Irla Flashcards
The Figure shows the response of a B. clausii-derived metE riboswitch
(reflected by the level of gene expression for a β-galactosidase reporter gene
fused to the 5′ UTR of the B. clausii metE mRNA) to supplementation of
growth media with methionine (Met) and adenosylcobalamin (AdoCbl).
Knowing that any decrease in the gene expression can be interpreted as
activation of the riboswitch, say what type of logic gate this riboswitch
represents, include 2-3 sentences of explanation.
We see that if both Met and Ado are absent, there is full gene expression. If there is gene expression, the output of the logic gate is 1. Thus, 0 and 0 = 1. If we interpret any downregulation of the transcription as activation of the riboswitch, and the riboswich is working as the opposite of a promoter, that means that for the other three, the output is zero. We can see that the presence of only one of the repressors is enough to activate the riboswitch, pointing to an OR gate being involved. However, the OR gate uses activators. As the two are repressors, it must therefore be a NOR gate. This is also supported by the “tables”:
Explain how the knowledge about regulation of gene expression can be
applied for design of synthetic pathways. Choose one example of functional
element for regulation of gene expression and explain which type of logic gate
it represents.
Knowledge about regulation of gene expression can be applied for design of synthetic pathways as it makes it possible to manipulate the pathways. One example of a functional element for regulation of gene expression is the LacI molecule. If this is bound to the DNA, then there is no expression. If it is absent, then there is expression. To gather these facts into a table:
NOT gate
What are the advantages of using synthetic microbial consortia over the
monocultures (at least 3)? What approaches can be used in design of
synthetic microbial consortia (at least 3), briefly explain them and give at least
one example of biotechnological applications where they have been applied
(one example for each approach in design listed)
The advantages of using synthetic microbial consortia rather than monocultures include the division of labor, spatial organization where different pathways can take place in different compartments, and multiple species increase the robustness of the whole consortia in regards to environmental changes and contaminations. Monocultures necessitate strict environmental control and sterilization, as one contaminant could potentially cause problems.
To engineer microbial communities, a synthetic biologist could utilize the following:
- Intercellular signaling to construct communication between organisms, like quorum sensing. In one example, a LuxI molecule is secreted by one cell and binds to a receptor in another cell, activating transcription of Plux in the receiver cell. - Exogenous molecules to control specific population behaviors, adding inducer molecules can affect gene expression in one strain that could affect multiple cells, like inducing ampicillin recistance gene (AmpR) in one strain, which could be transferred to the corresponsing QS receptor in another strain, enabling mutual survival. - Building co-dependent networks, like with one organism producing resources for others, or by deleting certain genes (like amino acid biosyntheis genes) in different members of the strain, thus making the survival of all the cells dependent on the survival of the others
What are the preffered properties of target organism used for top-down
approach in creation of minimal cell. Explain the process of creating a minimal
cell in a top-down approach.
The top-down approach takes a living cell and strips it of all non-essential functions, adding only those wanted. This saves the cell energy, as it does not perform any non-essential tasks, and creates an “artificial” cell. The cell also has different compartments for different tasks, and retains the function to replicate and divide.
Desired properties of a target organism for such a cell is small genomes that have been sequences, a well-characterized host, which is easy to cultivate and modify genetically.
The approach starts with sequencing a genome, isolating fragments encoding essential molecules for the processes of the cell, limiting the number chosen, and having the ends of the fragments overlap, thus enabling assembly into a cassette. This genome is then injected into a host cell.
Explain the process of designing a minimal cell bottom-up approach. What are
the essential features and processes that should be considered?
The bottom-up approach has not yet been realized, but the idea is to take biological molecules and put them together to make a functional cell. There are several aspects that needs to be considered, like energy-synthesis, metabolism in general, replication and division.
