Team:UESTC-China/Design

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<h1 style="color:#1b1b1b; position:relative; left:0px; padding:15 5px; font-size:40px; font-family: calibri, arial, helvetica, sans-serif; font-weight: bold;font-style: Italic; text-align:center; width:1140px;">Design</h1>
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<p style="color:#1b1b1b;"> 我们参赛的项目旨在通过植物吸收代谢甲醛,达到降低室内甲醛浓度的目的。我们通过将微生物和植物中代谢甲醛的关键酶基因3-hexulose-6-phosphate(HPS)、6-phospho-3-hexuloisomerase(PHI)、formaldehyde dehydrogenase(Faldh)、?formate dehydrogenase(FDH)、气孔调节基因(At AHA2),利用基因工程的手段在模式植物烟草中过量表达,最终达到加强植物对室内甲醛降解能力的目的。考虑到生物安全性,我们还将花粉败育基因(Ad CP)在烟草中过量表达,阻止花粉传播造成的基因污染。另外,我们还计划将微生物中代谢甲醛的关键酶基因转到烟草的叶绿体基因组中,保证生物安全性。
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<p style="color:#1b1b1b;">In order to further increase the plant ability of formaldehyde uptake and metabolism by synthetic biology technology, we choosed four enzyme-coding genes related to formaldehyde metabolic pathways from microorganism and plant: 3-hexulose-6-phosphate (HPS), 6-phospho-3-hexuloisomerase (PHI), formaldehyde dehydrogenase (FALDH) and formate-dehydrogenase (FDH). These genes are transformed into plants and will promote formaldehyde metabolism. For security reasons, we also induce <i>AdCP</i> gene into our plans because of its capability to lead to pollen abortion. At the same time, chloroplast transformation is taken into consideration to avoid gene flow and improve gene expression.
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  <h1 class="SectionTitles" style="width:245px;">Stomatal opening</h1>
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Stomata are microscopic pores surrounded by two guard cells and play an important role in the uptake of CO2 for photosynthesis. Recent researches revealed that light-induced stomatal  opening is mediated by at least three key components: blue light receptor phototropin, plasma membrane H+-ATPase, and plasma membrane inward-rectifying K+ channels.However, Yin Wang, et al[1]showed that only increasing the amount of H+-ATPase in guard cells had a significant effect on light-induced stomatal opening(Fig. 1). Transgenic Arabidopsis plants by overexpressing H+-ATPase in guard cells exhibited enhanced photosynthesis activity and plant growth. Therefore,in order to improve the ability of absorbing formaldehyde, we overexpresse H+-ATPase(At AHA2) in transgenic  tobacco guard cells ,resulting in a significant effect on light-induced stomatal opening.
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The ribulose monophosphate (RuMP) pathway is one of the formaldehyde-fixation pathways found in microorganisms called methylotrophs, which utilize one-carbon compounds as the sole carbon source. The key enzymes of this pathway are 3-hexulose-6-phosphate synthase (HPS), which fixes formaldehyde to D-ribulose-5-phosphate (Ru5P) to produce D-arabino-3-hexulose-6-phosphate (Hu6P), and 6-phospho-3-hexuloisomerase (PHI), which converts Hu6P to fructose 6-phosphate (F6P). The two key enzymes work in chloroplast both. We will use fusion expression method to conduct heterologous expression in tobacco (<i>Chen et al., 2010</i>).
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  <h1 class="SectionTitles" style="width:245px;">Biosafty</h1>
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<strong>Fig.1</strong>
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Schematic Representation of the Bacterial RuMP Pathway and the Plant Calvin-Benson Cycle. HPS and PHI denote 3-hexulose-6-phosphate synthase and 6-phospho-3-hexuloisomerase respectively. The abbreviations for several sugar phosphates are as follows: Ru5P, ribulose 5-phosphate; Hu6P, hexulose 6-phosphate; F6P, fructose 6-phosphate; FBP, fructose 1,6-bisphosphate; RuBP, ribulose1, 5-bisphosphate; 3-PGA, 3-phosphoglyce-rate. The other metabolites in the pathway are symbolized merely by their carbon numbers for simplicity <i></i>.  
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  <h1 class="SectionTitles" style="width:1100px;">FALDH</h1>
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In order to improve biology safety,we use male sterility systems which can be used as a biological safety containment to prevent horizontal transgene flow. Pawan Shukla[2] has used a plant pathogen-induced gene, cysteine protease for inducing male sterility. This gene was identified in the wild peanut, Arachis diogoi differentially expressed when it was challenged with the late leaf spot pathogen, Phaeoisariopsis personata.Arachis diogoi cysteine protease (AdCP) was expressed under the strong tapetum-specific promoter (TA29) and tobacco transformants were generated. Morphological and histological analysis of AdCP transgenic plants showed ablated tapetum and complete pollen abortion.
