Team:UNAM-CU/project
Project
Abstract
“Every 7 seconds one person dies from diabetes” (IDF, 2014). Among others, Type 1 Diabetes is the result of a partial or complete lack of insulin production that leads to deregulation of glucose levels in blood. Current available solutions for this disorder are based on complicated and expensive devices of external use. We propose the use of an innovative system based on the construction of a bacterial sensor capable to respond to glucose concentrations; secondly this sensor aims to induce the production of insulin according to glucose levels. The bacteria are going to be contained in a modular device composed by contention, communication, extraction and change sections. For the design of the device, a bio-compatible material was searched. This device is designed specifically to prevent an immune response of the patient. The system designed combines mechanical engineering and biotechnology, ensuring an appropriate and secure insulin dosage for the patient.
Diabetes mellitus is a metabolic disease characterized by the loss or alteration of the capability to regulate blood sugar levels (glycemia). Among other types of diabetes, type 1 diabetes (and in some cases type 2) can be treated by insulin dosage to the patient, which must be highly regulated. The ways of administering insulin are many, but the least uncomfortable happen to be the most expensive ones and all of them imply changes in the quality of life of the patient. Regarding to insulin production at industrial levels, it has been predicted that insulin large scale production technologies could be insufficient to satisfy the demand, so it’s still a challenge to improve the ways this protein is produced. For these reasons, it is our main goal to develop a device capable of sensing glucose levels and to produce insulin in response.
How could it be possible?
The idea is to integrate bacterial populations capable of doing the job within a special compartment .
The Design~
This project is an integrative work of students from different areas including engineering, biology, chemistry, medical, biomedical and genomic sciences.
For the device’s design, biocompatible materials were searched in order to be capable of containing the bacteria as well as allowing glucose levels’ information to pass through it and reach the bacteria, but this container also aims to prevent bacterial physical contact with the exterior.
About the bacterial populations job, we are building a circuit that consists of 2 mains parts:
For this circuit to work, the parts must be able to communicate with each other
Our main goals
Glucose levels detection:
Insulin production:
Theoretical basis
GGBP
GGBP is a monomeric protein that binds glucose with a dissociation constant (KD) in the µM range.
Punctual mutations have been made by research groups in order to diminish its KD to the mM range (Hsieh, 2004); these mutations make it possible to detect glucose levels in physiological concentrations from other organisms, giving the evidence that it could be possible to adjust the detection to human physiological glucose levels as well as abnormal glucose levels due to hyperglycemia in diabetics.
The EnvZ-OmpR Two Component System
Two component systems (TCS) are the major signal transduction mechanisms in bacteria; several receptors can sense some compounds in the media and respond with chemotaxis and metabolic changes.
The EnvZ-OmpR TCS has a chief role in osmoregulation in bacteria. By this mechanism, the bacteria can sense osmotic changes in the environment through the EnvZ receptor, which is bound in the inner membrane of the cell. When the environment osmolarity changes, the EnvZ receptor has a conformational change that leads to its phosphorylation, this phosphorylation lets EnvZ to phosphorylate OmpR , a transcription factor, which can then activate the expression of two porins under the OmpC promoter sequence.
Trg receptor
Trg is a receptor and is part of a TCS able to interact with many periplasmic binding proteins (PBPs); interestingly it interacts with GGBP when bound to glucose and it induces chemotaxis of the bacteria towards the glucose source
The TrgZ chimera
Since Trg and EnvZ share some structural characteristics, in 1994 Baumgartner, et al designed and stably expressed a chimera that puts together the Trg periplasmic domain with the EnvZ citoplasmic domain.
As a consequence, this chimera is able to bind GGBP when the latter is bound to its ligand and this causes a conformational change that activates the EnvZ citoplasmic domain, which in turn activates the transcription factor OmpR activating the expression of any gene under the OmpC promoter sequence.
Insulin
Insulin is a peptidic hormone with many important roles in many organisms’ physiology with short and long term effects. It is produced mainly in the pancreas by beta pancreatic cells, and its active structure is composed of two peptidic chains (A and B) linked by two disulfide bonds; its structure also contains an intrachain disulfide bond within the A chain.
Insulin is began synthesized as preproinsulin, a single peptidic chain with a secretion signal that translocates it to the endoplasmic reticulum (ER), where this signal is proteolyzed before the protein’s translation is finished. Once in the ER, the protein can be folded and the disulfide bonds can be made due to the ER’s oxidative environment. Since the hormone is going to be released to the extracellular matrix, it is involved in a secretion pathway through secretory vesicles, where an intermediate aminoacid sequence is proteolyzed by a carboxypeptidase, giving rise to the final and functional structure of the hormone.
Insulin's MW is about 9kDa when it is still as proinsulin and about 6kDa when it is functional
TAT secretion system
Many secretion systems exist in all organisms, in bacteria, we can find two main pathways by which proteins are secreted to the media.
