ''B. subtilis'' strains incl. NCIB3610: {{PubMed|20300532}} | * transformation of wild-type ''B. subtilis'' strains incl. NCIB3610: {{PubMed|20300532}} | ||
| + | * efficient electroporation of ''B. subtilis'' {{PubMed|22387342}} | ||
| + | * a novel transformation protocol for ''B. subtilis'' DB104 {{PubMed|22395911}} | ||
==General procedures== | ==General procedures== | ||
* Standard operation procedures ([[SOP]]s) of the SYSMO-BACELL consortium | * Standard operation procedures ([[SOP]]s) of the SYSMO-BACELL consortium | ||
| − | == | + | ==Microscopic techniques== |
* Live cell imaging of ''B. subtilis'' cells using automated time-lapse microscopy {{PubMed|21841760}} | * Live cell imaging of ''B. subtilis'' cells using automated time-lapse microscopy {{PubMed|21841760}} | ||
* Assay of gene expression dynamics using live cell imaging {{PubMed|22179594}} | * Assay of gene expression dynamics using live cell imaging {{PubMed|22179594}} | ||
| + | * Visualization and quantification of gene expression heterogeneity in growing microbial cells {{PubMed|23874729}} | ||
| + | * GFP variants specifically optimizd for use in ''B. subtilis'' {{PubMed|23956387}} | ||
| + | * Quantitative analysis of cell types by comparing microscoy images {{PubMed|25448819}} | ||
| + | * Semi-automated single cell analysis using membrane or DNA staining {{PubMed|27008090}} | ||
==Transposon mutagenesis== | ==Transposon mutagenesis== | ||
| Line 31: | Line 59: | ||
==Protein-DNA interactions== | ==Protein-DNA interactions== | ||
* ChAP-chip: A modified ChIP-chip protocol for the ''in vivo'' identification of binding sites of DNA-binding proteins {{PubMed|17932079}} | * ChAP-chip: A modified ChIP-chip protocol for the ''in vivo'' identification of binding sites of DNA-binding proteins {{PubMed|17932079}} | ||
| + | |||
| + | ==Genome engineering== | ||
| + | * generalized bacterial genome editing using mobile group II introns and Cre-lox {{PubMed|24002656}} | ||
| + | * genome engineering using a synthetic gene circuit {{PubMed|25552415}} | ||
| + | * Ordered Gene Assembly in Bacillus subtilis (OGAB) {{PubMed|25990947}} | ||
| + | * construction of a super-competent strain {{PubMed|26732353}} | ||
| + | * use of the CRISPR-Cas system {{PubMed|27260361,27255973,27238023,27342565}} | ||
| + | |||
| + | * A review on genome engineering: | ||
| + | <pubmed>23340847 </pubmed> | ||
| + | |||
| + | == Visual descriptions of methods for ''B. subtilis'' in the ''Journal of Visual Experimentation'' == | ||
| + | <pubmed> 24473333 24457605 24300024 24300445 22371091 20142799 21841760 </pubmed> | ||
==Key references== | ==Key references== | ||
| − | + | <pubmed>22179594 20057169 20134232 21542786 20300532 19698693 17932079 21841760 17994626 23956387 22285978,22113911 24002656 24282588 26238998 25990947 26732353</pubmed> | |
| − | <pubmed>20057169 20134232 21542786 20300532 19698693 17932079 21841760 17994626 22113911 </pubmed> | ||
Latest revision as of 10:31, 10 November 2017
Here you can find a list of methods for working with Bacillus subtilis:
Contents
- 1 Media
- 2 A collection of mutant strains
- 3 Toolboxes for the work with B. subtilis
- 4 Analysis of protein-protein interactions
- 5 Analysis of membrane proteins
- 6 Antibodies
- 7 Protein expression
- 8 Strain construction
- 9 RNA analysis
- 10 Genetic work with non-standard strains
- 11 General procedures
- 12 Microscopic techniques
- 13 Transposon mutagenesis
- 14 Protein-DNA interactions
- 15 Genome engineering
- 16 Visual descriptions of methods for B. subtilis in the Journal of Visual Experimentation
- 17 Key references
Media
A collection of mutant strains
- the complete mutant strain collection from the Koo et al. paper is now available: get access here
Toolboxes for the work with B. subtilis
- the biobrick box PubMed
- the biobrick box 2.0 PubMed
- a part toolbox to tune genetic expression PubMed
Analysis of protein-protein interactions
- Bacterial Two Hybrid: BACTH
- SPINE: A method to detect in vivo protein-protein interactions
- in vivo detection of protein-protein interactions using DivIVA and GFP PubMed
Analysis of membrane proteins
- application of a split green fluorescent protein reporter PubMed
Antibodies
- List of available Antibodies
Protein expression
- the LIKE system PubMed
Strain construction
- introduction of markerfree deletions: PubMed
- generation of markerfree mutations: PubMed
- an improved method for transformation: PubMed
RNA analysis
- Mechanical cell disruption and extraction of RNA from B. subtilis: Media:SOP-RNA.pdf
Genetic work with non-standard strains
- transformation of wild-type B. subtilis strains incl. NCIB3610: PubMed
- efficient electroporation of B. subtilis PubMed
- a novel transformation protocol for B. subtilis DB104 PubMed
General procedures
- Standard operation procedures (SOPs) of the SYSMO-BACELL consortium
Microscopic techniques
- Live cell imaging of B. subtilis cells using automated time-lapse microscopy PubMed
- Assay of gene expression dynamics using live cell imaging PubMed
- Visualization and quantification of gene expression heterogeneity in growing microbial cells PubMed
- GFP variants specifically optimizd for use in B. subtilis PubMed
- Quantitative analysis of cell types by comparing microscoy images PubMed
- Semi-automated single cell analysis using membrane or DNA staining PubMed
Transposon mutagenesis
- mariner transposon mutagenesis for random inducible-expression insertions and transcriptional reporter fusion insertions PubMed
Protein-DNA interactions
- ChAP-chip: A modified ChIP-chip protocol for the in vivo identification of binding sites of DNA-binding proteins PubMed
Genome engineering
- generalized bacterial genome editing using mobile group II introns and Cre-lox PubMed
- genome engineering using a synthetic gene circuit PubMed
- Ordered Gene Assembly in Bacillus subtilis (OGAB) PubMed
- construction of a super-competent strain PubMed
- use of the CRISPR-Cas system PubMed
- A review on genome engineering:
Kevin M Esvelt, Harris H Wang
Genome-scale engineering for systems and synthetic biology.