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The glutathione-dependent formaldehyde dehydrogenase (FALDH) plays a key role in formaldehyde metabolism (Fig.3). FALDH is identified as an enzyme expressed in the cytoplasm. If we make <i>FALDH</i> over-express in plants, we can enhance plants’ tolerance to formaldehyde and increase the ability of plants to absorb formaldehyde. In the process of metabolism of formaldehyde, the formaldehyde may first combined with glutathione (GSH) to form the product of S-hydroxymethyl glutathione (HM-GSH), then FALDH in cytoplasm will catalyzes the formation of a S-formyl glutathione (F-GSH). Next the F-GSH will be hydrolyzed to formate (HCOOH) and GSH by S-formyl glutathione hydrolase (FGH).
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Fig.1 Typical stomata in the epidermis illuminated with light for 30 min[1].
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<strong>Fig.2</strong>  a. <img align="top" src="https://static.igem.org/mediawiki/2014/0/04/C13-nmr.gif"> spectra from leaf extracts of transgenic tobacco plant treated with gaseous <img align="top" src="https://static.igem.org/mediawiki/2014/e/e7/H13CHO.gif"> for 2 h. b. <img align="top" src="https://static.igem.org/mediawiki/2014/0/04/C13-nmr.gif"> spectra from leaf extracts of WT treated with gaseous <img align="top" src="https://static.igem.org/mediawiki/2014/e/e7/H13CHO.gif"> for 2 h. c. The extract from WT plant leaves without <img align="top" src="https://static.igem.org/mediawiki/2014/e/e7/H13CHO.gif"> treatment was used to monitor the background <img align="top" src="https://static.igem.org/mediawiki/2014/0/04/C13-nmr.gif"> signal levels <i>(Nian et al., 2013)</i>.  
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Fig. 2 In vitro pollen germination of untransformed control plant and sterile transgenic plants. Pollen grains were germinated on sucrose-boric acid medium and >500 pollen grains were observed.a Untransformed control plant pollen, b Sterile pollen.Scale bar 25 μm[2]
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  <h1 class="SectionTitles" style="width:1100px;">FDH</h1>
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In order to measure the ability of different genes in the metabolism of formaldehyde ,We constructed 11 gene expression vectors(Table 1 and Fig. 3),including 2 backbone vectors,6 single gene expression vectors and 3 multi-gene expression vectors.
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Formate dehydrogenase is a mitochondrial-localized NAD-requiring enzyme while the HCOOH is getting into the mitochondrial, FDH will oxidize the formic acid into CO2, and reduce NAD+ to NADH with a high degree of specificity. In our project, the heterologous expression of Arabidopsis <i>FDH</i> gene in tobacco was completed.
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piGEM001: P35S+P2A+T2A+F2A+nptII+T-HSP+T-35S+T-nos
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<strong>Fig.3</strong> Folate-independent pathway. The abbreviations are as follows: FALDH:glutathione-dependent formaldehyde dehydrogenase; FDH: Formate dehydrogenase; HM-GSH: S-Hydroxymethyl glutathione; Forml-GSH: Formyl glutathione; SMM cycle: Methionine cycle.
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piGEM002: piGEM001+AtAHA2+PGC1+PTA29+AdCP
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piGEM003: piGEM002+TCP02-HPS-PHI
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piGEM004: piGEM002+TCP03-AtFDH
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piGEM005: piGEM002+TCP01-BbFALDH
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piGEM006: piGEM002+HPS-PHI
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piGEM008: piGEM002+BbFALDH
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piGEM009: piGEM002+HPS-PHI+AtFDH+BbFALDH
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piGEM010: piGEM002+TCP02-HPS-PHI+TCP03-AtFDH+FALDH
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piGEM011: piGEM002+TCP02-HPS-PHI+TCP03-AtFDH+TCP01-BbFALDH
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piGEM012: piGEM001+TCP02-HPS-PHI+TCP03-AtFDH+TCP01-BbFALDH
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2A peptide sequences were found in Picornaviruses to mediate "cleavage" between two proteins. We use 2A peptide-linked multicistronic vectors to express multiple proteins from a single open reading frame (ORF) effectively.
