Team:SCUT-China/Project/PPS

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<p class="head">PPS-Programmed Polyketide Synthesis</p>
 
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<p class="title"id="label1">Overview</p>
 
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<p>The fidelity and efficiency of acyl transfer on the interfaces of the individual PKS proteins is thought to be governed by helical regions, termed Docking Domains
 
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(DD), which are located at the C-terminus of the upstream and N-terminus of downstream polypeptide chains. The length of docking domain is about thirty to ninety amino
 
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acids (Figure 1) <sup>[1]</sup>. It not only participates in the regulation of protein function, but also completes the transshipment of upstream intermediate, and
 
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forecasts its vast prospects in the development of new drugs <sup>[2]</sup>.
 
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<p><img src="https://static.igem.org/mediawiki/2014/f/ff/DD-fig1_%E5%89%AF%E6%9C%AC.jpg" /width=750px,height=450px></p><br/>
 
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<p>Figure 1: The picture of docking domains</p>
 
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<p>There are two types of docking domains. Class 1 is from actinomycetes and mucous bacteria while class 2 is from cyanobacteria mostly <sup>[3]</sup>. Class 1 DD is
 
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also in the form of dimer just like the polyketide synthase. At present, the class 2 DD is seen to be a genetic engineering tool because of its shorter length and
 
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tight combination, and it will has great application prospect for deeper researches.
 
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Docking domain consists of ACP-side docking domain (ACP DD) at the C-terminus of the upstream and KS-side docking domain (KS DD) at the N-terminus of downstream. The
 
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two parts locate in the downstream of ACP and upstream of KS respectively, and lie in the different modules. Each DD has formed specificity of the binding because it
 
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has specific connection site. Namely each docking domain is unique in the whole polyketone synthesis pathway. With this important feature, we can ensure the connection
 
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between adjacent modules does not have randomness, which makes the product unique.
 
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ACP of class 2 DD is about 40 animo acids shorter than class 1, which cannot form a polymerization area. Having the similar length with class 1 DD, KS of class 2 is
 
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unable to form a spiral structure domain coiled coil due to its strong polarity. Therefore, the class 2 DD have no dimer, even though all of their structures are of
 
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even numbers.
 
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There are two alpha helix existing in the upstream and downstream of the class 2 DD separately. KS has alpha A and alpha B at the head of domain, while ACP has alpha 1
 
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and alpha 2 at its end (Figure. 2). In order to get closer and form tighter combinations, the alpha helices between alpha A and alpha B or between alpha 1 and alpha 2
 
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form a sharp turn (sharp bend). This structure makes class 2 DD different from class 1 <sup>[3][4]</sup>.
 
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<p><img src="https://static.igem.org/mediawiki/2014/7/72/DD-fig2.png" /width=750px,height=450px></p><br/>
 
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<p>Figure 2: Structure of class 2 docking domain</p>
 
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<p class="title"id="label1">Design:</p>
 
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<p>As introduced, it is obvious that the Class 2 DD has more advantages, such as its shorter lengths, closer combinations, clearer effect of regulating protein
 
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function and higher transfer efficiency in completing upstream intermediate. Therefore, we have selected the Class 2 Docking Domain as our part. Because of its
 
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specificity as mentioned, the connections between different sets of ACP and KS are different. Typical PKS subunits are tightly homodimeric and contain one to six
 
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modules each. They are thought to associate with other multienzyme subunits through contacts at their C and N termini to form the overall PKS complexes. For example,
 
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the 6-deoxyerythronolide B synthase (DEBS), assembling the polyketide core of erythromycin A, contains three multienzyme subunits as DEBS 1, DEBS 2, and DEBS3, each of
 
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which includes two extension modules <sup>[1][5]</sup>. We get the interest sequence of six pairs of DDs (DD1, DD2, DD3, DD4, DD5, DD6) by sequencing synthesis, and we
 
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also add RFC 23 to insert restriction enzyme cutting sizes(Figure 3). At last, we built them to pSB1C3 vector.
 
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<p><img src="https://static.igem.org/mediawiki/2014/e/e2/DD-figb3.jpg></p><br/>
 
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<p>Figure 3: The design of docking domains in our experiment. At each set of docking domain, the top was connected with ACP that its upstream joined in the PFC 23 and
 
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its downstream joined in the RFC 10. The following came close to KS that the upstream joined in the RFC 10 and the downstream joined in the RFC 23. The following has
 
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no linker generally.</p>
 
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<p class="title"id="label1">Results</p>
 
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<p>After long exploration, we have got the standard DDs that can be used in different connections of ACP and KS. All docking domain are class 2 in our project. At each
 
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set of docking domain, the top was connected with ACP that its upstream added the RFC 23 and its downstream added the RFC 10. The following came close to KS that the
 
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upstream added the RFC 10 and the downstream added the RFC 23. The following has no linker generally. With dedicated efforts, we have built out the different modules
 
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by using the same docking domains. With the upstream and downstream added for assembly, it has been constructed into pSB1C3 vector for further use.
 
