Team:Valencia/Parts

From 2012.igem.org

(Difference between revisions)
Line 10: Line 10:
<div id="HomeCenterCenter">
<div id="HomeCenterCenter">
<p align="justify">
<p align="justify">
-
<h2><b>psbAI promoter</b></h2>
+
<h2><b><i>psbAI</i> promoter</b></h2>
<br>
<br>
-
We have placed the strong psbAI promoter of Synechococcus elongatus into the Standard Biobrick, <a href="http://partsregistry.org/wiki/index.php/Part:pSB1C3" target="_blank">pSB1C3</a>, in order to create an assembly standard for this promoter and allow other users to use and assemble it together with other parts to create longer and more complex parts suitable to work in Cyanobacteria and photosynthetic organisms. You can find more information about standards <a href="http://partsregistry.org/Help:Standards/Assembly/RFC10" target="_blank">here</a>.
+
We have placed the strong <i>psbAI</i> promoter of <i>Synechococcus elongatus</i> PCC7942 into the Standard Biobrick, <a href="http://partsregistry.org/wiki/index.php/Part:pSB1C3" target="_blank">pSB1C3</a>, in order to create an assembly standard for this promoter and allow other users to assemble it together with other parts to create longer and more complex parts suitable to work in cyanobacteria and photosynthetic organisms. You can find more information about standards <a href="http://partsregistry.org/Help:Standards/Assembly/RFC10" target="_blank">here</a>.
<br><br>
<br><br>
<center>
<center>
Line 31: Line 31:
<br><br>
<br><br>
<h3><u>Descrption</u></h3>
<h3><u>Descrption</u></h3>
-
The psbAI gene of Synechococcus elongatus PCC 7942 is one of three psbA genes involved in the coding of a fundamental PSII reaction center protein: D1.  This family of genes is regulated distinctly in response to changes in the light environment resulting in an interchange of two different forms of the D1 protein.  The expression of psbAI is downregulated under high intensity light, while the other two members are induced. (Nair et al. 2001).
+
The <i>psbAI</i> gene of <i>Synechococcus elongatus</i> PCC 7942 is one of three <i>psbA</i> genes involved in the coding of a fundamental PSII reaction center protein: D1.  This family of genes is regulated distinctly in response to changes in the light environment resulting in an interchange of two different forms of the D1 protein.  The expression of <i>psbAI</i> is downregulated under high intensity light, while the other two members are induced. (Nair et al. 2001).
<br><br>
<br><br>
<h3><u>Function</u></h3>
<h3><u>Function</u></h3>
<br>
<br>
<img align="right" src="https://static.igem.org/mediawiki/2012/8/8f/Subpa2.png" width="310" height="210">
<img align="right" src="https://static.igem.org/mediawiki/2012/8/8f/Subpa2.png" width="310" height="210">
-
Cyanobacteria, as well as algae and higher plants, carry out oxygenic photosynthesis, which requires multiprotein complexes that driven by solar energy produce reducing power (NADPH) and chemical energy (ATP). In this system water is the source of electrons in reducing C02 to various organic compounds. The PSII is involved in the water oxidation reaction and the release of oxygen and its core is composed of two critical proteins D1 and D2, which coordinate the cofactors of light-driven charge separation (Andersson and Styring, 1991).  Due to the strong oxidative chemistry of the PSII, the D1 protein is subjected to constant photooxidation stress and therefore requires regular replacement to guarantee a steady-state level of D1 protein under different environmental conditions. Under low light growth, the rate of replenishment is 5h, while under intense illumination, the protein is replaced every 20 minutes (Tyystjärvi et al. 1994).  In cyanobacteria the three psbA genes that encode the D1 protein are under strict regulation to guarantee the proper functioning of the PSII.  In Synechococcus elongatus PCC7942 this three genes encode two distinct D1 protein isoforms: D1:1 being encoded by psbAI and D1:2 by psbAII and psbAIII (Golden et al. 1986).
+
Cyanobacteria, as well as algae and higher plants, carry out oxygenic photosynthesis, which requires multiprotein complexes that driven by solar energy produce reducing power (NADPH) and chemical energy (ATP). In this system water is the source of electrons in reducing C02 to various organic compounds. The PSII is involved in the water oxidation reaction and the release of oxygen and its core is composed of two critical proteins D1 and D2 (figure 1), which coordinate the cofactors of light-driven charge separation (Andersson and Styring, 1991).  Due to the strong oxidative chemistry of the PSII, the D1 protein is subjected to constant photooxidation stress and therefore requires regular replacement to guarantee a steady-state level of D1 protein under different environmental conditions. Under low light growth, the rate of replenishment is 5h, while under intense illumination, the protein is replaced every 20 minutes (Tyystjärvi et al. 1994).  In cyanobacteria the three <i>psbA</i> genes that encode the D1 protein are under strict regulation to guarantee the proper functioning of the PSII.  In <i>Synechococcus elongatus</i> PCC7942 this three genes encode two distinct D1 protein isoforms: D1:1 being encoded by <i>psbAI</i> and D1:2 by <i>psbAII</i> and <i>psbAIII</i> (Golden et al. 1986).
