Answers.Body: <p>The green protein is called GFP of 238 amino acid residues (26.9 kDa) and produced by:</p>
  
  <ol>
  <li>the jellyfish Aequorea victoria, It has a major excitation peak at a wavelength of 395 nm. </li>
  <li>the sea pansy, Renilla reniformis of 498 nm. </li>
  </ol>
  
  <p>However, the protein is widespread and not restricted to these species.</p>
  
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Answers.CreationDate: 2020-02-23T15:48:48.633Z
Answers.Text: Green Florescent Protein, thanks. Do you know the 'Ascension number' of the gene or where I can find the sequence?
Answers.UserDisplayName: TristanSC90
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Answers.Text: Looking up the sequence, I found this site: https://www.uniprot.org/uniprot/P42212 that had  one listing for this gene here: https://www.ebi.ac.uk/ena/data/view/M62654 so then I looked up "M62654" in the NIH's BLAST database to pull up a list of 100 results:   https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome    There were 5 from the jellyfish, one from a species Azotobacter vinelandii, and a listing for a synthetically derived version from E. coli. There were several related genes that were vectors, like a promotor vector at the end of the list
Answers.UserDisplayName: TristanSC90
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Answers.CreationDate: 2020-02-24T02:07:36.780Z
Answers.Text: There are also other versions of GFP (such as "enhanced GFP") that are more commonly used in the lab.
Answers.UserDisplayName: burger
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Answers.CreationDate: 2020-02-23T08:32:00.970Z
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Answers.UserDisplayName: M__
Answers.Body: <p>There appears to be a dinoflagellate with Luciferase and the diversity of their genes was studied in the Baltic, found described in an article here: <a href="https://www.tandfonline.com/doi/full/10.1080/09670262.2016.1160441" rel="nofollow noreferrer">https://www.tandfonline.com/doi/full/10.1080/09670262.2016.1160441</a></p>
  
  <p>This article by Smithsonian: <a href="https://ocean.si.edu/ocean-life/fish/bioluminescence" rel="nofollow noreferrer">https://ocean.si.edu/ocean-life/fish/bioluminescence</a> describes a lot of Luciferin metabolizing species in the oceans, saying that different species independently evolved the forms they use. It describes some of the systems like endosymbiotic bacteria, special tissue, and photo-proteins. </p>
  
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Answers.CreationDate: 2020-02-23T16:32:28.027Z
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Answers.UserDisplayName: TristanSC90
Answers.Body: <p>There are three processes wherein light is emitted.</p>
  
  <ul>
  <li><strong>Bioluminescence</strong>: a chemical reaction releases light. The enzyme that does this is luciferase, while its substrate is luciferin, a small molecule. There are half a dozen organisms that have analogous (evolved independently) enzymes and totally different substrates, such as fireflies, Alivibrio bacteria, diatomes, deep sea fish, some mushrooms etc. The <a href="https://en.wikipedia.org/wiki/Luciferin" rel="noreferrer">wiki article</a> has a list of these and their small molecules.</li>
  <li><strong>Fluorescence</strong>: light is absorbed by the molecule and is emitted at a lower energy (wider wavelength, redshifted). Green fluorescent protein of Aequorea victoria jellyfish is the classic example of this. It is excited with UV and emits green light. Here is <a href="https://michelanglo.sgc.ox.ac.uk/data/5bb431b4-e2b6-49ac-aef8-71370bec04e8" rel="noreferrer">an interactive model</a>, I threw together. Variants exists for biotech reasons that span the whole of the visible spectrum. Other species have a homologous beta barrel, such as corals (red).</li>
  <li><strong>Phosphorescence</strong>: light is absorbed by the molecule and emitted later.  Ignoring the picosecond delay in fluorescent small molecules (cf. fluorescent lifetime microscopy), this is exclusively a properties of lanthanide elements (e.g. Europium). Lathanide binding domains have been designed, but do no exist in nature.</li>
  </ul>
  