Mol Syst Biol: 2013, 9;641
[PubMed:23340847]
[WorldCat.org]
[DOI]
(I p)
Visual descriptions of methods for B. subtilis in the Journal of Visual Experimentation
Lorena Stannek, Richard Egelkamp, Katrin Gunka, Fabian M Commichau
Monitoring intraspecies competition in a bacterial cell population by cocultivation of fluorescently labelled strains.
J Vis Exp: 2014, (83);e51196
[PubMed:24473333]
[WorldCat.org]
[DOI]
(I e)
Samantha M Desmarais, Felipe Cava, Miguel A de Pedro, Kerwyn Casey Huang
Isolation and preparation of bacterial cell walls for compositional analysis by ultra performance liquid chromatography.
J Vis Exp: 2014, (83);e51183
[PubMed:24457605]
[WorldCat.org]
[DOI]
(I e)
Ewa Król, Dirk-Jan Scheffers
FtsZ polymerization assays: simple protocols and considerations.
J Vis Exp: 2013, (81);e50844
[PubMed:24300445]
[WorldCat.org]
[DOI]
(I e)
Elizabeth Anne Shank
Using coculture to detect chemically mediated interspecies interactions.
J Vis Exp: 2013, (80);e50863
[PubMed:24300024]
[WorldCat.org]
[DOI]
(I e)
Juan C Garcia-Betancur, Ana Yepes, Johannes Schneider, Daniel Lopez
Single-cell analysis of Bacillus subtilis biofilms using fluorescence microscopy and flow cytometry.
J Vis Exp: 2012, (60);
[PubMed:22371091]
[WorldCat.org]
[DOI]
(I e)
Imke G de Jong, Katrin Beilharz, Oscar P Kuipers, Jan-Willem Veening
Live Cell Imaging of Bacillus subtilis and Streptococcus pneumoniae using Automated Time-lapse Microscopy.
J Vis Exp: 2011, (53);
[PubMed:21841760]
[WorldCat.org]
[DOI]
(I e)
Andrew D Klocko, Kaleena M Crafton, Brian W Walsh, Justin S Lenhart, Lyle A Simmons
Imaging mismatch repair and cellular responses to DNA damage in Bacillus subtilis.
J Vis Exp: 2010, (36);
[PubMed:20142799]
[WorldCat.org]
[DOI]
(I e)
Key references
Regine Rahmer, Kambiz Morabbi Heravi, Josef Altenbuchner
Construction of a Super-Competent Bacillus subtilis 168 Using the P mtlA -comKS Inducible Cassette.
Front Microbiol: 2015, 6;1431
[PubMed:26732353]
[WorldCat.org]
[DOI]
(P e)
Marian Wenzel, Josef Altenbuchner
Development of a markerless gene deletion system for Bacillus subtilis based on the mannose phosphoenolpyruvate-dependent phosphotransferase system.
Microbiology (Reading): 2015, 161(10);1942-1949
[PubMed:26238998]
[WorldCat.org]
[DOI]
(I p)
Kenji Tsuge, Yukari Sato, Yuka Kobayashi, Maiko Gondo, Masako Hasebe, Takashi Togashi, Masaru Tomita, Mitsuhiro Itaya
Method of preparing an equimolar DNA mixture for one-step DNA assembly of over 50 fragments.
Sci Rep: 2015, 5;10655
[PubMed:25990947]
[WorldCat.org]
[DOI]
(I e)
Ting Shi, Guanglu Wang, Zhiwen Wang, Jing Fu, Tao Chen, Xueming Zhao
Establishment of a markerless mutation delivery system in Bacillus subtilis stimulated by a double-strand break in the chromosome.