<br><br>
<br><br>
<center><img src="https://static.igem.org/mediawiki/2012/2/21/Subpa4.png" width="300" height="150"></center><br>
<center><img src="https://static.igem.org/mediawiki/2012/2/21/Subpa4.png" width="300" height="150"></center><br>
Line 42: Line 42:
<br><br>
<br><br>
<h3><u>Regulation</u></h3><br>
<h3><u>Regulation</u></h3><br>
-
One strategy of the psbA regulation is to replace the D1 protein under unstressed conditions with a different form when high-light intensity is detected. The other strategy is upon stress, to increase the turn-over of the same D1 protein produced under basic growth conditions (Mulo et al. 2009) (figure 2). The three psbA genes are regulated at both transcriptional and posttranscriptional levels. Under low light conditions (125 μE m-2 s-1) over 80% of the transcripts are from psbAI, however after high light conditions (750μE m-2 s-1) psbAII and psbAIII message levels increase (Bustos et al. 1991).
+
One strategy of the <i>psbA</i> regulation is to replace the D1 protein under unstressed conditions with a different form when high-light intensity is detected. The other strategy is upon stress, to increase the turn-over of the same D1 protein produced under basic growth conditions (Mulo et al. 2009) (figure 2). The three <i>psbA</i> genes are regulated at both transcriptional and posttranscriptional levels. Under low light conditions (125 μE m-2 s-1) over 80% of the transcripts are from <i>psbAI</i>, however after high light conditions (750μE m-2 s-1) <i>psbAII</i> and <i>psbAIII</i> message levels increase (Bustos et al. 1991).
<br><br>
<br><br>
-
<u>Regulation of the psbAI gene and functional elements of the psbAI promoter</u><br><br>
+
<u>Regulation of the <i>psbAI</i> gene and functional elements of the <i>psbAI</i> promoter</u><br><br>
-
One of the most crucial determinants of gene expression in cyanobacteria is the initiation of transcription, where several sigma factors are involved in promoter recognition (Mulo et al. 2009).  The psbAI promoter has characteristic -35 spaced elements from the E. coli σ70  promoter, but has an atypical -10bp element TCTCCT (Golden et al. 1986), which entails that this promoter doesn´t  work in E. coli (Schaefer and Golden, 1989) making it difficult to characterize it properly. The smallest psbAI functional promoter region comprises nucleotides -54 to +1, and one or more proteins bind specifically to the psbAI upstream region stimulating, rather than inactivating the transcription (+1 to + 43) (Nair et al. 2001), unlike typical σ70  promoters. A segment of approximately 20bp of the consensus -35 element has been shown to be implicated in both, promoter activation per se and light-responsive expression, this region is characterized by being AT-rich (Nair et al. 2001).  
+
One of the most crucial determinants of gene expression in cyanobacteria is the initiation of transcription, where several sigma factors are involved in promoter recognition (Mulo et al. 2009).  The <i>psbAI</i> promoter has characteristic -35 spaced elements from the E. coli σ70  promoter, but has an atypical -10bp element TCTCCT (Golden et al. 1986), which entails that this promoter doesn´t  work in <i>E. coli</i> (Schaefer and Golden, 1989) making it difficult to characterize it properly. The smallest <i>psbAI</i> functional promoter region comprises nucleotides -54 to +1, and one or more proteins bind specifically to the <i>psbAI</i> upstream region stimulating, rather than inactivating the transcription (+1 to + 43) (Nair et al. 2001), unlike typical σ70  promoters. A segment of approximately 20bp of the consensus -35 element has been shown to be implicated in both, promoter activation per se and light-responsive expression, this region is characterized by being AT-rich (Nair et al. 2001).  
<br><br>
<br><br>
<center><img src="https://static.igem.org/mediawiki/2012/d/d8/Subpa5.png" width="400" height="75"></center>
<center><img src="https://static.igem.org/mediawiki/2012/d/d8/Subpa5.png" width="400" height="75"></center>
<br>
<br>
<h3><u>Behaviour</u></h3><br>
<h3><u>Behaviour</u></h3><br>
-
Some studies show that psbAI transcript is actively destabilized when shift to high light (Kulkarni et al. 1992), but prolonged exposure of Synechococcus 7942 cells to high light leads to an increased accumulation of all psbA transcripts, including psbAI (Kulkarni and Golden, 1994). This is an electronic flow independent response implying a response to light rather than to redox changes (Tsinoremas et al. 1996). Extensive assays suggest that the psbAI promoter in S. elongatus is among the strongest in this organism (Andersson et al. 2000).
+
Some studies show that <i>psbAI</i> transcript is actively destabilized when shift to high light (Kulkarni et al. 1992), but prolonged exposure of <i>S. elongatus</i> PCC 7942 cells to high light leads to an increased accumulation of all <i>psbA</i> transcripts, including <i>psbAI</i> (Kulkarni and Golden, 1994). This is an electronic flow independent response implying a response to light rather than to redox changes (Tsinoremas et al. 1996). Extensive assays suggest that the <i>psbAI</i> promoter in <i>S. elongatus</i> is among the strongest in this organism (Andersson et al. 2000).
<br>
<br>
-
Gráficas y Northerns del paper (Blue and red Light....)
+
 
