Paris/Introduction
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====Dealing with complexity==== | ====Dealing with complexity==== | ||
| - | A major challenge for synthetic biology | + | A major challenge for synthetic biology is to tackle complexity ''(Simpson 2004)''. If one wants to modify an organism so that it can perform complex tasks, the standard approach is to implement a complex circuit within a single cell. But unwanted interactions may happen between parts of the system, either because of unknown or unavailable interactions. An alternative approach may be to implement small simple parts of your circuit within different types of cells that would work together. |
For the moment only very few parts in the registry are well characterized. This leads to a situation in which almost all the devices are made out of the same biobricks (plac, pBad, ptet, plambda, luxI, luxR…), and are thus incompatible (you cannot implement them in the same cell). Implementing them in different cell types could alleviate this problem… | For the moment only very few parts in the registry are well characterized. This leads to a situation in which almost all the devices are made out of the same biobricks (plac, pBad, ptet, plambda, luxI, luxR…), and are thus incompatible (you cannot implement them in the same cell). Implementing them in different cell types could alleviate this problem… | ||
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====A new tool for metabolic engineering==== | ====A new tool for metabolic engineering==== | ||
| - | In most multicellular organisms, there is a distinction between the cell line devoted to reproduction, the | + | In most multicellular organisms, there is a distinction between the cell line devoted to reproduction, the germline, and the one devoted to support the germline, the soma (''Weismann, 1892''). The particularity of somatic cells is that, in a sense, they sacrifice themselves for the benefit of the organism. In the same way, implementing a soma/germ line separation in a bacterial species could allow using the soma to produce compounds noxious for itself. In this perspective, our multicellular organism could become a great tool for metabolic engineering, and to synthetic biology at large. |
==== Studying fundamental features of multicellularity ==== | ==== Studying fundamental features of multicellularity ==== | ||
| - | A separation between | + | A separation between germline and soma is a basic feature of multicellular organisms. Although the fitness of the organism essentially depends on the phenotype of the soma, only the germline is perpetuated. For instance skin cells die for the sake of the organism. Our SMB could be a phenomenological model to study the relationship between those two cell types. |
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[[Paris/Definitions#Organism|Organisms]] are living complex adaptive system composed of [[Paris/Definitions#Cell|cells]]. Some organisms, such as bacteria or protozoa, are unicellular. Other organisms, such as humans, are multicellular. But providing a clear definition of multicellularity is not obvious.<br> | [[Paris/Definitions#Organism|Organisms]] are living complex adaptive system composed of [[Paris/Definitions#Cell|cells]]. Some organisms, such as bacteria or protozoa, are unicellular. Other organisms, such as humans, are multicellular. But providing a clear definition of multicellularity is not obvious.<br> | ||
| - | ''E. coli'' is a bacterium able to form colonies but is a unicellular organism since a single cell is able to survive on its own if separated from the colony. Colonial organisms, such as ''Volvox'', are considered being an evolutionary intermediate between the unicellularity and multicellularity, living in colonies most of the time, even if individual cells can survive on their own if separated from the colony (click [[/Paris/colonial theory of evolution of multicellularity|here]] to know more about the colonial theory of evolution of multicellularity). | + | ''E. coli'' is a bacterium able to form colonies but is a unicellular organism since a single cell is able to survive on its own if separated from the colony. Colonial organisms, such as ''Volvox'', are considered being an evolutionary intermediate between the unicellularity and multicellularity, living in colonies most of the time, even if individual cells can survive on their own if separated from the colony (click [[/Paris/colonial theory of evolution of multicellularity|here]] to know more about the colonial theory of evolution of multicellularity). Another example is the one of recently discovered Magnetobacter that seem to necessarily live in colony (''Keim, 2004''). Consequently, it can be discussed whether the grouping of identical cells constitute a multicellular organism. |
Since there is no consensus on the subject, our design of a synthetic multicellular organism will include two cells types and we '''will define a multicellular organism as the necessary and sufficient existence of at least 2 cell types'''. <br> | Since there is no consensus on the subject, our design of a synthetic multicellular organism will include two cells types and we '''will define a multicellular organism as the necessary and sufficient existence of at least 2 cell types'''. <br> | ||