The model
Due to the complexity of the system we want to develop and test, it is extremely interesting to predict how it will behave in different contexts, and that’s why it is important to involve mathematical modeling in the project.
The modeling can be related to a lot of parts of the system, such as the bacterial populations growth rate, glucose detection and insulin synthesis, the circuit flux of information and the effects a device like the one we are developing would have in a patient.
For details of the modeling, please check that Section in the wiki
Our accomplishments until now
What remains to be done
Lab Journal
Weeks 1 and 2 (June 1st - June 12th)
After many months of looking for a lab where we could work and after planning our project, we arrived to our lab with the Wetlab assesor and began sterilizing some material and locating many things we are going to use.
Also, our guests from the UNAH arrived and we were pleased to teach them some Molecular Biology and Protein’s Physicochemistry principles, as well as how to use scientific software and how to navigate in iGEM’s databases. They are staying in Mexico for 4 weeks.
Weeks 3 and 4 (June 15th - June 26th)
We went to Cuernavaca in order to speak with many researchers about our projects (ours and the one of our guests); we went to the Biotechnology Institute, the Center for Genomic Sciences and the Physics Institute.
We began some Wetlab practices with our UNAH guests and we inoculated the E. coli strains that we are going to use in our project. These strains are:
EnvZ -/- An E. coli strain with a deleterious mutation in the EnvZ receptor, which senses osmotic changes in the media and is part of the EnvZ/OmpR two component system.SHuffle A strain with a cytoplasmic oxidative environment capable of making disulphide bonds in many peptides (which a WT strain is no able to form).
Rosettagami A strain used to synthesize many folded proteins which cannot be right folded by a WT strain.
DH5α Typical WT strain used for molecular biology steps like cloning vectors and amplifying plasmids. This strain methylates its DNA.
JM110 WT strain which doesn’t methylate its DNA, it is used mainly to obtain plasmids for digestion reactions.
All strains were cultured in LB medium
After we amplified our cultures, we were able to make competent cells with CaCl2 and we tried to transform EnvZ-/- and DH5α with our main reporter gene, RFP under OmpR promoter, but got only a single colony in DH5α strain, so we are going to make competent cells again.
Weeks 5 and 6 (June 29th - July 10th)
We followed DH5α, EnvZ-/-, SHuffle and Rosettagami’s growing rates by measuring absorbance at 600nm. They were cultured in complete LB medium.
We made competent cells again with CaCl2 and were able to transform a constitutive GFP and YFP to confirm that our cells were competent. After this confirmation, we transformed our reporter RFP from part BBa_M30011 in DH5α and EnvZ-/- strains.
Weeks 7 and 8 (July 13th - July 24th)
We prepared the solutions needed for a homemade Miniprep and got much more BBa_M30011 plasmid, so we transformed more EnvZ-/- strain with it and amplified both DH5α and EnvZ-/- cultures containing the reporter gene; we kept amplifying cultures with constitutive GFP and YFP in order to use those plasmids to test other techniques.
We measured the LB medium’s osmolarity, since it is important for our project to control it; our LB medium’s osmolarity was 420 mOsm/L so we are going to dilute it to reach an osmolarity of 300mOsm/L, which is the osmolarity of intersticial fluid. We planned the curve we are going to measure in an ELISA plate in order to see how this reporter gene (“OmpR controlled mRFP”) behaves in different conditions of glucose concentration and medium osmolarity.
Weeks 9 and 10 (July 27th - August 7th)
We measured our reporter gene’s expression by measuring it’s absorbance. RFP’s excitation wave length is 560nm and it’s emission wavelength is 612nm. The curve was made for 5 hours and measurements were made every half an hour.
Weeks 11 and 12 (August 10th - August 21st)
Our DNA fragments and oligos finally arrived along with the NEB’s Gibson Assembly Mix so we could finally assemble both of our parts, the Trg-EnvZ chimera and Insulin Lispro, both of them are built under a constitutive promoter to test wether or not they are expressed in our strains.
Weeks 13 and 14 (August 24th - September 4th)
We confirmed the assembly of our parts and we transformed them in our strains to obtain a large quantity of plasmid; we also assembled the parts in PSB1C3 backbone to deliver it to iGEM Headquarters while we test their expression by Western Blot (in the case of insulin) and by stimuli response (in the case of the chimera). We assembled our constructs and after transformation and selection of three clones on the plates, minipreps were performed and subsequent digestión with Xbal was done.
Tar-EnvZ chimera assembly:
Expected bands after Xbal digestion
Obtained bands after Xbal digestion
Obtained band after Xbal digestion
Parts
Parts were designed by Alejandro Rodríguez and Lizbeth Bolaños mainly using the Serial Cloner software.
