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Team:Paris/Transduction overview
From 2009.igem.org
Overview
Aim:
- to enable gene transcription after fusionning OMVs with the outer membrane of the receiving bacterium.
We also hope that we could achieve this aim without sacrifying important proprieties of our message : specific, repeatable , multidirectional.
It seems that we have two possible ways : the ABC transporters or the two component systems .
ABC transporters and two component systems are natural transport system (export or import) of information, nutriments or toxines.
There is another possibility but the mecanism is mostly unknown : the DNA-containing OMVs which could be a useful mean of information transport.
ABC transporter
Overview:
The ABC transporter is a major class of cellular translocation machinery encoded in the largest set of paralogous genes.
The ABC (ATP binding cassette) transporter is one of the active transport systems of the cell,
which is widespread in archaea, eubacteria, and eukaryotes. It is also known as the
periplasmic binding protein-dependent transport system in Gram-negative bacteria and the binding-
lipoprotein-dependent transport system in Gram positive bacteria. The transporter shows a common
global organization with three types of molecular components. Typically, it consists of two integral membrane proteins (permeases)
each having six transmembrane segments, two peripheral membrane proteins that bind and hydrolyze ATP,
and a periplasmic (or lipoprotein) substrate-binding protein. The ATP-binding protein component is the most
conserved, the membrane protein component is somewhat less conserved, and the substrate-binding protein
component is most divergent in terms of the sequence similarity. The ABC transporters form the largest group of paralogous genes in bacterial
and archaeal genomes , and the genes for the three components frequently form an operon.
the following scheme shows a typical ABC mechanism :
uses:
transport the protein directly into the cytolpasm to activate the transcription.
advantages/drawbacks:
advantages:
the protein of interest is directly translocated in the cytoplasm and if it is a transcription factor it could activated immediatly the response.
drawbacks:
It is a nutriment uptake system, so basically only small molecules are able to pass throught the membranes and it is a very specific.
the trick :
Few ABC transporter such as FecABCD (iron transporter) are able to induce à response regardless of the tranlocation, due to the activity of FecA, some mutant can also have a constitutive expression of FecABCD . We could use FecA- mutant receiver and FecA+ mutant donor to transfert working FecA to the receiver. In this case the receiver will express the FecABCD operon, and so we could place under the control of the Fec ABCD promoter the gene sequence encoding for the response.
problems : the message is unidirectionnal and unrepeatable. It would just be a proof of principle that a vesicle-mediated controlled communication is possible.
Two-component system
overview:
The TCS can be cosidered as a widely spread class of biosensor knowing that adaptive signal transduction within microbial cells involving a multi-faceted regulated phosphotransfer mechanism that comprises structural rearrangements of sensor histidine kinases upon ligand-binding and phosphorylation-induced conformational changes in response regulators of versatile two-component systems (TCS), arisen early in bacterial evolution.
In most eubacteria, two-component proteins typically constitute *1% of encoded peptides. In
pathogenic bacteria they control the expression of important pathogenetic factors, in addition to regulating basic
housekeeping functions. The widespread distribution of two-component signal transduction systems in Bacteria and
Achaea reflect their biological value as major sensing and response elements to a wide range of environmental insults
that are tuned to respond from within milliseconds to hours . Although TCSs are probably the most
efficient means of adaptation to conventional stressful stimuli encountered by bacteria during their lifespan, the
plasticity of some of these sophisticated systems may contribute to strain-specific cellular processes and to the
acquisition of distinct features and phenotypes, particularly in pathogens .
To put the structure in a nutshell : A typical TCS consists of a transmembrane dimeric sensor histidine kinase (HK) and a cytoplasmic cognate response regulator (RR). In gram negative bacteria there is often a Periplasmic Binding Protein which optimize the dectection of the molecule localized in the periplasm by a high affinity for the HK after binding the specific molecule.
the following scheme shows a typical ABC mechanism :
uses:
By transferring a packet of molecule synthesize by the donnor but not present in the medium, the arrival could activate the transcription of gene of interest.
advantages/drawbacks:
advantages:
This mecanism is dedicated to the transription of gene under a specific promoter, the difficulty is to find an easily exportable and detectable signal.
drawbacks:
The biosensor are generaly sensible to high diffusible molecule for which the vesicles transport is useless.
the trick:
We could with the help of Alfonso Jaramillo design a synthetic PBP which could detect the substrate we choosed and activate a specific HK. The previous work (Valencia 2006) design a vanilin-sensitive PBP and a network for a graduated response whereas we just need a proteic sensitive PBP and a binary type of response.
strain and part needed: strain : E.coli MRi7 (unable to translocate ribose from periplasm to cytoplasme) part :
référence :
- 1995- Cosima Harle & Volkmar Braun - Signal transfer through three compartments transcription initiation of the Escherichia coiferric citrate transport system from the cell surface
- 2000 - Stock & Goudreau – Two-component signal transduction
- 2001 - Mishima & Murata - Super-channel in bacteria function and structure of the macromolecule import system mediated by a pit-dependent ABC transporter
- 2009 - Akyriakidis & Tiligada – signal transduction TCS the AtoSC paradigm
- 2009 - Tomii & Kanehisa – comparative analysis of ABC transporter