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A basic property of multicellular organisms is the occurrence of [[Paris/Definitions#Cellular_differentiation_.2F_cell_type|cellular differentiation]] leading to complementary specialized functions and interdependency between different cell types. Cellular differentiation is the process by which a cell acquires a new cell type. A cell type is a distinct functional and/or morphological form of a cell. A cell able to differentiate into many cell types is known as pluripotent. Generally, differentiation leads to progressive restriction of the developmental potential and increased specialization of function (NCBI MeSH). | A basic property of multicellular organisms is the occurrence of [[Paris/Definitions#Cellular_differentiation_.2F_cell_type|cellular differentiation]] leading to complementary specialized functions and interdependency between different cell types. Cellular differentiation is the process by which a cell acquires a new cell type. A cell type is a distinct functional and/or morphological form of a cell. A cell able to differentiate into many cell types is known as pluripotent. Generally, differentiation leads to progressive restriction of the developmental potential and increased specialization of function (NCBI MeSH). | ||
| - | Differentiation needs signalling between and within cells leading ultimately to changes in gene expression patterns: some genes are turned on and other are turned off. Considering how gene expression may change, we can distinguish 2 forms of differentiations. Most of the time, it is epigenetic differentiation where mechanisms do not involve changes to DNA sequence: "classical" cis and trans gene regulation involving transcription factors, enhancers, repressors but also DNA methylations, DNA replication timing... The second form of differentiation involves changes to DNA sequence by recombination processes, for example during lymphocyte differentiation (V-D-J recombination). | + | Differentiation needs signalling between and within cells leading ultimately to changes in gene expression patterns: some genes are turned on and other are turned off. Considering how gene expression may change, we can distinguish 2 forms of differentiations. Most of the time, it is epigenetic differentiation where mechanisms do not involve changes to DNA sequence: "classical" cis and trans gene regulation involving transcription factors, enhancers, repressors but also DNA methylations, DNA replication timing... The second form of differentiation involves changes to DNA sequence by recombination processes, for example during lymphocyte differentiation (V-D-J recombination; ''Tonegawa, 1976''). |
==== '''Germ cells and somatic cells'''==== | ==== '''Germ cells and somatic cells'''==== | ||
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[[Image:Paris_Germline-Soma.jpg|400px|center]] | [[Image:Paris_Germline-Soma.jpg|400px|center]] | ||
| - | Our organism, | + | Our organism, is be composed of 2 cell types. The first one is the germ cell (G cell). It is unable to live alone but able to give an entire organism (both cell types). It needs the second cell type to survive: the somatic cell. Somatic cells (S cell) are derived from G cells by a single irreversible differentiation step and concomitantly acquire a new function necessary for supporting G cells survival. Therefore, the S cell is unable to give an entire organism. |
Thus, our system is composed of an undifferentiated G cell type and a differentiated S cell type. Obligatory interdependency between these two cell types must ensure the stability of the system. The nature of this interdependency will be discussed below. | Thus, our system is composed of an undifferentiated G cell type and a differentiated S cell type. Obligatory interdependency between these two cell types must ensure the stability of the system. The nature of this interdependency will be discussed below. | ||
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| + | ===References=== | ||
| + | 1. Keim, C. N., J. L. Martins, et al. (2004). "Multicellular life cycle of magnetotactic prokaryotes." FEMS Microbiol Lett 240(2): 203-8. | ||
| + | |||
| + | 2. Simpson, M. L. (2004). "Rewiring the cell: synthetic biology moves towards higher functional complexity." Trends Biotechnol 22(11): 555-7. | ||
| + | |||
| + | 3. Tonegawa, S. (1976). "Reiteration frequency of immunoglobulin light chain genes: further evidence for somatic generation of antibody diversity." Proc Natl Acad Sci U S A 73(1): 203-7. | ||
| + | |||
| + | 4. Weismann, A. (1893). The Germ-Plasm - A Theory of Heredity. New York, Charles Scribner's Sons. | ||
| + | |||
| + | ---- | ||
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| + | Go to [[Paris/DesignProcess|Design process>]] | ||
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Latest revision as of 23:37, 26 October 2007
Contents |
Introduction
Why a Synthetic Multicellular Bacterium ?
Dealing with complexity
A major challenge for synthetic biology is to tackle complexity (Simpson 2004). If one wants to modify an organism so that it can perform complex tasks, the standard approach is to implement a complex circuit within a single cell. But unwanted interactions may happen between parts of the system, either because of unknown or unavailable interactions. An alternative approach may be to implement small simple parts of your circuit within different types of cells that would work together.
For the moment only very few parts in the registry are well characterized. This leads to a situation in which almost all the devices are made out of the same biobricks (plac, pBad, ptet, plambda, luxI, luxR…), and are thus incompatible (you cannot implement them in the same cell). Implementing them in different cell types could alleviate this problem…
The aim of our project is to provide a practical tool for such an approach, making a jump in complexity scale, from single cells to multicellular synthetic biology, and for the first time engineering a multicellular bacterium.
