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.
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2$\begingroup$ Hi, I think this is better moved to se.biology $\endgroup$– M__ ♦Feb 23, 2020 at 8:25
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$\begingroup$ 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. $\endgroup$– TristanSC90Feb 23, 2020 at 15:31
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$\begingroup$ 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) $\endgroup$– Kamil S JaronFeb 24, 2020 at 13:14
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3 Answers
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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 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, 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.
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$\begingroup$ 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? $\endgroup$ Feb 23, 2020 at 16:05
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$\begingroup$ Cuddlefish chromatophores are simply pigments, i.e. small molecules with a resonant structure but do not release the excited energy as a photon. $\endgroup$ Feb 23, 2020 at 16:31
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1$\begingroup$ Fungal bioluminescence was described fairly recently (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 pubs.rsc.org/en/content/articlelanding/2010/np/c004593d/… discusses some enzymes. N. gardneri is not sequenced, but other funghi are. $\endgroup$ Feb 23, 2020 at 16:39
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1$\begingroup$ In terms of gene sequences. You'll just have to do a search for luciferin, which is a generic name. Although most may not be sequenced, eg. glow-worm genome. $\endgroup$ Feb 23, 2020 at 16:43
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$\begingroup$ 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. $\endgroup$ Feb 23, 2020 at 16:47
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The green protein is called GFP of 238 amino acid residues (26.9 kDa) and produced by:
- the jellyfish Aequorea victoria, It has a major excitation peak at a wavelength of 395 nm.
- the sea pansy, Renilla reniformis of 498 nm.
However, the protein is widespread and not restricted to these species.
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1$\begingroup$ Green Florescent Protein, thanks. Do you know the 'Ascension number' of the gene or where I can find the sequence? $\endgroup$ Feb 23, 2020 at 15:48
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1$\begingroup$ Looking up the sequence, I found this site: uniprot.org/uniprot/P42212 that had one listing for this gene here: 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: blast.ncbi.nlm.nih.gov/… 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 $\endgroup$ Feb 23, 2020 at 15:54
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1$\begingroup$ There are also other versions of GFP (such as "enhanced GFP") that are more commonly used in the lab. $\endgroup$– burgerFeb 24, 2020 at 2:07
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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.