Difference between revisions of "Part:BBa K343001"
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<partinfo>BBa_K343001 short</partinfo> | <partinfo>BBa_K343001 short</partinfo> | ||
| − | This coding region encodes a beta-carotene | + | This coding region encodes a beta-carotene 15,15'-monooxygenase. |
| + | |||
| + | =Beta-carotene monooxygenase= | ||
| + | |||
| + | β,β-carotene-15,15′-monooxygenase is an enzyme that cleaves beta-carotene into two molecules of retinal, via the following reaction: Beta-carotene + O(2) <=> 2 retinal [https://parts.igem.org/Part:BBa_K343001#References [1]]. | ||
| + | |||
| + | Beta-carotene monooxygenase plays an important role in animal vision, as retinal forms the chemical basis for vision in animals [https://parts.igem.org/Part:BBa_K343001#References [2]]. Animals cannot synthesize retinal ''de novo'' and thus relies on beta-carotene monooxygenase to transform carotenoids (beta-carotene, alpha-carotene, gamma-carotene, and beta-cryptoxanthin) into retinal [https://parts.igem.org/Part:BBa_K343001#References [3]]. | ||
| + | |||
| + | Here we present a BioBrick containing the gene encoding this enzyme, and show that it produces retinal both when beta-carotene is added directly to bacteria containing this BioBrick; and in bacteria double transformed with this BioBrick and the [https://parts.igem.org/Part:BBa_K274210 Cambridge 2009 BBa_K274210] (CrtEBIY under constitutive promoter) BioBrick [https://parts.igem.org/Part:BBa_K343001#References [4]] which produces beta-carotene ''in vivo''. | ||
| + | |||
| + | ==Background== | ||
| + | |||
| + | [[Image:SDU-Denmark-2010-retinal-synthesis.gif|200px|thumb|right|Retinal synthesis pathway]] | ||
| + | |||
| + | Only two mechanisms for collecting light energy and converting it into chemical energy have been found in nature so fare. The first mechanism depends upon photochemical reaction centers (a multisubunit protein complex containing chlorophylls or bacteriochlorophylls, in which light energy is transduced into redox chemistry). The second mechanism uses rhodopsins, retinal-binding proteins that respond to light stimuli [https://parts.igem.org/Part:BBa_K343001#References [5]]. | ||
| + | |||
| + | The latter mechanism is found extensively througout nature, which has been speculated to be because of the ease, with which this system works; lateral transfer of rhodopsin-based photosystems requires only the genes encoding the rhodopsin apoprotein and a carotenoid oxygenase that produces retinal [https://parts.igem.org/Part:BBa_K343001#References [5]]. | ||
| + | |||
| + | The use of rhodopsin photosystems could be of great use in synthetic biology, but this also requires a retinal-forming brick, which we present here. | ||
| + | |||
| + | ===Beta-carotene monooxygenase gene=== | ||
| + | |||
| + | The beta-carotene monooxygenase gene (also called "neither inactivation nor afterpotential B" or ''NinaB'' for short) was cloned from ''Drosophila melanogaster'' cDNA [https://parts.igem.org/Part:BBa_K343001#References [7]]. This gene was the first beta-carotene monooxygenase to be molecularly identified and studied for its function [https://parts.igem.org/Part:BBa_K343001#References [8]]. Formerly, this enzyme has been called beta-caroten dioxygenase, but it is now known that only one atom of the dioxygen is incorporated into retinal, hence the name change [https://parts.igem.org/Part:BBa_K343001#References [9]]. | ||
| + | |||
| + | The enzyme requires Fe(II) and bile salts as co-factors. In the presence of FeSO4/ascorbate and using varying amounts of substrate of beta-caroten (800 pmol to 100 pmol), the apparent Km value of the enzyme was estimated to be 5 mM [https://parts.igem.org/Part:BBa_K343001#References [8]]. | ||
| + | |||