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<p><img src="https://static.igem.org/mediawiki/2014/b/b2/DD-fig4.png" /width=750px,height=450px></p><br/>
 
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<p>Figure 4: Gel Electrophoresis of our amplified fragments needed for Docking Domains. Each fragment showed the different DD and the”M” is stand for 100bp maker. In
 
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the picture (a), number 1 to 3 refer to the” DD1上” . Number 1 to 4 refer to the “DD2上、DD2下、DD3下、DD3上” separately in the picture (b). For (c), number 1 to 5
 
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refer to the “DD4上、DD4下、DD6上、DD6上、DD6下” separately.</p>
 
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<p class="title"id="label1">Conclusion</p>
 
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<p>In our initial design, we aimed to create the standard general DD that can connect different Module (get more information about Module, please click here). Now, we
 
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have got the standard biobricks of DD but without strict verification. Then, we will continue completing the remaining parts of the experiment.
 
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<p class="title" id="label4">Reference</p>
 
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[1]Broadhurst RW, Nietlispach D, Wheatcroft MP, Leadlay PF, Weissman KJ(2003) The structure of docking domains in modular polyketide synthases. Chem Biol 10: 723–731.
 
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[2] Worthington, A. S., Hur, G. H., Meier, J. L., Cheng, Q., Moore, B. S.and Burkart, M. D. (2008) Probing the compatibility of  type II ketosynthase-carrier protein
 
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partners,ChemBioChem 9, 2096 –2103
 
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[3]onia JB, Todd WG, Frank EB Kevin AR, Janet LS, and David HS(2009)Structural Basis for Binding Specificity between Subclasses of Modular Polyketide Synthase Docking
 
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Domains. ACS Chem Biol Vol.4 No.1
 
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[4]Jonathan RW, Sarah SS, Douglas AH, William CB, William HG,David HS and Janet LS(2013)Cyanobacterial PolyketideSynthase Docking Domains:A Tool for Engineering
 
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Natural Product Biosynthesis. Chem Biol 20:1340–1351.
 
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[5][Tang, Y., Kim, C.-Y., Mathews, I. I., Cane, D. E. and  Khosla, C. (2006)The 2.7-angstrom crystal structure of a 194-kDa homodimeric fragment of the 6-
 
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deoxyerythronolide B synthase,Proc. Natl. Acad. Sci. U.S.A. 103, 11124 -11129.
 
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Revision as of 02:03, 18 October 2014

PPS-Programmed Polyketide Synthesis

The domain in type I polyketide synthase(PKS) can work independently without losing their function[1]. We want to standardize the domain and assemble them in correct order and finally we can rational design and produce new-to-nature polyketide as we want.


1.What kind of polyketide synthase do we choose as our candidate?

Polyketide almost exist in every organisms but many of their synthesis processes are unclear[2]. First thing we did is to search suitable PKS. Erythromycin PKS modular 6-deoxyerythronolide B synthase(DEBS) from Saccharopolyspora erythraea is a good candidate[3]. It has served as a module system for researching to engineer PKSs and to explore their structural plasticity and substrate tolerance[4] for long. DEBS, encoded by the gene eryA, are divided into three part including totally six module. DEBS1 which include three module, is the first part of DEBS[5]. (figure.1)


2.How to search the boundary between the domains and linker in a module?

The domains in PKS have independent functions[6]. We tried to separate different domains in the sequence of erythromycin type I polyketide synthase. To make sure that the integrity of domains are unbroken, it’s important that searching for the boundary between domain precisely. We find out the boundary between two domain, each domain are connected by the short adhesion.We search two database ASMPKS (Analysis System for Modular Polyketide Synthases:http://gate.smallsoft.co.kr:8008/~hstae/asmpks/pks_prediction.pl ) and MAPSI (Management and Analysis for Polyketide Synthase type I: http://gate.smallsoft.co.kr:8008/pks/ ), both of which provide the information for researching type I polyketide synthase[4]. According to the information provided on two websites, we identify and seperate all the domains from DEBS1.


3. Generating new polyketide by “programming” domain in module.

After identifying and obtaining the sequence of each domains, we assemble the domain in the order of what we want. Then we can test whether the PKS are expressed correctly and the polyketide synthesized as we want.(figure.2) GC content of PKS DEBS1 sequence is very high, so we have the codon optimized to make it suitable for E.coli[7].

3.1 Standardzing the domain.

We first assemble the domain as original DEBS1+TE, to find whether our reconstructed domain works.(figure1)



Figure1: Standardzing of domains


At the same time, we try to exchange position of domain with the same function. We exchange the domain KR and ACP and insert the didomain DH+ER into different module to know whether our standardized domains works[8].(figure2)



Figure2: Repositioning and insert of domain inside module.