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Stomata are microscopic pores surrounded by two guard cells and play an important role in the uptake of CO2 for photosynthesis. Recent researches revealed that light-induced stomatal opening is mediated by at least three key components: blue light receptor phototropin, plasma membrane H+-ATPase, and plasma membrane inward-rectifying K+ channels. However, Wang et al (2014) showed that only increasing the amount of H+-ATPase in guard cells had a significant effect on light-induced stomatal opening (Fig. 4). Transgenic Arabidopsis plants by overexpressing H+-ATPase in guard cells exhibited enhanced photosynthesis activity and plant growth. Therefore, in order to strengthen the ability of absorbing formaldehyde, we overexpressed H+-ATPase (<i>AtAHA2</i>) in transgenic tobacco guard cells, resulting in a significant effect on light-induced stomatal opening.
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Fig. 4 schematic of 2A peptide 
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<strong>Fig.4</strong> Typical stomata in the epidermis illuminated with light for 30 min (<i>Wang et al., 2014</i>).
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The 18~22 amino acids 2A self-cleaving oligopeptides can be used for co-expression of multiple, discrete proteins from a single ORF.Based on highly inefficient peptide bond formation between glycine and proline residues within the 2A peptide, placement of 2A peptide sequence as a linker region between tandem cDNA’s allows the stoichiometric translation of multiple unfused protein products. These sequences were first discovered in the foot-and-mouth disease virus (FMDV).And since than many 2A-like sequences have been identified in other viruses and some parasites.To minimize the risk of homologous recombination, it is important to use different 2A peptide sequences if more than two genes are being linked. The 2A peptide system has thus far worked successfully in all eukaryotic systems tested, from mammalian cells, yeast, and plants.In our project,we use F2A(from foot-and-mouth disease virus), P2A(from porcine teschovirus-1) and T2A(from Thosea asigna virus) to achieve our goal.
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  <h1 class="SectionTitles" style="width:1100px;">Biosafty</h1>
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  <h1 class="SectionTitles" style="width:245px;">Gibson Assemble</h1>
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In 2009 Dr. Daniel Gibson and colleagues at the J. Craig Venter Institute developed a novel method for the easy assembly of multiple linear DNA fragments (Nat Methods 2009;6(5):343-5).(Fig. 5) Regardless of fragment length or end compatibility, multiple overlapping DNA fragments can be joined in a single isothermal reaction. With the activities of three different enzymes, the product of a Gibson Assembly is a fully ligated double-stranded DNA molecule. This has proven to be an efficient and effective method for the assembly of plasmids, and molecular biologists now use this method extensively
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In order to promise biology safety, we use male sterility systems which can be used as a biological safety containment to prevent horizontal transgene flow. Shukla et al (2014) has used a plant pathogen-induced gene, cysteine protease for inducing male sterility. This gene was identified in the wild peanut, <i>Arachis diogoi</i> differentially expressed when it was challenged with the late leaf spot pathogen, <i>Phaeoisariopsis personata</i>. <i>Arachis diogoi</i> cysteine protease (AdCP) was expressed under the strong tapetum-specific promoter (TA29) and tobacco transformants were generated. Morphological and histological analysis of <i>AdCP</i> transgenic plants showed ablated tapetum and complete pollen abortion.
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Fig. 5 schematic of Gibson Assemble
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The Gibson Cloning Master Mix consists of three different enzymes within a single buffer. Each enzyme has a specific and unique function for the reaction:
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T5 Exonuclease?-creates single-strand DNA 3’ overhangs by chewing back from the DNA 5’ end. Complementary DNA fragments can subsequently anneal to each other.
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Phusion DNA Polymerase?-incorporates nucleotides to “fill in” the gaps in the annealed DNA fragments.
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Taq DNA Ligase?-covalently joins the annealed complementary DNA fragments, removing any nicks and creating a contiguous DNA fragment.
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  <h1 class="SectionTitles" style="width:245px;">Reference</h1>
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<div align="center"><img style="width:50% ;" src="https://static.igem.org/mediawiki/2014/1/1c/New_fig5.png">
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<strong>Fig.5</strong> Pollen germination of untransformed control plant and sterile transgenic plants <i>in vitro</i>. Pollen grains were germinated on sucrose-boric acid medium and over 500 pollen grains were observed. a. Untansformed control plant pollen, b. Sterile pollen. Scale bar 25 μm (<i>Shukla et al., 2014</i>).
