IGEM:MIT/2007/Ideas

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Ideas to chew on

Some ideas from 4/23/07 meeting

M1. Bacteria with squid reflecting protein (reflectin)

  • comments:
    • Brian: 6 family members, all highly homologous
    • Brian: biggest issue could be solubility problems (E. Coli)
    • Brian: try expression in different systems where folding more likely to be correct (yeast, streptomyces, etc)
    • Brian: only 1 major publication, so very little known about possible chaperones (see reference)
    • Forrest: Paper on Methionine-Rich Repeat Proteins (MRRPs)


M2. Self mini-prepping bacteria

  • comments: once triggered, will lyse, express RNases, and precipitate proteins and genomic DNA


M3. Bacteria with limited lifetime (telomeres)

  • comments:
    • Brian: streptomyces bacteria have linear genome
    • Brian: e. coli w/ linear genomes have been constructed (see reference)
    • tk: The N15 plasmid (works in E. coli, commercially available from Lucigen) is linear.


M4. Bacteria with removed/non-functional DNA

  • comments: "minicells" will grow for several weeks


M5. Incorporating biobrick parts into minicell

  • comments: difficult to produce in large quatities


M6. Magnetic alignment of bacteria

  • comments:
    • Brian: surface display of peptide which binds magnetic nanoparticles (iron oxide, cobalt oxide)
    • Brian: can we control number of bound nanoparticles via concentration (i.e. one NP per bacteria)?
    • Brian: feasibility: can we generate enough force and torque on NP to align bacteria (calculations)
    • Forrest: Iron oxide nanoparticles tend to fall off the protein surface near neutral pH; cobalt oxide adheres better, but the synthesis conditions are quite toxic for cells


M7. Bacteria that illuminate when dark

  • comments:


M8. Bacteria which synthesize vitamins

  • comments: Major vitamin deficiencies
    • Brian: One of the most serious vitamin deficiencies in the current world is that of vitamin D (described as an epidemic in the USA). Although it can be produced by humans, the synthesis requires sunlight and many people do not receive sufficient UV radiation to produce the minimum daily requirement. Vitamin D is required for efficient calcium absorption in the gut, and deficiency leads to many bone disorders (rickets, osteoporosis, etc) as well as increasing the risk of autoimmune disease, diabetes, cancer, and cardiovascular disease. Current methods to synthesize vitamin D use extraction from sheep's wool. For more info on vitamin D, see wikipedia page epidemic cancer
    • Brian: Another option is Vitamin B12, which is the main vitamin lacking in vegan diets (deficiency causes pernicious anemia). It is produced ONLY in prokaryotic organisms...
    • Brian: Beriberi is caused by deficiency in thiamine (vitamin B1). It is very prevalent in Asian countries where many people rely entirely on white rice for their diet.


M9. Sensing pH

  • comments:
    • Brian: idea -- use anthocyanins as pH sensor (expressed in plants such as red cabbage)
    • Brian: E. Coli have been metabolically engineered to produce anthocyanin (see reference)


M10. Bacteria with kill switch

  • comments:


M11. Bacteria battle

  • comments:
    • Forrest: Austin mentioned during the 4/23/07 meeting that this could be done in 2-D (on a dish)
    • Forrest: Environmental conditions/stimuli can skew the outcome (e.g. shinning light or lowering pH causes on colony to have advantage over another)
    • Brian: Could use F factor (bacterial conjugation) as the "weapon", where Strain A delivers a repressor gene lethal to Strain B and so on.
    • Brian: Could have multiple fighting strains (e.g., A kills B, B kills C, C kills A)
    • Brian: Possible to see population oscillations? Could easily model the system...
    • tk: The idea of "phage wars" was an early incarnation of the IGEM competition. We rejected it because it seemed too yucky.