| + | β,β-carotene-15,15′-monooxygenase cleaves beta-carotene into two molecules of retinal, via the following reaction: Beta-carotene + O(2) <=> 2 retinal (1). | ||
| + | |||
| + | The reaction proceeds in three stages, epoxidation of the 15,15′-double bond, hydration of the double bond leading to ring opening, and oxidative cleavage of the diol formed [https://parts.igem.org/Part:BBa_K343001#References [9]]. | ||
| + | |||
| + | ====Protein structure==== | ||
| + | |||
| + | The protein has a calculated molecular weight of 69.94 kilodaltons. The protein structure of beta-carotene monooxygenase is not known. | ||
| + | |||
| + | ===Retinal=== | ||
| + | |||
| + | [[Image:SDU-Denmark-2010-all-trans-retinal.png|130px|thumb|right|Retinal]] | ||
| + | |||
| + | In the presence of beta-carotene, this BioBrick creates retinal. Retinal (also called retinaldehyde, vitamin A aldehyde or RAL) has the molecular formular C20H28O and weighs 284.43572 [g/mol]. C 84.45%, H 9.92%, O 5.63%. Melting point at 61-64 degrees celcius. The molecule can exist in four stereoisomeric forms [https://parts.igem.org/Part:BBa_K343001#References [6]]. | ||
| + | |||
| + | The apperence of the molecule is orange crystals (in petr ether). UV max is 373 nm (in cyclohexane). Soluble in ethanol, chloroform, cyclohexane, petr ether and oils [https://parts.igem.org/Part:BBa_K343001#References [6]]. | ||
| + | |||
| + | ==Composite part== | ||
| + | This part has been assembled into the [https://parts.igem.org/Part:BBa_K343006 K343006] ''ninaB'' generator. | ||
| + | |||
| + | ==Risk-assessment== | ||
| + | |||
| + | This risk assessment follows the [http://2010.igem.org/Team:SDU-Denmark/safety-c SDU-Denmark 2010 Risk Assessment Protocol]. A general risk assessment of our used ''E. coli'' strains can be found at our team [http://2010.igem.org/Team:SDU-Denmark/safety-c#Risk-assessment_2 homepage]. | ||
| + | |||
| + | ===General use=== | ||
| + | This BioBrick poses no treat to the welfare of people working with it, as long as this is done in at least a level 1 safety lab by trained people. No special care is needed when working with this BioBrick. | ||
| + | |||
| + | ===Potential pathogenicity=== | ||
| + | We do not recommend using this BioBrick for any type of system in humans or animals for the following reasons: | ||
| + | #Retinoic acid, which retinal can degrade into, can affect gene expression and function of almost any cell, including cells of the immune system; it also plays a fundamental role in cellular functions by activating nuclear receptors [https://parts.igem.org/Part:BBa_K343001#References [11]]. | ||
| + | #Vitamin A toxicity can lead to hepatic congestion and fibrosis [https://parts.igem.org/Part:BBa_K343001#References [12]]. | ||
| + | #Vitamin A and its derivatives have been implicated as chemopreventive and differentiating agents in a variety of cancers [https://parts.igem.org/Part:BBa_K343001#References [13]]. | ||
| + | |||
| + | These effects have been observed in humans. Please see references for more information. | ||
| + | |||
| + | ===Environmental impact=== | ||
| + | Beta-carotene monooxygenase is found in a wide variety of different bacteria, insects and animals [https://parts.igem.org/Part:BBa_K343001#References [5]]. As such, we would be cautious as to letting a system containing this BioBrick into the wild, since its function might conflict with existing systems. On the other hand, one might argue that since it's function is already available in nature, the function is widely available. | ||
| + | |||
| + | The product of the BioBrick, retinal, also plays an important function in nature and animals. For this reason we believe that the BioBrick could be used in controlled settings, but not in the wild. | ||
| + | |||
| + | ==Resources== | ||
| + | |||
| + | Datasheet for BioBrick: please refer to composite part [https://parts.igem.org/Part:BBa_K343006 K343006]. | ||