<br><br>
<br><br>
-
<h3><u>Using this part in S. elongatus</u></h3><br>
+
<h3><u>Using this part in <i>S. elongatus</i></u></h3><br>
-
If you would like to use this part in Synechococcus elongatus PCC7942 you should be aware that the transformation of S. elongatus is based on homologous recombination between two sites on the chromosome (neutral sites) that have been developed as cloning locus. Ectopic sequences can be homologous recombinant without any apparent aberrant phenotype (Clerico et al. 2007).<br>
+
If you would like to use this part in <i>Synechococcus elongatus</i> PCC7942 you should be aware that the transformation of <i>S. elongatus</i> is based on homologous recombination between two sites on the chromosome (neutral sites) that have been developed as cloning locus. Ectopic sequences can be homologous recombinant without any apparent aberrant phenotype (Clerico et al. 2007).<br>
-
Thus, to use this part you should cloned it within the S. elongatus neutral sites sequences to move it into the cyanobacterial chromosome.<br>
+
Thus, to use this part you should cloned it within the <i>S. elongatus</i> neutral sites sequences to move it into the cyanobacterial chromosome.<br>
-
When transforming, the selective marker and the part of interest flanked with the neutral site sequences are inserted into the neutral site of S. elongatus chromosome and the backbone is lost.<br>
+
When transforming, the selective marker and the part of interest flanked with the neutral site sequences are inserted into the neutral site of <i>S. elongatus</i> chromosome and the backbone is lost.<br>
-
To read more about techniques concerning site-directed mutagenesis in Cyanobacteria, please take a look at this paper.
+
To read more about techniques concerning site-directed mutagenesis in Cyanobacteria, please take a look at this paper
<br><br>
<br><br>
<h3><u>Using this part in other photosynthetic organisms</u></h3>
<h3><u>Using this part in other photosynthetic organisms</u></h3>
Line 64: Line 64:
<br><br>
<br><br>
<h3><u>Promoter source</u></h3><br>
<h3><u>Promoter source</u></h3><br>
-
We sincerely want to thank Prof. Susan Golden for providing us with a psbAI:luxABCDE fusion construct ready to use in Synechococcus elongatus PCC7942 and the appropriate protocols and papers to achieve our goal. Furthermore, her research on this promoter helped us to prepare a standard characterization report for the registry.<br>
+
We sincerely want to thank Prof. Susan Golden for providing us with a <i>psbAI:luxABCDE</i> fusion construct ready to use in <i>Synechococcus elongatus</i> PCC7942 and the appropriate protocols and papers to achieve our goal. Furthermore, her research on this promoter helped us to prepare a standard characterization report for the registry.<br>
-
The synthesis of the psbAI promoter for our Biobrick was carried out by Genscript (link). In the protocols page you will find the ligation protocol we followed to assemble our part into psb1C3.
+
The synthesis of the <i>psbAI</i> promoter for our Biobrick was carried out by Genscript. In the protocols page you will find the ligation protocol we followed to assemble our part into psb1C3.
<br><br><br>
<br><br><br>
<b>References</b>
<b>References</b>

Revision as of 21:28, 25 September 2012



Submitted Parts

psbAI promoter


We have placed the strong psbAI promoter of Synechococcus elongatus PCC7942 into the Standard Biobrick, pSB1C3, in order to create an assembly standard for this promoter and allow other users to assemble it together with other parts to create longer and more complex parts suitable to work in cyanobacteria and photosynthetic organisms. You can find more information about standards here.

<groupparts>iGEM012 Valencia</groupparts>
This section is dedicated to properly document this part so that any interested user can use it successfully without the need to search in primary literature.

Secuence


1   ggactagagg ctggatttag cgtcttctaa tccagtgtag acagtagttt tggctccgtt
61 gagcactgta gccttgggcg atcgctctaa acattacata aattcacaaa gttttcgtta
121 cataaaaata gtgtctactt agctaaaaat taagggtttt ttacaccttt ttgacagtta
181 atctcctagc ctaaaaagca agagttttta actaagactc ttgcccttta caacctcaag
241 atcgat


Descrption

The psbAI gene of Synechococcus elongatus PCC 7942 is one of three psbA genes involved in the coding of a fundamental PSII reaction center protein: D1. This family of genes is regulated distinctly in response to changes in the light environment resulting in an interchange of two different forms of the D1 protein. The expression of psbAI is downregulated under high intensity light, while the other two members are induced. (Nair et al. 2001).

