Team:Paris/Perspectives

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Latest revision as of 04:52, 30 October 2008

Perspectives

As for the flagella biosynthesis, our FIFO could be useful for many bottom-up assembled molecular machines that needs to be assembled in a precise order. Moreover, as we will show on an example, the FIFO could also be useful in many biosynthetic pathways subject to competitive alternative pathways and for wich intermediate products must be avoided. We will develop below two examples: type III secretion injectisome and PHA biosynthesis pathway.

Example 1: type III secretion injectisome

The injectisome is a complex nanomachine that allows bacteria to deliver protein effector across eucaryotic cellular membranes. The injectisome consists of a basal structure, which resembles the basal structure of the flagellum, surmounted by either a needle, a needle and a filament or a long pilus.

The injectisome is related to the flagellum genetically. Studies show that a core of eight proteins share significant similarity with components of the flagellum. From this studies, we can expect that the genes expression is ruled by a sequential FIFO order so we can express it with our bacteriO'clock system . Moreover, the injectisome will find a lot of applications for example ,bacteria that express this kinds of structure could :

induce apoptosis of Eukaryote cells so we can developed by our system new kinds of in-vivo compatible anticancer therapy,
be a new way to liberate substances produced by bacteria (see bioplastic application).

In conclusion, our BacteriO'Clock can be used in a lot of new applications like for instance, bottom-up molecular machines self-assembly or new kinds of optimized chemoreactor.

Example 2: metabolic engineering of polyhydroxyalkanoate biosynthesis pathways

Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials. One illustrative example is polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions. The biosynthesis of this polymer is currently subject to intensive work. It consists in expressing in appropriate quantities 3 enzymes PhaA ,PhaB and PhaC that sequentially process AcetoacetylcoA into its final product PHA. This biosynthesis os subjected to 2 constraints :

Intermediate products of this pathway are used in alternatives competing metabolic pathways,
Only the final product is of interest,so that all intermediates products need to be transformed into PHA.

Two strategies are commonly used in bioengineering of metabolic pathways :

Sequential expression of enzymes involved in the pathways,
Or constitutive expressions of all enzymes.

Because of the above mentioned limitations, none of these approaches are adapted here . Using the sequential expression, intermediate products would accumulate and thus be consumed by competing pathways. Using the constitutive expression a mixture of final and intermediate product would necessarily be obtained.

Our FIFO could be useful here. Indeed a FIFO expression pattern is intermediate between a purely sequential and a purely constitutive expression. At some point all enzymes are presents ( no accumulation of intermediate products ) and during the last step only the last enzyme (PhC) is presents ( all intermediate products are consumed).

Moreover, the fact that our system oscillate could provide to the cell a metabolic recovering phase.

Bibliography

The type III secretion injectisome Guy R.Cornelis Nature reviews

Process design for microbial plastic factories: metabolic engineering of polyhydroxyalkanoates

Ilana S Aldor and Jay D Keasling Department of Chemical Engineering, 201 Gilman Hall, University of California, Berkeley, 94720-1462, USA 23 September 2003

PHA synthase engineering toward superbiocatalysts for custom-made biopolymers.

Nomura CT, Taguchi S. Department of Chemistry, State University of New York - College of Environmental Science and Forestry, 121 Jahn Laboratory, Syracuse, NY 13210, USA.