| + | |||
| + | ==References== | ||
| + | |||
| + | #ENZYME entry 1.14.99.36 [Internet]. [cited 2010 Oct 13];Available from: http://www.expasy.org/cgi-bin/nicezyme.pl?1.14.99.36 | ||
| + | #von Lintig J, Dreher A, Kiefer C, Wernet MF, Vogt K. Analysis of the blind Drosophila mutant ninaB identifies the gene encoding the key enzyme for vitamin A formation in vivo. Proceedings of the National Academy of Sciences of the United States of America. 2001 Jan 30;98(3):1130 -1135. | ||
| + | #Retinal - Wikipedia, the free encyclopedia [Internet]. [cited 2010 Oct 13];Available from: http://en.wikipedia.org/wiki/Retinal | ||
| + | #Part:BBa K274210 - parts.igem.org [Internet]. [cited 2010 Oct 13];Available from: https://parts.igem.org/Part:BBa_K274210 | ||
| + | #Bryant DA, Frigaard N. Prokaryotic photosynthesis and phototrophy illuminated. Trends Microbiol. 2006 Nov;14(11):488-496. | ||
| + | #Retinaldehyde - PubChem Public Chemical Database [Internet]. [cited 2010 Oct 13];Available from: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=1070 | ||
| + | #ninaB neither inactivation nor afterpotential B [Drosophila melanogaster] - Gene result [Internet]. [cited 2010 Oct 13];Available from: http://www.ncbi.nlm.nih.gov/gene/41678 | ||
| + | #von Lintig J, Vogt K. Filling the Gap in Vitamin A Research. Journal of Biological Chemistry. 2000 Apr 21;275(16):11915 -11920. | ||
| + | #ENZYME: 1.14.99.36 [Internet]. [cited 2010 Oct 13];Available from:http://www.genome.jp/dbget-bin/www_bget?ec:1.14.99.36 | ||
| + | #Kelley LA & Sternberg MJE. Protein structure prediction on the web: a case study using the Phyre server. Nature Protocols. 4, 363 - 371 (2009). | ||
| + | #Spiegl N, Didichenko S, McCaffery P, Langen H, Dahinden CA. Human basophils activated by mast cell-derived IL-3 express retinaldehyde dehydrogenase-II and produce the immunoregulatory mediator retinoic acid. Blood. 2008 Nov 1;112(9):3762-71. | ||
| + | #Russell RM. The vitamin A spectrum: from deficiency to toxicity. American Journal of Clinical Nutrition, Vol. 71, No. 4, 878-884, April 2000. | ||
| + | #Pasquali D, Thaller C, Eichele G. Abnormal level of retinoic acid in prostate cancer tissues. J Clin Endocrinol Metab. 1996 Jun;81(6):2186-91. | ||
| + | |||
| + | ==Contribution == | ||
| − | + | *'''Group:''' [https://2020.igem.org/Team:SCU-WestChina SCU-WestChina iGEM team 2020] | |
| − | + | *'''Author:''' Kang Wang | |
| + | *'''Summary:''' function addition | ||
| − | + | Genetic analysis of visual circuit activity in the control of aggressiveness in DrosophilaThe research on this part is also helpful to promote the progress of neuroscience and ethology. Visual perception does not play a major role in social suppression of aggression in Drosophila. For single-housed individuals lacking social experience prior to behavioral tests, visual perception decreases the level of aggressiveness. | |
| − | + | [[File:T--SCU-WestChina--improved_part5.png]] | |
| − | + | ||
| + | Chronic visual loss does not affect aggressiveness of single-housed flies that lack social experience prior to behavioral tests. | ||
| − | + | *Reference | |
| − | + | Ramin M, Domocos C, Slawaska-Eng D, Rao Y. Aggression and social experience: genetic analysis of visual circuit activity in the control of aggressiveness in Drosophila. Mol Brain. 2014 Aug 13;7:55. doi: 10.1186/s13041-014-0055-0. PMID: 25116850; PMCID: PMC4237967. | |
| − | + | ||
| − | + | ||
Latest revision as of 03:33, 28 October 2020
B-carotene monooxygenase, Produces retinal from B-carotene. ninaB gene from Drosophila.
This coding region encodes a beta-carotene 15,15'-monooxygenase.
Beta-carotene monooxygenase
β,β-carotene-15,15′-monooxygenase is an enzyme that cleaves beta-carotene into two molecules of retinal, via the following reaction: Beta-carotene + O(2) <=> 2 retinal [1].