Thirdly, we obtain the loading module from diffenent organisms.
Loading module is the first module in polyketide synthase that recognize the starter unit of the polyketide chain and initiates the polyketide synthesis[9]. It include at least two domains that AT and ACP. Some loading modules may contain KS. The loading module influences the efficience of polyketide synthesis as it start the synthesis process.
We choose loading module of PKS of pyoluteorin[10] and amphotericin[11]. Erythromycin’s starter unit is propionyl-CoA and The starter unit of Amphotericin are acetyl-CoA. (Figure3)


Figure3: Exchange of loading module


Starter unit of Pyoluteorin in two PKS database is different that malonyl-CoA in ASMPKS and acetyl-CoA in MAPSI. We compare the efficience of that loading module between two concentration of substrates.
The loading module of Amphotericin contain an redundant domain DH that can’t modify the starter unit or any other polyketide unit[11]. We eliminate the DH domain of Amphotericin to optimize loading module.(figure.4)


Figure4: Elimation of redundant dh of amphotericin


Finally, we will test the seletivity of diffenent AT so that we can determine the structure by selecting the substrates. AT domain is responsible for selecting CoA linked extender as building blocks for constructing the polyketide chain[12].

3.2 "programming" the PKS

By all these work we do, we can control the structure of polyketide in three aspect: by choosing or engineering the appropriate host, the supplement of building blocks will be enough[13][14]; then, by choosing the suitable loading module and KS-AT domain, the PKS can select the building blocks of polyketide synthesis. Finally, according to the structure of polyketide, we can insert different modified domains into specific module, so that the building blocks can be modified correctly.
We will try to establish a database that can provide the information about the utilization of standardized domain. According to the structure of polyketide that user need, the database can provide the information about the assemble of standardization domains and host needed for synthsis. Achieving the programmed synthesis of polyketide.(figure5)


Figure5: how do we produce new polyketide. a) approriate host for producing substrate; b)choose suitable didomain KS-AT to select correct building blocks; c)arrange the suitable proccessing domains to modify the polyketide chain.


Reference

[1]Cane, David E. "Programming of erythromycin biosynthesis by a modular polyketide synthase." Journal of Biological Chemistry 285.36 (2010): 27517-27523.
[2]Komaki, Hisayuki, et al. "Genome based analysis of type-I polyketide synthase and nonribosomal peptide synthetase gene clusters in seven strains of five representative Nocardia species." BMC genomics 15.1 (2014): 323.
[3]Pfeifer, Blaine A., et al. "Biosynthesis of complex polyketides in a metabolically engineered strain of E. coli." Science 291.5509 (2001): 1790-1792.
[4]Tae, Hongseok, Jae Kyung Sohng, and Kiejung Park. "Development of an analysis program of type I polyketide synthase gene clusters using homology search and profile hidden Markov model." Journal of microbiology and biotechnology 19.2 (2009): 140-146.
[5]Cortes, Jesus, et al. "An unusually large multifunctional polypeptide in the erythromycin-producing polyketide synthase of Saccharopolyspora erythraea." (1990): 176-178.
[6]Khosla, Chaitan, Shiven Kapur, and David E. Cane. "Revisiting the modularity of modular polyketide synthases." Current opinion in chemical biology 13.2 (2009): 135-143.
[7]Menzella, Hugo G., et al. "Redesign, synthesis and functional expression of the 6-deoxyerythronolide B polyketide synthase gene cluster." Journal of Industrial Microbiology and Biotechnology 33.1 (2006): 22-28.
[8]Oliynyk, Markiyan, et al. "A hybrid modular polyketide synthase obtained by domain swapping." Chemistry & biology 3.10 (1996): 833-839.
[9]Lau, Janice, David E. Cane, and Chaitan Khosla. "Substrate specificity of the loading didomain of the erythromycin polyketide synthase." Biochemistry39.34 (2000): 10514-10520.
[10]Nowak-Thompson, Brian, et al. "Characterization of the pyoluteorin biosynthetic gene cluster of Pseudomonas fluorescens Pf-5." Journal of bacteriology 181.7 (1999): 2166-2174.
[11]Caffrey, Patrick, et al. "Amphotericin biosynthesis in Streptomyces nodosus deductions from analysis of polyketide synthase and late genes." Chemistry & biology 8.7 (2001): 713-723. [12]Dunn, Briana J., et al. "Comparative analysis of the substrate specificity of trans-versus cis-acyltransferases of assembly line polyketide synthases."Biochemistry (2014).
[13]Jiang, Ming, and Blaine A. Pfeifer. "Metabolic and pathway engineering to influence native and altered erythromycin production through E. Coli ."Metabolic engineering 19 (2013): 42-49. [14]Chen, Xianzhong, et al. "Metabolic engineering of Escherichia coli : A sustainable industrial platform for bio-based chemical production."Biotechnology advances 31.8 (2013): 1200-1223.