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Answers.CreationDate: 2020-02-23T16:05:27.823Z
Answers.Text: Thank you for classifying types of bioluminesence and connecting some species. I am wondering what the genes are so that I can search for the species. For example, many jellyfish, deep sea species like the lanternfish, and algae glow, and the cuddlefish utilizes chromatophores to change color. I dont think you mentioned fungus, any idea what kind of glow gene they have?
Answers.UserDisplayName: TristanSC90
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Answers.CreationDate: 2020-02-23T16:31:02.423Z
Answers.Text: Cuddlefish chromatophores are simply pigments, i.e. small molecules with a resonant structure but do not release the excited energy as a photon.
Answers.UserDisplayName: Matteo Ferla
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Answers.CreationDate: 2020-02-23T16:39:50.453Z
Answers.Text: Fungal bioluminescence was described fairly recently (https://advances.sciencemag.org/content/3/4/e1602847.full). There are two parts the enzyme and the pathway to synthesise the substrate (3-hydroxy hispidin). The pathway biosynthesis is quite clear, but https://pubs.rsc.org/en/content/articlelanding/2010/np/c004593d/unauth#!divAbstract discusses some enzymes. N. gardneri is not sequenced, but other funghi are.
Answers.UserDisplayName: Matteo Ferla
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Answers.CreationDate: 2020-02-23T16:43:01.807Z
Answers.Text: In terms of gene sequences. You'll just have to do a [search for luciferin](https://www.uniprot.org/uniprot/?query=luciferase&sort=score), which is a generic name. Although most may not be sequenced, eg. glow-worm genome.
Answers.UserDisplayName: Matteo Ferla
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Answers.Text: Right, I am figuring that out. How many species have been genomically evaluated, and just specifcially because they glow? rhetorical question) Especially because derivative molecules have already been innovated in labs, there isn't really a point. I think I was hoping that since it has been a few years and gene sequencing machines are easier to access, that more species would be on file with more data about their molecules and metabolism of the genes that regulate them.
Answers.UserDisplayName: TristanSC90
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Answers.Text: Well, it is not trivial finding the enzymes that encode a secondary metabolism pathway, so sequencing is not the discouraging step. In thermophilic bacteria they will be in the same operon and in fungi there will be some clustering, but elsewhere its horrid. Scientific effort goes into seeing what the small molecule substrate is and if it could be technologically useful. If it is, such as firefly (very bright) or bacterial (easily usable pathway in SynBio), it will get more attention.
Answers.UserDisplayName: Matteo Ferla
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Answers.CreationDate: 2020-02-23T09:37:44.257Z
Answers.LastActivityDate: 2020-02-23T09:37:44.257Z
Answers.UserDisplayName: Matteo Ferla
Body: <p>I know of the common green glow gene but I forgot the name and I also know that some algae glow blue. There are so many types of bioluminesent organisms, so I am wondering what species have which genes and what other genes are associated with their metabolism and the systems that regulate these genes.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-23T08:25:35.313Z
Comments.Text: Hi, I think this is better moved to se.biology
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-23T15:31:54.763Z
Comments.Text: I was hoping to compile a list of answers with genes and related species, or I could comment about the species after searching the BLAST database for each gene. Maybe someone would answer with a sequence that I could look up on the BLAST database. I need a review of discussion about genes and bioinformatics, and thought I would start with bioluminesence. Since some time has elapsed since I studied this, I was thinking more information has been developed about this topic, particularly Luciferin and related species. Answers shedding light on metabolism-related studies of genes are desired.
Comments.UserDisplayName: TristanSC90
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-24T13:14:38.643Z
Comments.Text: BLAST is a search algorithm, do you mean NCBI database? Would it make sense to reformulate the question as "how to find species with bioluminiscence and preferantially also parthways involved in the process?" - because that would have a good potential to have a decent bioinformatics answer. Note you can [edit] your question (and it's better than writing long comments)
Comments.UserDisplayName: Kamil S Jaron
Tags: <phylogenetics><phylogeny><gene><blast><systems-biology>
Title: What are the different kinds of bioluminescent genes?
ThreadText: # What are the different kinds of bioluminescent genes?
  
  (Asked by: username_0 on 2020-02-23)
  
  I know of the common green glow gene but I forgot the name and I also know that some algae glow blue. There are so many types of bioluminesent organisms, so I am wondering what species have which genes and what other genes are associated with their metabolism and the systems that regulate these genes.
  
  **Tags:** phylogenetics, phylogeny, gene, blast, systems-biology
  
  > **Comments:**
  > **username_1**: Hi, I think this is better moved to se.biology  
  > **username_0**: I was hoping to compile a list of answers with genes and related species, or I could comment about the species after searching the BLAST database for each gene. Maybe someone would answer with a sequence that I could look up on the BLAST database. I need a review of discussion about genes and bioinformatics, and thought I would start with bioluminesence. Since some time has elapsed since I studied this, I was thinking more information has been developed about this topic, particularly Luciferin and related species. Answers shedding light on metabolism-related studies of genes are desired.  
  > **username_2**: BLAST is a search algorithm, do you mean NCBI database? Would it make sense to reformulate the question as "how to find species with bioluminiscence and preferantially also parthways involved in the process?" - because that would have a good potential to have a decent bioinformatics answer. Note you can [edit] your question (and it's better than writing long comments)  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_4 on 2020-02-23. Score: 6 | Accepted answer
  
  There are three processes wherein light is emitted.
  