For both parts, the sequence was obtained by back-translating the aminoacid sequences of interest into nucleotides; then restriction sites like EcoRI, NotI, XbaI (among others) were removed maintaining the open reading frame and finally the nucleotide sequences were codon-optimized for E. coli.
Trg-EnvZ chimera
The Chimera Trg-EnvZ is part of a two component system and it constitutes a chimeric protein composed of the extracellular and transmembrane domains of chemoreceptor Trg and the cytosolic kinase domain of osmosensor EnvZ . Trg is activated by periplasmic binding proteins, and transduces the message to EnvZ to phosphorylate OmpR, a transcription factor which binds to the OmpC promoter driving transcription of whichever gene that is downstream.
Insulin lispro
Insulin lispro is a rapid-acting insulin analog capable of lowering blood glucose levels; it differs from native insulin in that it has an inversion between proline al position B28 and lysine al position B29. This part has a constitutive promoter and an excretion signal from TAT system at its N-terminus
BioBricks.
BBa_K1731001
Insulin lispro is a human insulin analog that dissociates more rapidly than human regular insulin after subcutaneous injection, resulting in higher insulin levels at an earlier point in time and a shorter duration of action[1]. We designed a sequence of constitutive expression for insulin lispro. Our aim is to express lispro as proinsulin containing peptide C and with a TAT sequence in its N terminus. This construct is expected to be expressed in Rossetagami and Shuffle strains, were eukaryotic protein expression and correct folding are enhanced.
In a future we would replace the promoter of this construct for an OmpC promoter so that its expression can be modulated by EnvZ activation.
1. HoweyDC, BowsherRR, BrunelleRL, Woodworth JR: [Lys(B28), Pro(B29)]- human insulin: a rapidly absorbed analogue of human insulin. Diabetes 43:396-402,1994
Results:
Insulin Expression in Rossetagami (R) and SHuffle strains. A western blot was performed with transformed strains with Lispro construct and controls from both strains not transformed. Our biobrick is expressed in the two strains, this result only confirms the protein is expressed but further analysis needs to be done in order to confirm fully formed insulin with disulfide bonds.
BBa_K1731000
Two component systems (TCS) are the major signal transduction mechanisms in bacteria; several receptors can sense some compounds in the media to respond with chemotaxis and metabolic changes. There are several periplasmic binding proteins that are the first sensors to a broad range of molecules; the one of our interest is Glucose Galactose Binding Protein (GGBP)(Dwyer and Hellinga 2004). Glucose is sensed by bacteria through the GGBP which has been proposed as a glucose sensor (Hsieh et al. 2004). Trg-EnvZ was initially created in 1994, in order to measure the carbohydrates concentration and using the EnvZ intracellular domain with a reporter gene, Trg chemoreceptor triggers the chemotaxis of the bacteria while the EnvZ is an osmoregulator which activates the transcription factor OmpR. This chimera allows an easy way to measure glucose concentration using a reporter for EnvZ(Tolosa and Rao 2006).
Dwyer M a., Hellinga HW. Periplasmic binding proteins: A versatile superfamily for protein engineering. Curr. Opin. Struct. Biol. 2004;14(4):495–504.
Hsieh H V., Pfeiffer Z a., Amiss TJ, Sherman DB, Pitner JB. Direct detection of glucose by surface plasmon resonance with bacterial glucose/galactose-binding protein. Biosens. Bioelectron. 2004;19(7):653–60.
Tolosa L, Rao G. The Glucose Binding Protein as Glucose Sensor: Protein engineering for low-cost optical sensing of glucose. Top. Fluoresc. Spectrosc. Vol. 11 Glucose Sens. 2006;11:323–31.
References:
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• Impact of Fat, Protein, and Glycemic Index on Postprandial Glucose Control in Type 1 Diabetes: Implications for Intensive Diabetes Management in the Continuous Glucose Monitoring EraDiabetes Care June 1, 2015 38:1008-1015
• American Diabetes Association. Standards of Medical Care in Diabetes-2015: Abridged for Primary Care Providers. Clinical Diabetes. 2015. 33(2)
• [Guideline] Diagnosis and classification of diabetes mellitus. Diabetes Care. 2010 Jan. 33 Suppl 1:S62-9.
• [Guideline] American Diabetes Association. Standards of medical care in diabetes. 2012. Diabetes Care. 2012 Jan. 35 Suppl 1:S11-63
• Frontiers in Diabetes. Technological Advances in the Treatment of type 1 diabetes; vol. 24. Germany 2014
• Boron, W. F., Boulpaep, E. L. Medical Physiology, 2nd Ed., Elsevier – Saunders. New York, 2012.
• Berne & Levy, Physiology, 6th Ed., Koeppen, B. M., Stanton, B. A. (Eds.),
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• Whoint. (2015). Whoint. Retrieved 13 September, 2015, from http://www.who.int/mediacentre/factsheets/fs312/en/