M12. Plastic binding bacteria

  • comments: credit to Reshma
    • Brian: bacteria bind to polymer plastic via surface display peptides
    • Brian: one idea: couple to growth phase -- bacteria in stationary phase bind to side of plastic tube, which those still growing can be poured out (easy separation)
    • Forrest: We have peptide sequences that bind to an electically conducting polymer (PPyCl) (NATURE MATERIALS 4 (6): 496-502 JUN 2005)
    • tk: wouldn't a plastic making bacterium be more interesting?
    • Forrest: Perhaps the bacteria can produce keratin, i.e. the plastic-like structural material in bird feathers; it would be very interesting to produce different keratin compositions (e.g. include pigments for color or strenghening) and microstructures (e.g. to diffract light like some feathers do)
    • Forrest: Plastic Made by Bacteria Commercialized (Apr '07)
    • Forrest: Some pionnering work is lead by MIT's Anthony Sinskey (Biopolymer Engineering)


M13. Luciferase Lava Lamp

  • comments: credit to Reshma


M14. Organic Transister?

  • comments:
    • using conductive M13 phage nanowires?
    • Forrest: For electrical transister, M13 phage is not suitable because it's difficult to program both the head and tail to bind to electrodes. In the past, someone has been able to bind the tail end to an electrode and play with flow to get the head to make contact with another electrode. Not sure how much more we can improve on...

Random ideas from Superphage (Forrest)

F1. Engineering bacteria to operate in extreme environment (extremophiles)

  • bacteria that die when not in artificially harsh environments (i.e. bacteria that 'escaped' from lab would not thrive)

http://environment.newscientist.com/article/dn11614-extremeliving-bacteria-has-genome-sequenced.html

  • comments:


F2. High protein bacteria/fungus

  • Easy to grow, and highly-nutritious
  • To be made into bread spread for poor or disaster-striken communities
  • comments:


F3. Blood clotting phage/bacteria

  • function like Chitosan bandaids

http://en.wikipedia.org/wiki/Chitosan

  • comments:


F4. Bacteria that process animal waste to recover nutrients

  • Recover proteins and other substances from pool of farm animal waste (e.g. the edible stuff floats to the top) and add back to animal feed
  • comments:


F5. Food spoilage detection

  • Add non-harmful bacteria to milk, meat packaging, etc; these bacteria grow slightly more easily that the usual bacteria that make people sick, and are highly visible (e.g. bright purple) when they grow
  • If consumer sees purple, if means that the food is possibly spoiled
  • comments:


F6. Fungus-based sensors

Random ideas from Cookb (Brian)

B1. RNA oligo synthesizing bacteria

  • bacteria that produce and secrete RNA (mRNA, siRNA, RNAi, microRNA, etc)
  • could be used to mass produce RNA-based therapies
  • benefit from high-fidelity biological production (no error-prone commercial synthesis)
  • commercial synthesis is limited to <20 bp (maybe 50 bp max)
  • purification by HPLC later (and analyze by MS)
  • protect RNA (chemicals protect 2'OH, could secrete as dsRNA)
  • F factor secretion?

Olfactory sensing systems

  • The idea is to capture the very wide diversity of the olfactory sensing systems in mammalian noses.
  • Like antibodies, there is a very wide range of sequenced olfactory systems, especially from the new Dog genome.
  • Here is a list of possible readings. Short version: proofs of concept in yeast have been made.
  1. Katada S, Nakagawa T, Kataoka H, and Touhara K. Odorant response assays for a heterologously expressed olfactory receptor. Biochem Biophys Res Commun. 2003 Jun 13;305(4):964-9. PubMed ID:12767924 | HubMed [Katada02]
  2. Pajot-Augy E, Crowe M, Levasseur G, Salesse R, and Connerton I. Engineered yeasts as reporter systems for odorant detection. J Recept Signal Transduct Res. 2003;23(2-3):155-71. DOI:10.1081/RRS-120025196 | PubMed ID:14626444 | HubMed [Pajot-Augy03]
  3. Levasseur G, Persuy MA, Grebert D, Remy JJ, Salesse R, and Pajot-Augy E. Ligand-specific dose-response of heterologously expressed olfactory receptors. Eur J Biochem. 2003 Jul;270(13):2905-12. PubMed ID:12823561 | HubMed [Levasseur03]
  4. Minic J, Sautel M, Salesse R, and Pajot-Augy E. Yeast system as a screening tool for pharmacological assessment of g protein coupled receptors. Curr Med Chem. 2005;12(8):961-9. PubMed ID:15853708 | HubMed [Minic05]
  5. Minic J, Persuy MA, Godel E, Aioun J, Connerton I, Salesse R, and Pajot-Augy E. Functional expression of olfactory receptors in yeast and development of a bioassay for odorant screening. FEBS J. 2005 Jan;272(2):524-37. DOI:10.1111/j.1742-4658.2004.04494.x | PubMed ID:15654890 | HubMed [Minic05a]
  6. Touhara K. Odor discrimination by G protein-coupled olfactory receptors. Microsc Res Tech. 2002 Aug 1;58(3):135-41. DOI:10.1002/jemt.10131 | PubMed ID:12203691 | HubMed [Touhara02]
  7. Shirokova E, Schmiedeberg K, Bedner P, Niessen H, Willecke K, Raguse JD, Meyerhof W, and Krautwurst D. Identification of specific ligands for orphan olfactory receptors. G protein-dependent agonism and antagonism of odorants. J Biol Chem. 2005 Mar 25;280(12):11807-15. DOI:10.1074/jbc.M411508200 | PubMed ID:15598656 | HubMed [Shirokova05]
  8. Radhika V, Proikas-Cezanne T, Jayaraman M, Onesime D, Ha JH, and Dhanasekaran DN. Chemical sensing of DNT by engineered olfactory yeast strain. Nat Chem Biol. 2007 Jun;3(6):325-30. DOI:10.1038/nchembio882 | PubMed ID:17486045 | HubMed [Radhika02]
All Medline abstracts: PubMed | HubMed