Beta-carotene monooxygenase plays an important role in animal vision, as retinal forms the chemical basis for vision in animals [2]. Animals cannot synthesize retinal de novo and thus relies on beta-carotene monooxygenase to transform carotenoids (beta-carotene, alpha-carotene, gamma-carotene, and beta-cryptoxanthin) into retinal [3].
Here we present a BioBrick containing the gene encoding this enzyme, and show that it produces retinal both when beta-carotene is added directly to bacteria containing this BioBrick; and in bacteria double transformed with this BioBrick and the Cambridge 2009 BBa_K274210 (CrtEBIY under constitutive promoter) BioBrick [4] which produces beta-carotene in vivo.
Background
Only two mechanisms for collecting light energy and converting it into chemical energy have been found in nature so fare. The first mechanism depends upon photochemical reaction centers (a multisubunit protein complex containing chlorophylls or bacteriochlorophylls, in which light energy is transduced into redox chemistry). The second mechanism uses rhodopsins, retinal-binding proteins that respond to light stimuli [5].
The latter mechanism is found extensively througout nature, which has been speculated to be because of the ease, with which this system works; lateral transfer of rhodopsin-based photosystems requires only the genes encoding the rhodopsin apoprotein and a carotenoid oxygenase that produces retinal [5].
The use of rhodopsin photosystems could be of great use in synthetic biology, but this also requires a retinal-forming brick, which we present here.
Beta-carotene monooxygenase gene
The beta-carotene monooxygenase gene (also called "neither inactivation nor afterpotential B" or NinaB for short) was cloned from Drosophila melanogaster cDNA [7]. This gene was the first beta-carotene monooxygenase to be molecularly identified and studied for its function [8]. Formerly, this enzyme has been called beta-caroten dioxygenase, but it is now known that only one atom of the dioxygen is incorporated into retinal, hence the name change [9].
The enzyme requires Fe(II) and bile salts as co-factors. In the presence of FeSO4/ascorbate and using varying amounts of substrate of beta-caroten (800 pmol to 100 pmol), the apparent Km value of the enzyme was estimated to be 5 mM [8].
β,β-carotene-15,15′-monooxygenase cleaves beta-carotene into two molecules of retinal, via the following reaction: Beta-carotene + O(2) <=> 2 retinal (1).
The reaction proceeds in three stages, epoxidation of the 15,15′-double bond, hydration of the double bond leading to ring opening, and oxidative cleavage of the diol formed [9].
Protein structure
The protein has a calculated molecular weight of 69.94 kilodaltons. The protein structure of beta-carotene monooxygenase is not known.
Retinal
In the presence of beta-carotene, this BioBrick creates retinal. Retinal (also called retinaldehyde, vitamin A aldehyde or RAL) has the molecular formular C20H28O and weighs 284.43572 [g/mol]. C 84.45%, H 9.92%, O 5.63%. Melting point at 61-64 degrees celcius. The molecule can exist in four stereoisomeric forms [6].
The apperence of the molecule is orange crystals (in petr ether). UV max is 373 nm (in cyclohexane). Soluble in ethanol, chloroform, cyclohexane, petr ether and oils [6].
Composite part
This part has been assembled into the K343006 ninaB generator.
Risk-assessment
This risk assessment follows the [http://2010.igem.org/Team:SDU-Denmark/safety-c SDU-Denmark 2010 Risk Assessment Protocol]. A general risk assessment of our used E. coli strains can be found at our team [http://2010.igem.org/Team:SDU-Denmark/safety-c#Risk-assessment_2 homepage].
General use
This BioBrick poses no treat to the welfare of people working with it, as long as this is done in at least a level 1 safety lab by trained people. No special care is needed when working with this BioBrick.
Potential pathogenicity
We do not recommend using this BioBrick for any type of system in humans or animals for the following reasons:
- Retinoic acid, which retinal can degrade into, can affect gene expression and function of almost any cell, including cells of the immune system; it also plays a fundamental role in cellular functions by activating nuclear receptors [11].