A new tool for metabolic engineering
In most multicellular organisms, there is a distinction between the cell line devoted to reproduction, the germline, and the one devoted to support the germline, the soma (Weismann, 1892). The particularity of somatic cells is that, in a sense, they sacrifice themselves for the benefit of the organism. In the same way, implementing a soma/germ line separation in a bacterial species could allow using the soma to produce compounds noxious for itself. In this perspective, our multicellular organism could become a great tool for metabolic engineering, and to synthetic biology at large.
Studying fundamental features of multicellularity
A separation between germline and soma is a basic feature of multicellular organisms. Although the fitness of the organism essentially depends on the phenotype of the soma, only the germline is perpetuated. For instance skin cells die for the sake of the organism. Our SMB could be a phenomenological model to study the relationship between those two cell types.
What is a multicellular organism and what is needed to create one ?
Grouping of cells
Organisms are living complex adaptive system composed of cells. Some organisms, such as bacteria or protozoa, are unicellular. Other organisms, such as humans, are multicellular. But providing a clear definition of multicellularity is not obvious.
E. coli is a bacterium able to form colonies but is a unicellular organism since a single cell is able to survive on its own if separated from the colony. Colonial organisms, such as Volvox, are considered being an evolutionary intermediate between the unicellularity and multicellularity, living in colonies most of the time, even if individual cells can survive on their own if separated from the colony (click here to know more about the colonial theory of evolution of multicellularity). Another example is the one of recently discovered Magnetobacter that seem to necessarily live in colony (Keim, 2004). Consequently, it can be discussed whether the grouping of identical cells constitute a multicellular organism.
Since there is no consensus on the subject, our design of a synthetic multicellular organism will include two cells types and we will define a multicellular organism as the necessary and sufficient existence of at least 2 cell types.
Cellular differentation
A basic property of multicellular organisms is the occurrence of cellular differentiation leading to complementary specialized functions and interdependency between different cell types. Cellular differentiation is the process by which a cell acquires a new cell type. A cell type is a distinct functional and/or morphological form of a cell. A cell able to differentiate into many cell types is known as pluripotent. Generally, differentiation leads to progressive restriction of the developmental potential and increased specialization of function (NCBI MeSH).
Differentiation needs signalling between and within cells leading ultimately to changes in gene expression patterns: some genes are turned on and other are turned off. Considering how gene expression may change, we can distinguish 2 forms of differentiations. Most of the time, it is epigenetic differentiation where mechanisms do not involve changes to DNA sequence: "classical" cis and trans gene regulation involving transcription factors, enhancers, repressors but also DNA methylations, DNA replication timing... The second form of differentiation involves changes to DNA sequence by recombination processes, for example during lymphocyte differentiation (V-D-J recombination; Tonegawa, 1976).
Germ cells and somatic cells
In multicellular organisms, two categories of cells can be found. Germ cells are responsible for the reproduction of the organism while the others, the somatic cells, are unable to generate a new organism but are essential for the germ line viability. Most multicellular organisms reproduce through sex, and the germ line is responsible for gamete production. We will not attempt to reproduce sexual behaviors, only separation between a line dedicated to reproduction, and one dedicated to support the other will be implemented. These will be named the germ line and the soma. Also, we realize we are overextending the proper definition of those terms.
What will our synthetic multicellular organism look like?
Our organism, is be composed of 2 cell types. The first one is the germ cell (G cell). It is unable to live alone but able to give an entire organism (both cell types). It needs the second cell type to survive: the somatic cell. Somatic cells (S cell) are derived from G cells by a single irreversible differentiation step and concomitantly acquire a new function necessary for supporting G cells survival. Therefore, the S cell is unable to give an entire organism.
Thus, our system is composed of an undifferentiated G cell type and a differentiated S cell type. Obligatory interdependency between these two cell types must ensure the stability of the system. The nature of this interdependency will be discussed below.
References
1. Keim, C. N., J. L. Martins, et al. (2004). "Multicellular life cycle of magnetotactic prokaryotes." FEMS Microbiol Lett 240(2): 203-8.
2. Simpson, M. L. (2004). "Rewiring the cell: synthetic biology moves towards higher functional complexity." Trends Biotechnol 22(11): 555-7.
3. Tonegawa, S. (1976). "Reiteration frequency of immunoglobulin light chain genes: further evidence for somatic generation of antibody diversity." Proc Natl Acad Sci U S A 73(1): 203-7.
4. Weismann, A. (1893). The Germ-Plasm - A Theory of Heredity. New York, Charles Scribner's Sons.
Go to Design process>