Comments:

  • Brian -- I work on olfactory receptors (ORs), so I have a good deal of experience with them. But they are difficult to express (especially in bacteria and yeast) and this could be tricky to do in a summer, especially if trying to use multiple OR proteins.


Stick-to-everything proteins from mussels

  1. Hwang DS, Yoo HJ, Jun JH, Moon WK, and Cha HJ. Expression of functional recombinant mussel adhesive protein Mgfp-5 in Escherichia coli. Appl Environ Microbiol. 2004 Jun;70(6):3352-9. DOI:10.1128/AEM.70.6.3352-3359.2004 | PubMed ID:15184131 | HubMed [Hwang04]
  2. Hwang DS, Gim Y, and Cha HJ. Expression of functional recombinant mussel adhesive protein type 3A in Escherichia coli. Biotechnol Prog. 2005 May-Jun;21(3):965-70. DOI:10.1021/bp050014e | PubMed ID:15932281 | HubMed [Hwang05]
  3. Hwang DS, Gim Y, Yoo HJ, and Cha HJ. Practical recombinant hybrid mussel bioadhesive fp-151. Biomaterials. 2007 Aug;28(24):3560-8. DOI:10.1016/j.biomaterials.2007.04.039 | PubMed ID:17507090 | HubMed [Hwang07]
  4. Hwang DS, Gim Y, Kang DG, Kim YK, and Cha HJ. Recombinant mussel adhesive protein Mgfp-5 as cell adhesion biomaterial. J Biotechnol. 2007 Jan 20;127(4):727-35. DOI:10.1016/j.jbiotec.2006.08.005 | PubMed ID:16979252 | HubMed [Hwang07a]
  5. Lee H, Scherer NF, and Messersmith PB. Single-molecule mechanics of mussel adhesion. Proc Natl Acad Sci U S A. 2006 Aug 29;103(35):12999-3003. DOI:10.1073/pnas.0605552103 | PubMed ID:16920796 | HubMed [Lee06]
  6. Lin Q, Gourdon D, Sun C, Holten-Andersen N, Anderson TH, Waite JH, and Israelachvili JN. Adhesion mechanisms of the mussel foot proteins mfp-1 and mfp-3. Proc Natl Acad Sci U S A. 2007 Mar 6;104(10):3782-6. DOI:10.1073/pnas.0607852104 | PubMed ID:17360430 | HubMed [Lin07]
  7. Wang J, Liu C, Lu X, and Yin M. Co-polypeptides of 3,4-dihydroxyphenylalanine and L-lysine to mimic marine adhesive protein. Biomaterials. 2007 Aug;28(23):3456-68. DOI:10.1016/j.biomaterials.2007.04.009 | PubMed ID:17475323 | HubMed [Wang07]
All Medline abstracts: PubMed | HubMed