  * **Bioluminescence**: a chemical reaction releases light. The enzyme that does this is luciferase, while its substrate is luciferin, a small molecule. There are half a dozen organisms that have analogous (evolved independently) enzymes and totally different substrates, such as fireflies, Alivibrio bacteria, diatomes, deep sea fish, some mushrooms etc. The [wiki article](https://en.wikipedia.org/wiki/Luciferin) has a list of these and their small molecules.
  * **Fluorescence**: light is absorbed by the molecule and is emitted at a lower energy (wider wavelength, redshifted). Green fluorescent protein of Aequorea victoria jellyfish is the classic example of this. It is excited with UV and emits green light. Here is [an interactive model](https://michelanglo.sgc.ox.ac.uk/data/5bb431b4-e2b6-49ac-aef8-71370bec04e8), I threw together. Variants exists for biotech reasons that span the whole of the visible spectrum. Other species have a homologous beta barrel, such as corals (red).
  * **Phosphorescence**: light is absorbed by the molecule and emitted later. Ignoring the picosecond delay in fluorescent small molecules (cf. fluorescent lifetime microscopy), this is exclusively a properties of lanthanide elements (e.g. Europium). Lathanide binding domains have been designed, but do no exist in nature.
  
  > **Comments:**
  > **username_0**: Thank you for classifying types of bioluminesence and connecting some species. I am wondering what the genes are so that I can search for the species. For example, many jellyfish, deep sea species like the lanternfish, and algae glow, and the cuddlefish utilizes chromatophores to change color. I dont think you mentioned fungus, any idea what kind of glow gene they have?  
  > **username_4**: Cuddlefish chromatophores are simply pigments, i.e. small molecules with a resonant structure but do not release the excited energy as a photon.  
  > **username_4**: Fungal bioluminescence was described fairly recently (https://advances.sciencemag.org/content/3/4/e1602847.full). There are two parts the enzyme and the pathway to synthesise the substrate (3-hydroxy hispidin). The pathway biosynthesis is quite clear, but https://pubs.rsc.org/en/content/articlelanding/2010/np/c004593d/unauth#!divAbstract discusses some enzymes. N. gardneri is not sequenced, but other funghi are.  
  > **username_4**: In terms of gene sequences. You'll just have to do a [search for luciferin](https://www.uniprot.org/uniprot/?query=luciferase&sort=score), which is a generic name. Although most may not be sequenced, eg. glow-worm genome.  
  > **username_0**: Right, I am figuring that out. How many species have been genomically evaluated, and just specifcially because they glow? rhetorical question) Especially because derivative molecules have already been innovated in labs, there isn't really a point. I think I was hoping that since it has been a few years and gene sequencing machines are easier to access, that more species would be on file with more data about their molecules and metabolism of the genes that regulate them.  
  > **username_4**: Well, it is not trivial finding the enzymes that encode a secondary metabolism pathway, so sequencing is not the discouraging step. In thermophilic bacteria they will be in the same operon and in fungi there will be some clustering, but elsewhere its horrid. Scientific effort goes into seeing what the small molecule substrate is and if it could be technologically useful. If it is, such as firefly (very bright) or bacterial (easily usable pathway in SynBio), it will get more attention.  
  
  ---
  
  ### Answer by username_1 on 2020-02-23. Score: 2
  
  The green protein is called GFP of 238 amino acid residues (26.9 kDa) and produced by:
  
  1. the jellyfish Aequorea victoria, It has a major excitation peak at a wavelength of 395 nm.
  2. the sea pansy, Renilla reniformis of 498 nm.
  
  However, the protein is widespread and not restricted to these species.
  
  > **Comments:**
  > **username_0**: Green Florescent Protein, thanks. Do you know the 'Ascension number' of the gene or where I can find the sequence?  
  > **username_0**: Looking up the sequence, I found this site: https://www.uniprot.org/uniprot/P42212 that had  one listing for this gene here: https://www.ebi.ac.uk/ena/data/view/M62654 so then I looked up "M62654" in the NIH's BLAST database to pull up a list of 100 results:   https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome    There were 5 from the jellyfish, one from a species Azotobacter vinelandii, and a listing for a synthetically derived version from E. coli. There were several related genes that were vectors, like a promotor vector at the end of the list  
  > **username_3**: There are also other versions of GFP (such as "enhanced GFP") that are more commonly used in the lab.  
  
  ---
  
  ### Answer by username_0 on 2020-02-23. Score: 1
  
  There appears to be a dinoflagellate with Luciferase and the diversity of their genes was studied in the Baltic, found described in an article here: <https://www.tandfonline.com/doi/full/10.1080/09670262.2016.1160441>
  
  This article by Smithsonian: <https://ocean.si.edu/ocean-life/fish/bioluminescence> describes a lot of Luciferin metabolizing species in the oceans, saying that different species independently evolved the forms they use. It describes some of the systems like endosymbiotic bacteria, special tissue, and photo-proteins.
  
  
  ---
  
  