- Vitamin A toxicity can lead to hepatic congestion and fibrosis [12].
- Vitamin A and its derivatives have been implicated as chemopreventive and differentiating agents in a variety of cancers [13].
These effects have been observed in humans. Please see references for more information.
Environmental impact
Beta-carotene monooxygenase is found in a wide variety of different bacteria, insects and animals [5]. As such, we would be cautious as to letting a system containing this BioBrick into the wild, since its function might conflict with existing systems. On the other hand, one might argue that since it's function is already available in nature, the function is widely available.
The product of the BioBrick, retinal, also plays an important function in nature and animals. For this reason we believe that the BioBrick could be used in controlled settings, but not in the wild.
Resources
Datasheet for BioBrick: please refer to composite part K343006.
References
- ENZYME entry 1.14.99.36 [Internet]. [cited 2010 Oct 13];Available from: http://www.expasy.org/cgi-bin/nicezyme.pl?1.14.99.36
- von Lintig J, Dreher A, Kiefer C, Wernet MF, Vogt K. Analysis of the blind Drosophila mutant ninaB identifies the gene encoding the key enzyme for vitamin A formation in vivo. Proceedings of the National Academy of Sciences of the United States of America. 2001 Jan 30;98(3):1130 -1135.
- Retinal - Wikipedia, the free encyclopedia [Internet]. [cited 2010 Oct 13];Available from: http://en.wikipedia.org/wiki/Retinal
- Part:BBa K274210 - parts.igem.org [Internet]. [cited 2010 Oct 13];Available from: https://parts.igem.org/Part:BBa_K274210
- Bryant DA, Frigaard N. Prokaryotic photosynthesis and phototrophy illuminated. Trends Microbiol. 2006 Nov;14(11):488-496.
- Retinaldehyde - PubChem Public Chemical Database [Internet]. [cited 2010 Oct 13];Available from: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=1070
- ninaB neither inactivation nor afterpotential B [Drosophila melanogaster] - Gene result [Internet]. [cited 2010 Oct 13];Available from: http://www.ncbi.nlm.nih.gov/gene/41678
- von Lintig J, Vogt K. Filling the Gap in Vitamin A Research. Journal of Biological Chemistry. 2000 Apr 21;275(16):11915 -11920.
- ENZYME: 1.14.99.36 [Internet]. [cited 2010 Oct 13];Available from:http://www.genome.jp/dbget-bin/www_bget?ec:1.14.99.36
- Kelley LA & Sternberg MJE. Protein structure prediction on the web: a case study using the Phyre server. Nature Protocols. 4, 363 - 371 (2009).
- Spiegl N, Didichenko S, McCaffery P, Langen H, Dahinden CA. Human basophils activated by mast cell-derived IL-3 express retinaldehyde dehydrogenase-II and produce the immunoregulatory mediator retinoic acid. Blood. 2008 Nov 1;112(9):3762-71.
- Russell RM. The vitamin A spectrum: from deficiency to toxicity. American Journal of Clinical Nutrition, Vol. 71, No. 4, 878-884, April 2000.
- Pasquali D, Thaller C, Eichele G. Abnormal level of retinoic acid in prostate cancer tissues. J Clin Endocrinol Metab. 1996 Jun;81(6):2186-91.
Contribution
- Group: SCU-WestChina iGEM team 2020
- Author: Kang Wang
- Summary: function addition
Genetic analysis of visual circuit activity in the control of aggressiveness in DrosophilaThe research on this part is also helpful to promote the progress of neuroscience and ethology. Visual perception does not play a major role in social suppression of aggression in Drosophila. For single-housed individuals lacking social experience prior to behavioral tests, visual perception decreases the level of aggressiveness.
Chronic visual loss does not affect aggressiveness of single-housed flies that lack social experience prior to behavioral tests.
- Reference
Ramin M, Domocos C, Slawaska-Eng D, Rao Y. Aggression and social experience: genetic analysis of visual circuit activity in the control of aggressiveness in Drosophila. Mol Brain. 2014 Aug 13;7:55. doi: 10.1186/s13041-014-0055-0. PMID: 25116850; PMCID: PMC4237967.