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 {{Paris/Menu}}
+{{Paris/Header|Perspectives}}
-<font color=red>''Un petit texte pour expliquer la motivation de cette page''  ne serait-ce que tout simplement:
-On this page we report some possible uses of the FIFO device in synthetic applications.
-General comment: I am not at all against an explorative, speculative section. But it's purpose must be clear very clearly focussed on the interest of the FIFO for putative applications. Discuss each time why the FIFO could be especially interesting for your application. This must be very clear in order for this section to fulfill it's purpose.</font>
+As for the flagella biosynthesis, our FIFO could be useful for many '''bottom-up assembled molecular machines''' that needs to be assembled in a precise order.
+Moreover, as we will show on an example, the FIFO could also be useful in many '''biosynthetic pathways''' subject to competitive alternative pathways and for wich intermediate products must be avoided.
+We will develop below two examples: type III secretion injectisome and PHA biosynthesis pathway.
+== Example 1: type III secretion injectisome ==
+The injectisome is a complex nanomachine that allows bacteria to deliver protein effector across eucaryotic cellular membranes.
+The injectisome consists of a basal structure, which resembles the basal structure of the flagellum, surmounted by either a needle, a needle and a filament or a long pilus.
+[[Image:injectisome.JPG]]
-== Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==
-Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials such as polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.
-we hope that if we applied our system  to  pathways that have differentes cross linked intermediaries like the biosynthesis of PHA (figure 1), by the FIFO we will optimized the expression of the differentes genes in order to avoid waste producte that will increase impurities.
-Our strategy consists on replacing  the RFP,CFP and YFP genes by the PhaA ,PhaB and PhaC genes in our final system (containing oscillation,FIFO,synchronisation modules).
-This strategy is more efficient than a constitutive activation for 3 main reasons:
+The injectisome is related to the flagellum genetically. Studies show that a core of eight proteins share significant similarity with components of the flagellum. From this studies, we can expect that the genes expression is ruled by a  sequential FIFO order so we can express it with our bacteriO'clock system .
-*First, in this application the NADPH, which is a cellular metastable  fuel, is used by  the PhaB to  synthesize bioplastic. This molecule is very important for many metabolic pathways in bacteria. A NADPH recuperation step is then needed to ensure other metabolic activities to go on. We can then make the hypothesis that if the PhaB is always  activated the bacteria will get exhausted and die quickly. In our system, the bacteria will have a NADPH recuperation step, this is why we hope bacteria will live more than in an usual chemoreactor.
+Moreover, the injectisome will find a lot of applications for example ,bacteria that express this kinds of structure  could :
+* induce apoptosis of Eukaryote cells so we can developed  by our system new kinds of  in-vivo compatible anticancer therapy,
+* be a new way to liberate substances produced by bacteria (see bioplastic application).
-*Secondly, we hope that our system will increase the purity  and the rate of PHA obtain because we don't activate the 3 genes simultaneously, instead of that we activate by a FIFO order  system the 3 genes  so we will avoid lost of acetoacetylcoA or others important intermediary product  in  others metabolic pathways.
+In conclusion, our BacteriO'Clock can be used in a lot of new applications like for instance, bottom-up  molecular machines self-assembly or new kinds of optimized chemoreactor.
+==  Example 2: metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==
+Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials.
+One illustrative example is polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.
+The biosynthesis of this polymer is currently subject to intensive work.
+It consists in expressing in appropriate quantities 3 enzymes  PhaA ,PhaB and PhaC that sequentially process AcetoacetylcoA into its final product PHA.
+This biosynthesis os subjected to 2 constraints :
+* Intermediate products of this pathway are used in alternatives competing metabolic pathways,
+* Only the final product is of interest,so that all intermediates products need to be transformed into PHA.
 [[Image:PHA.jpg|center]]
-In conclusion,our bacterioclock can be use to obtain many polymers or proteins fibers that their production pass by a lot of methabolic cross linked intermediary, in those situations the FIFO order may optimized the purity and the rate of the final products.
+Two strategies are commonly used in bioengineering of metabolic pathways :
+* Sequential expression of enzymes involved in the pathways,
+* Or constitutive expressions of all enzymes.
+Because of the above  mentioned limitations, none of these approaches are adapted here .
+Using the sequential expression, intermediate products would accumulate and thus be consumed by competing pathways.
+Using the constitutive expression a mixture of final and intermediate product would necessarily be obtained.
+Our FIFO could be useful here.
+Indeed a FIFO expression pattern is intermediate between a purely sequential and a purely constitutive expression.
+At some point all enzymes are presents ( no accumulation of intermediate products ) and during the last step only the last enzyme (PhC) is presents ( all intermediate products are consumed).
+Moreover, the fact that our system oscillate could provide to the cell a metabolic recovering phase.
 == Bibliography ==
+* The type III secretion injectisome  Guy R.Cornelis Nature reviews
+* Process design for microbial plastic factories: metabolic engineering of polyhydroxyalkanoates
+Ilana S Aldor and Jay D Keasling
+Department of Chemical Engineering, 201 Gilman Hall, University of California, Berkeley, 94720-1462, USA
+September 2003
+* PHA synthase engineering toward superbiocatalysts for custom-made biopolymers.
+Nomura CT, Taguchi S.
+Department of Chemistry, State University of New York - College of Environmental Science and Forestry, 121 Jahn Laboratory, Syracuse, NY 13210, USA.