Function


Cyanobacteria, as well as algae and higher plants, carry out oxygenic photosynthesis, which requires multiprotein complexes that driven by solar energy produce reducing power (NADPH) and chemical energy (ATP). In this system water is the source of electrons in reducing C02 to various organic compounds. The PSII is involved in the water oxidation reaction and the release of oxygen and its core is composed of two critical proteins D1 and D2 (figure 1), which coordinate the cofactors of light-driven charge separation (Andersson and Styring, 1991). Due to the strong oxidative chemistry of the PSII, the D1 protein is subjected to constant photooxidation stress and therefore requires regular replacement to guarantee a steady-state level of D1 protein under different environmental conditions. Under low light growth, the rate of replenishment is 5h, while under intense illumination, the protein is replaced every 20 minutes (Tyystjärvi et al. 1994). In cyanobacteria the three psbA genes that encode the D1 protein are under strict regulation to guarantee the proper functioning of the PSII. In Synechococcus elongatus PCC7942 this three genes encode two distinct D1 protein isoforms: D1:1 being encoded by psbAI and D1:2 by psbAII and psbAIII (Golden et al. 1986).


Figure: Simplified scheme of the PSII repair cycle (Mulo et al. 2009)


Regulation


One strategy of the psbA regulation is to replace the D1 protein under unstressed conditions with a different form when high-light intensity is detected. The other strategy is upon stress, to increase the turn-over of the same D1 protein produced under basic growth conditions (Mulo et al. 2009) (figure 2). The three psbA genes are regulated at both transcriptional and posttranscriptional levels. Under low light conditions (125 μE m-2 s-1) over 80% of the transcripts are from psbAI, however after high light conditions (750μE m-2 s-1) psbAII and psbAIII message levels increase (Bustos et al. 1991).

Regulation of the psbAI gene and functional elements of the psbAI promoter

One of the most crucial determinants of gene expression in cyanobacteria is the initiation of transcription, where several sigma factors are involved in promoter recognition (Mulo et al. 2009). The psbAI promoter has characteristic -35 spaced elements from the E. coli σ70 promoter, but has an atypical -10bp element TCTCCT (Golden et al. 1986), which entails that this promoter doesn´t work in E. coli (Schaefer and Golden, 1989) making it difficult to characterize it properly. The smallest psbAI functional promoter region comprises nucleotides -54 to +1, and one or more proteins bind specifically to the psbAI upstream region stimulating, rather than inactivating the transcription (+1 to + 43) (Nair et al. 2001), unlike typical σ70 promoters. A segment of approximately 20bp of the consensus -35 element has been shown to be implicated in both, promoter activation per se and light-responsive expression, this region is characterized by being AT-rich (Nair et al. 2001).


Behaviour


Some studies show that psbAI transcript is actively destabilized when shift to high light (Kulkarni et al. 1992), but prolonged exposure of S. elongatus PCC 7942 cells to high light leads to an increased accumulation of all psbA transcripts, including psbAI (Kulkarni and Golden, 1994). This is an electronic flow independent response implying a response to light rather than to redox changes (Tsinoremas et al. 1996). Extensive assays suggest that the psbAI promoter in S. elongatus is among the strongest in this organism (Andersson et al. 2000).


Using this part in S. elongatus


If you would like to use this part in Synechococcus elongatus PCC7942 you should be aware that the transformation of S. elongatus is based on homologous recombination between two sites on the chromosome (neutral sites) that have been developed as cloning locus. Ectopic sequences can be homologous recombinant without any apparent aberrant phenotype (Clerico et al. 2007).
Thus, to use this part you should cloned it within the S. elongatus neutral sites sequences to move it into the cyanobacterial chromosome.
When transforming, the selective marker and the part of interest flanked with the neutral site sequences are inserted into the neutral site of S. elongatus chromosome and the backbone is lost.
To read more about techniques concerning site-directed mutagenesis in Cyanobacteria, please take a look at this paper:

Using this part in other photosynthetic organisms





Promoter source


We sincerely want to thank Prof. Susan Golden for providing us with a psbAI:luxABCDE fusion construct ready to use in Synechococcus elongatus PCC7942 and the appropriate protocols and papers to achieve our goal. Furthermore, her research on this promoter helped us to prepare a standard characterization report for the registry.
The synthesis of the psbAI promoter for our Biobrick was carried out by Genscript. In the protocols page you will find the ligation protocol we followed to assemble our part into psb1C3.


References