Team:Cambridge/BioluminescenceLinks

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Rough notes: Bioluminescence

Emily's Section

Spectra:
- Spectral Emissions of different species - [http://jgp.rupress.org/content/48/1/95.full.pdf+html Different Species Spectra]
- Fluorescent Protein Spectra - [http://jcs.biologists.org/cgi/reprint/114/5/837 Spectra]
- Small amount of blue-shift - [http://pubs.acs.org/doi/pdfplus/10.1021/bi7015052 Blue Shift]
- More blue-shift - [http://www.conncoll.edu/ccacad/zimmer/GFP-ww/Research.html Blue Shift 2]
Metridia: (luciferase requires CBP Protein)
- Metridia luciferase link - http://www.ncbi.nlm.nih.gov/pubmed/18754048
- CBP link - http://www.ncbi.nlm.nih.gov/pubmed/18264586
- CBP amino acid sequence http://www.rsc.org/ej/PP/2008/b713109g.pdf
Firefly:
- Oxyluciferin reduction - http://www.ncbi.nlm.nih.gov/pubmed/19872330
- Luciferin Regenerating Enzyme (LRE) - [http://www.ncbi.nlm.nih.gov/pubmed/11457857 LRE] (in Photinus pyralis)
- Firefly luciferin reaction - http://pubs.acs.org/doi/pdf/10.1021/ja00529a051
- Light Emission Quanta - [http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WB5-4DXBGFJ-D5-1&_cdi=6701&_user=1495569&_pii=0003986160902083&_orig=search&_coverDate=05%2F31%2F1960&_sk=999119998&view=c&wchp=dGLbVzz-zSkzV&md5=f1b9d348749d1304c05f85d9290e3b90&ie=/sdarticle.pdf Spectral Emission and Quantum Yield of Firefly Bioluminescence]
  - One light quantum emitted for every luciferin molecule oxidized
- CoA stimulation - [http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B73G9-47G3TGV-1S9-1&_cdi=11521&_user=1495569&_pii=0006300258903810&_orig=search&_coverDate=12%2F31%2F1958&_sk=999729999&view=c&wchp=dGLbVzb-zSkzV&md5=4420b38ef24aba8ca23e0b8ce2b3a953&ie=/sdarticle.pdf CoA in Luminescence]
- D-cysteine powerfully inhibits E.Coli growth [http://www.ncbi.nlm.nih.gov/pubmed/11527960 D-cysteine]
Aequorin:
- Regeneration of Aequorin in Aequorea Aequorea jellyfish - http://www.nature.com/nature/journal/v256/n5514/pdf/256236a0.pdf
Bacteria:
- Bacterial luciferase reaction - [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC357244/?page=1 Bacterial Luciferin]
- Beetle luciferin - [http://www3.interscience.wiley.com/cgi-bin/fulltext/107615738/PDFSTART Putative Beetle Luciferin Synthesis]
- V. Fischeri Plasmid - [http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WSN-4C7WG76-M-1&_cdi=7051&_user=1495569&_pii=0092867483900636&_orig=search&_coverDate=03%2F31%2F1983&_sk=999679996&view=c&wchp=dGLzVlz-zSkWb&md5=97c3a918d59cbd913da5c00b6805deb9&ie=/sdarticle.pdf V. Fischeri Plasmid]
- KCal/Mol luciferin in Lightning Bugs - [http://www.springerlink.com/content/w184700gj8767ww7/fulltext.pdf Luciferin KCal/Mol]
- Photinus Pyralis (firefly) spectrum, 562nm - [http://jgp.rupress.org/content/48/1/95.full.pdf+html Reference]
- Different Coloured Firefly Luciferases - [http://peds.oxfordjournals.org/cgi/reprint/18/12/581 Colours]
Gaussia Princeps (copepod):
- GLuc - [http://aem.asm.org/cgi/content/abstract/71/7/3427 GLuc]
- 100 Times Brighter than P. Pyrilus!! - [http://www.nature.com/nmeth/journal/v3/n12/full/nmeth979.html So bright]
- GLuc expression in E. Coli [http://pubs.acs.org/doi/pdfplus/10.1021/ac025742k E.GLuc]

Theo's section

Self contained part for Photorhabdus luminescens lux operon: http://partsregistry.org/Part:BBa_J70008:Design
Firefly diagram from Emily's paper:

Fireflow luciferin normally emits at 560nm but at higher temperatures at 630nm
http://pubs.acs.org/doi/pdf/10.1021/bi00702a015 Kinetics
Mg2+ required
A nice background summary: http://irishmarinelife.com/bioluminescence-symbioses/
The guy who made the biobrick's logbook: http://openwetware.org/wiki/User:Spenser_Skates/Notebook/pTKX_luciferase_biobrick/2008/04/14

Vibrio

luxC = acyl coA reductase

Firefly

The awesome paper http://www.springerlink.com/content/67w1q80435537747/fulltext.pdf

Biobricks related to light

Luciferases=

Coelentrazine using
- [http://partsregistry.org/Part:BBa_J52008 Renilla luciferase]
Firefly luciferin using
- [http://partsregistry.org/Part:BBa_I712019 Firefly luciferase]
Produces all parts of pathway:
- [http://partsregistry.org/Part:BBa_J70008 Lux operon from photorhabdus]
Click beetle:
- [http://partsregistry.org/Part:BBa_J70005 Red]