Comments:

  • Forrest -- ref.13 points:
    • adhesive properties are from an "unusual amino acid 3,4-dihydroxy-l-phenylalanine (dopa)"
    • "On inorganic surfaces the unoxidized dopa forms high-strength yet reversible coordination bonds, whereas on organic surfaces oxidized dopa is capable of adhering via covalent bond formation."
  • Forrest --
    • could perhaps express dopa on p3 (tail) or p8 (main body) protein of M13 phage
    • after discussing with Rana, it seems that phage is probably not appropriate b/c 1) it is difficult/impossible to engineer phage to express tyrosine (perhaps too bulky) and 2) a phagemid approach would incorporate dopa arbitrarily and sparsely on phage; our best bet would be to engineer p3 of phage (p3 engineering is generally more forgiving than p8)
  • Brian -- could express on E. Coli using fusion to surface proteins (e.g., OmpA, OmpX, FhuA, or LamB). see references below
    • also possible to express on flagella via the Invitrogen FliTrx system
    • a good consensus peptide appears to be AKPSYPPTYK, with tyrosines getting converted to L-DOPA. Also reported to have prolines converted to hydroxyproline, but not sure if required for stickiness.
    • can convert tyrosine residues to L-DOPA by adding tyrosine hydroxylase (later could have bacteria secrete it)
    • main question/concern is will bacteria stick to each other and clump up? separations obviously won't work if sticky (+) bacteria adhere to the non-sticky (-) bacteria we are trying to separate from.
    • some papers on bacterial surface display:
  1. Rice JJ, Schohn A, Bessette PH, Boulware KT, and Daugherty PS. Bacterial display using circularly permuted outer membrane protein OmpX yields high affinity peptide ligands. Protein Sci. 2006 Apr;15(4):825-36. DOI:10.1110/ps.051897806 | PubMed ID:16600968 | HubMed [Rice07]
  2. Bessette PH, Rice JJ, and Daugherty PS. Rapid isolation of high-affinity protein binding peptides using bacterial display. Protein Eng Des Sel. 2004 Oct;17(10):731-9. DOI:10.1093/protein/gzh084 | PubMed ID:15531628 | HubMed [Bessette04]
  3. Etz H, Minh DB, Schellack C, Nagy E, and Meinke A. Bacterial phage receptors, versatile tools for display of polypeptides on the cell surface. J Bacteriol. 2001 Dec;183(23):6924-35. DOI:10.1128/JB.183.23.6924-6935.2001 | PubMed ID:11698382 | HubMed [Etz01]
  4. Hall SS, Mitragotri S, and Daugherty PS. Identification of peptide ligands facilitating nanoparticle attachment to erythrocytes. Biotechnol Prog. 2007 May-Jun;23(3):749-54. DOI:10.1021/bp060333l | PubMed ID:17469847 | HubMed [Hall07]
  5. Samuelson P, Gunneriusson E, Nygren PA, and Ståhl S. Display of proteins on bacteria. J Biotechnol. 2002 Jun 26;96(2):129-54. PubMed ID:12039531 | HubMed [Samuelson02]
  6. Wernérus H and Ståhl S. Biotechnological applications for surface-engineered bacteria. Biotechnol Appl Biochem. 2004 Dec;40(Pt 3):209-28. DOI:10.1042/BA20040014 | PubMed ID:15035661 | HubMed [Wernerus04]
All Medline abstracts: PubMed | HubMed

Adhesive bacteria with surface specificity

  • Brian-- Non-specific binding (mussel peptide) has certain disadvantages, such as exotic amino acids (DOPA, hydroxyproline) and possibility of cell clumping.
  • Instead could investigate adhesive peptides which specifically bind common plastic/polymer surfaces.
    • Polystyrene/polyurethane binding peptide WxxWxxxW, related to fibrinogen
  1. Gebhardt K, Lauvrak V, Babaie E, Eijsink V, and Lindqvist BH. Adhesive peptides selected by phage display: characterization, applications and similarities with fibrinogen. Pept Res. 1996 Nov-Dec;9(6):269-78. PubMed ID:9048419 | HubMed [Gebhart96]