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  <h1 class="SectionTitles" style="width:1100px;">Vectors</h1>
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[1] Yin Wang,et al.(2014) Overexpression of plasma membrane H+-ATPase in guard cells promotes light-induced stomatalopening and enhances plant growth. 111(1):533-8. doi: 10.1073/pnas.1305438111
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The product of <i>HPS</i>, <i>PHI</i>, and <i>FDH</i> are located in chloroplast, while the product of <i>FALDH</i> are located in cytoplasm. We used chloroplast transit peptides to locate these products of genes. So we constructed different vectors with and without transit peptide. We hope to compare the ability of metabolizing formaldehyde of transgenic tobacco between different transgenic lines. We planned to constructed 11 vectors (Fig. 6), including two backbones, six mono-gene expression vectors and three multi-gene expression vectors (Fig. 7). piGEM003, piGEM004 and piGEM005 are individual mono-gene expression vectors with transit peptides, while piGEM006, piGEM006, piGEM008 are individual multi-gene expression vectors without transit peptides. piGEM009 is a multi-gene expression vector without any transit peptides, while piGEM011 is a multi-gene expression vector with three peptides. piGEM010 is a multi-gene expression vector with two transit peptides.
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<strong>Fig.6</strong>  The procedure of vectors construction.
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<div align="center"><img width="70%" src="https://static.igem.org/mediawiki/2014/b/bd/Uestc_vector.png">
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<strong>Fig.7</strong> Schematic of vectors construction.
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<h1 class="SectionTitles" style="width:1100px;">References</h1>
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Chen, L. M., H. Yurimoto, K. Z. Li, I. Orita, M. Akita, N. Kato, Y. Sakai and K. Izui (2010). "Assimilation of formaldehyde in transgenic plants due to the introduction of the bacterial ribulose monophosphate pathway genes." Biosci Biotechnol Biochem 74(3): 627-635.<br/>
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Nian, H., Q. Meng, W. Zhang and L. Chen (2013). "Overexpression of the formaldehyde dehydrogenase gene from Brevibacillus brevis to enhance formaldehyde tolerance and detoxification of tobacco." Appl Biochem Biotechnol 169(1): 170-180.<br/>
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Shukla, P., N. K. Singh, D. Kumar, S. Vijayan, I. Ahmed and P. B. Kirti (2014). "Expression of a pathogen-induced cysteine protease (AdCP) in tapetum results in male sterility in transgenic tobacco." Funct Integr Genomics 14(2): 307-317.<br/>
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Wang, Y., K. Noguchi, N. Ono, S. Inoue, I. Terashima and T. Kinoshita (2014). "Overexpression of plasma membrane H+-ATPase in guard cells promotes light-induced stomatal opening and enhances plant growth." Proc Natl Acad Sci U S A 111(1): 533-538.
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[2]Pawan Shukla et al. Expression of a pathogen-induced cysteine protease (AdCP) in tapetum results in male sterility in transgenic tobacco Funct Integr Genomics DOI 10.1007/s10142-014-0367-2
 
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[3][3]Andrea?L.?Szymczak-Workman,?Kate?M.?Vignali,?and?Dario?A.A.?Vignali.Design?and?construction?of?2A?vectors.Cold?Spring?Harb?Protoc?2012;doi:10.1101/pdb.ip067876 <br/>T5 Exonuclease?-creates single-strand DNA 3’ overhangs by chewing back from the DNA 5’ end. Complementary DNA fragments can subsequently anneal to each other.
 
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[4]Abdelhak?El?Amrani,Abdellah?Barakate,Barak?M.?Askari,?Xuejun?Li,?Alison?G.?Roberts,Martin?D.?Ryan,?and?Claire?Halpin.Coordinate?Expression?and?Independent?Subcellular?Targeting?of?Multiple?Proteins?from?a?Single?Transgene.Plant?Physiology,?May?2004,?Vol.?135,?pp.?16–24
 
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[5] Pablo?de?Felipe,?Lorraine?E.?Hughes,?Martin?D.?Ryan,?and?Jeremy?D.?Brown.Co-translational,?Intraribosomal?Cleavage?of?Polypeptides?by?the?Foot-and-mouth?Disease?Virus?2A?Peptide.J.?Biol.?Chem.?2003,?278:11441-11448
 
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[6]Andrea?L?Szymczak,?Creg?J?Workman1,Yao?Wang,?Kate?M?Vignali,?Smaroula?Dilioglou,?Elio?F?Vanin&?Dario?A?A?Vignali.�Correction?of?multi-gene?deficiency?in?vivo?using?a�single?‘self-cleaving’?2A?peptide–based?retroviral?vector.Nature?Biotechnology?22,?589?-?594?(2004)
 
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