PLoS One: 2013, 8(11);e81370
[PubMed:24282588]
[WorldCat.org]
[DOI]
(I e)
Peter J Enyeart, Steven M Chirieleison, Mai N Dao, Jiri Perutka, Erik M Quandt, Jun Yao, Jacob T Whitt, Adrian T Keatinge-Clay, Alan M Lambowitz, Andrew D Ellington
Generalized bacterial genome editing using mobile group II introns and Cre-lox.
Mol Syst Biol: 2013, 9;685
[PubMed:24002656]
[WorldCat.org]
[DOI]
(I p)
Wout Overkamp, Katrin Beilharz, Ruud Detert Oude Weme, Ana Solopova, Harma Karsens, Ákos T Kovács, Jan Kok, Oscar P Kuipers, Jan-Willem Veening
Benchmarking various green fluorescent protein variants in Bacillus subtilis, Streptococcus pneumoniae, and Lactococcus lactis for live cell imaging.
Appl Environ Microbiol: 2013, 79(20);6481-90
[PubMed:23956387]
[WorldCat.org]
[DOI]
(I p)
Arturo Rodríguez-Banqueri, Lukasz Kowalczyk, Manuel Palacín, José Luis Vázquez-Ibar
Assessment of membrane protein expression and stability using a split green fluorescent protein reporter.
Anal Biochem: 2012, 423(1);7-14
[PubMed:22285978]
[WorldCat.org]
[DOI]
(I p)
Jonathan W Young, James C W Locke, Alphan Altinok, Nitzan Rosenfeld, Tigran Bacarian, Peter S Swain, Eric Mjolsness, Michael B Elowitz
Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy.
Nat Protoc: 2011, 7(1);80-8
[PubMed:22179594]
[WorldCat.org]
[DOI]
(I e)
Eric R Pozsgai, Kris M Blair, Daniel B Kearns
Modified mariner transposons for random inducible-expression insertions and transcriptional reporter fusion insertions in Bacillus subtilis.
Appl Environ Microbiol: 2012, 78(3);778-85
[PubMed:22113911]
[WorldCat.org]
[DOI]
(I p)
Imke G de Jong, Katrin Beilharz, Oscar P Kuipers, Jan-Willem Veening
Live Cell Imaging of Bacillus subtilis and Streptococcus pneumoniae using Automated Time-lapse Microscopy.
J Vis Exp: 2011, (53);
[PubMed:21841760]
[WorldCat.org]
[DOI]
(I e)
Chong Zhang, Xiaohui Zhang, Zhengying Yao, Yaping Lu, Fengxia Lu, Zhaoxin Lu
A new method for multiple gene inactivations in Bacillus subtilis 168, producing a strain free of selectable markers.
Can J Microbiol: 2011, 57(5);427-36
[PubMed:21542786]
[WorldCat.org]
[DOI]
(I p)
Reindert Nijland, J Grant Burgess, Jeff Errington, Jan-Willem Veening
Transformation of environmental Bacillus subtilis isolates by transiently inducing genetic competence.
PLoS One: 2010, 5(3);e9724
[PubMed:20300532]
[WorldCat.org]
[DOI]
(I e)
Haojie Yu, Xin Yan, Weiliang Shen, Yujia Shen, Ji Zhang, Shunpeng Li
Efficient and precise construction of markerless manipulations in the Bacillus subtilis genome.
J Microbiol Biotechnol: 2010, 20(1);45-53
[PubMed:20134232]
[WorldCat.org]
(P p)
Takuya Morimoto, Katsutoshi Ara, Katsuya Ozaki, Naotake Ogasawara
A new simple method to introduce marker-free deletions in the Bacillus subtilis genome.
Genes Genet Syst: 2009, 84(4);315-8
[PubMed:20057169]
[WorldCat.org]
[DOI]
(P p)
A Nicole Edwards, Jason D Fowlkes, Elizabeth T Owens, Robert F Standaert, Dale A Pelletier, Gregory B Hurst, Mitchel J Doktycz, Jennifer L Morrell-Falvey
An in vivo imaging-based assay for detecting protein interactions over a wide range of binding affinities.
Anal Biochem: 2009, 395(2);166-77
[PubMed:19698693]
[WorldCat.org]
[DOI]
(I p)
Christina Herzberg, Lope Andrés Flórez Weidinger, Bastian Dörrbecker, Sebastian Hübner, Jörg Stülke, Fabian M Commichau
SPINE: a method for the rapid detection and analysis of protein-protein interactions in vivo.
Proteomics: 2007, 7(22);4032-5
[PubMed:17994626]
[WorldCat.org]
[DOI]
(P p)
Shu Ishikawa, Yoshitoshi Ogura, Mika Yoshimura, Hajime Okumura, Eunha Cho, Yoshikazu Kawai, Ken Kurokawa, Taku Oshima, Naotake Ogasawara
Distribution of stable DnaA-binding sites on the Bacillus subtilis genome detected using a modified ChIP-chip method.
DNA Res: 2007, 14(4);155-68
[PubMed:17932079]
[WorldCat.org]
[DOI]
(P p)