Fluorescent proteins

Bill's section

[http://sciencelinks.jp/j-east/article/200514/000020051405A0424228.php Conversion of normal luciferin into firefly luciferin]
Don't use luciferinol, it r teh suckage
[http://jeb.biologists.org/cgi/reprint/137/1/39.pdf Glowing fish what?]
Some actual numbers on luciferin [http://pubs.acs.org/doi/abs/10.1021/bi060475o]
D-cysteine is bad for e-coli [http://www.jbc.org/content/276/44/40864.full]
luminaze - good for brighter and longer wavelength light [http://pubs.acs.org/doi/abs/10.1021/bi00327a026]

Will's section

[http://www.ncbi.nlm.nih.gov/pubmed/15162459 Kinetic analysis and modeling of firefly luciferase as a quantitative reporter gene in live mammalian cells.]

[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WB5-4DXBGFJ-D5&_user=1495569&_coverDate=05%2F31%2F1960&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000053194&_version=1&_urlVersion=0&_userid=1495569&md5=8d7118ece7966e711eb16425e94285cf "Spectral emission and quantum yield of firefly bioluminescence" One rxn=>one photon]

General Notes for emission estimation

Anja's section

[http://www.ncbi.nlm.nih.gov/pubmed/17540326 Paper on mutant luciferase with increased activity]
Aequorin wavelength= 469 nm
Low leakage rate
Does not disrupt cell functions/ devt.
Requires continual addition of luciferin
[http://pubs.acs.org/doi/pdfplus/10.1021/ac9007286 Dr Laura Rowe's Paper on Bioluminescent Proteins]
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-4KVXNDX-6&_user=1495569&_coverDate=10%2F02%2F2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1402310626&_rerunOrigin=google&_acct=C000053194&_version=1&_urlVersion=0&_userid=1495569&md5=9470d4cd213e5e5b263d357951485be8 Paper on Biosynthesis of Firefly D-Luciferin]
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6THS-45514JT-4&_user=1495569&_coverDate=03%2F25%2F2002&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1402284823&_rerunOrigin=google&_acct=C000053194&_version=1&_urlVersion=0&_userid=1495569&md5=25863faa508182606b6e59eee65333d5 Paper on L-Tryptophan in Biosynthesis of Sea Firefly Luciferase]

Peter's section

[http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.mi.42.100188.001055?cookieSet=1 Paper on various bacterial luciferase and luciferin synthesis pathways]

Ben's section

Flashlight fish symbiont luciferase genes have been sequenced but cannot be successfully expressed in E. Coli
Suggested application http://www.yankodesign.com/2010/05/28/illuminate-your-influenza/
The firefly luciferin regenerating enzyme is patented http://www.freepatentsonline.com/EP0825257.html
Firefly luciferin biosynthesis appears not to be known. Vibrio Ficheri Lux operon is known. Would VF luciferin work with other luciferases? http://www3.interscience.wiley.com/cgi-bin/fulltext/89014035/PDFSTART

L-luciferin can be oxidised to produce light but with half the efficiency http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1217473/

Paul's section

Precursor to luciferin: http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&N4=261858|ALDRICH&N5=SEARCH_CONCAT_PNO|BRAND_KEY&F=SPEC
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6THS-4HWX8NX-C&_user=1495569&_coverDate=02%2F13%2F2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1402624057&_rerunOrigin=google&_acct=C000053194&_version=1&_urlVersion=0&_userid=1495569&md5=b2ccca6fb4c15f90120534c45c40bc8e Construction of a new firefly bioluminescence system using l-luciferin as substrate]
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6W9V-4DYN47Y-NX&_user=1495569&_origUdi=B6T21-3XX6W2J-18&_fmt=high&_coverDate=08%2F01%2F1992&_rdoc=1&_orig=article&_acct=C000053194&_version=1&_urlVersion=0&_userid=1495569&md5=84b46718e73359df8c6aea608dde9f15 stuff to do with ATP in the cycle]
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6THS-4HWX8NX-C&_user=1495569&_coverDate=02%2F13%2F2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1402624057&_rerunOrigin=google&_acct=C000053194&_version=1&_urlVersion=0&_userid=1495569&md5=b2ccca6fb4c15f90120534c45c40bc8e Applications of luciferin biosynthesis: Bioluminescence assays for l-cysteine and luciferase]
Biobrick for the Firefly luciferase for Slovenia '07: http://partsregistry.org/Part:BBa_I712019:Design
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T39-46RN5P2-H&_user=1495569&_coverDate=07%2F10%2F2002&_rdoc=17&_fmt=high&_orig=browse&_srch=doc-info%28%23toc%234941%232002%23997059998%23338594%23FLA%23display%23Volume%29&_cdi=4941&_sort=d&_docanchor=&_ct=31&_acct=C000053194&_version=1&_urlVersion=0&_userid=1495569&md5=0522f6433170194d4a35ad67a99dab7f Molecular cloning and expression of the cDNAs encoding luciferin-regenerating enzyme from Luciola cruciata and Luciola lateralis]