ProteInProgress: a cellular assembly line for protein manufacturing

References

A general bibliography about industrial protein manufacturing is reported here:

1. Banki MR, Wood DW (2005), Inteins and affinity resin substitutes for protein purification and scale up. Microbial Cell Factories 2005, 4:32.
2. Gellissen G, Melber K, Janowicz ZA, Dahlems UM, Weydemann U, Piontek M, Strasser AW, Hollenberg CP (1992), Heterologous protein production in yeast. Antonie Van Leeuwenhoek. 1992 Aug;62(1-2):79-93.
3. Jana S, Deb JK (2005), Strategies for efficient production of heterologous proteins in Escherichia coli, Appl Microbiol Biotechnol (2005) 67: 289–298.
4. Kroll J, Klinter S, Schneider C, Voss I, Steinbuchel A (2010), Plasmid addiction systems: perspectives and applications in biotechnology. Microbial Biotechnology. doi:10.1111/j.1751-7915.2010.00170.x.

A specific bibliography about the synthetic biological solutions we have adopted for our project can be found in the sections below.

Self-inducible promoters

1. Anderson JC, Clarke EJ, Arkin AP, Voigt CA (2006). Environmentally controlled invasion of cancer cells by engineered bacteria. J. Mol. Biol. 355 (4): 619–27.
2. Andrianantoandro A, Basu S, Karig DK, Weiss R (2006), Synthetic biology: new engineering rules for an emerging discipline. Molecular Systems Biology 2 Article number: 2006.0028 doi:10.1038/msb4100073
3. Canton B, Labno A, Endy D (2008), Refinement and standardization of synthetic biological parts and devices. Nat Biotechnol. Jul;26(7):787-93.
4. Collins CH, Arnold FH, Leadbetter JR (2005) Directed evolution of Vibrio fischeri LuxR for increased sensitivity to a broad spectrum of acyl-homoserine lactones. Mol Microbiol 55: 712–723
5. Fussenegger M (2010), Synthetic biology: Synchronized bacterial clocks, Nature 463, 301-302 (21 January).
6. Garcia-Ojalvo J, Elowitz MB, Strogatz SH (2004) Modeling a synthetic multicellular clock: repressilators coupled by quorum sensing. Proc Natl Acad Sci USA 101: 10955–10960
7. Hanzelka BM, Stevens AM, Parsek MR, Crone TJ, Greenberg EP (1997), Mutational Analysis of the Vibrio fischeri LuxI Polypeptide: Critical Regions of an Autoinducer Synthase, Journal of Bacteriology, Aug., p. 4882–4887.
8. Jayaraman A, Wood TK (2008). Bacterial quorum sensing: signals, circuits, and implications for biofilms and disease. Annu Rev Biomed Eng. 10:145-67.
9. Kobayashi H, Kaern M, Araki M, Chung K, Gardner TS, Cantor CR, and Collins JJ(2004), Programmable cells: Interfacing natural and engineered gene networks. PNAS 22, 8418-8419.
10. McMillen D, Kopell N, Hasty J, Collins J (2002). Synchronizing genetic relaxation oscillators by intercell signaling. PNAS, 99(2):679-684.
11. Miller MB, Bassler BL (2001), Quorum sensing in bacteria, Annu Rev Microbiol. 2001;55:165-99.
12. Stevens AM, Greenberg EP (1997), Quorum Sensing in Vibrio fischeri: Essential Elements for Activation of the Luminescence Genes. Journal of Bacteriology, Jan., p. 557–562.
13. Weiss R, Knight TF (2000) Engineered communications for microbial robotics. DNA6: Sixth International Meeting on DNA Based Computers, pp 1–55.
14. You L, Cox RS 3rd, Weiss R, Arnold FH (2004), Programmed population control by cell–cell communication and regulated killing. Nature Apr 22;428(6985):868-71.

Integrative standard vector for E. coli

1. Anderson JC, Dueber JE, Leguia M, Wu GC, Goler JA, Arkin AP, Keasling JD (2010), BglBricks: A flexible standard for biological part assembly. Journal of Biological Engineering 2010 4:1.
2. Bernard P (1995), New ccdB positive-selection cloning vectors with kanamycin or chloramphenicol selectable markers. Gene, Aug 30; 162(1) 159-60.
3. Cherepanov PP, Wackernagel W (1995), Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant. Gene 158(1):9-14.
4. Datsenko KA, Wanner BL (2000), One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A., Jun 6;97(12):6640-5.
5. DeLoache W (2009), Constructing and Implementing a Transcription-Based XOR Gate in Escherichia coli through Promoter Engineering. Honors Thesis, Davidson College, Department of Biology, April 6.
6. Diederich L, Rasmussen LJ, Messer W (1992), New cloning vectors for integration in the lambda attachment site attB of the Escherichia coli chromosome. Plasmid. Jul;28(1):14-24.
7. Doublet B, Douard G, Targant H, Meunier D, Madec JY, Cloeckaert A (2008), Antibiotic marker modifications of lambda Red and FLP helper plasmids, pKD46 and pCP20, for inactivation of chromosomal genes using PCR products in multidrug-resistant strains. J Microbiol Methods. Oct;75(2):359-61. Epub 2008 Jun 21.
8. Haldimann A, Wanner BL (2001), Conditional-replication, integration, excision, and retrieval plasmid-host systems for gene structure-function studies of bacteria. Journal of Bacteriology, 183(21), p.6386-6393.
9. Knight T (2003), Idempotent Vector Design for Standard Assembly of Biobricks, MIT DSpace [http://web.mit.edu/synbio/release/docs/biobricks.pdf].
10. Lutz R, Bujard H (1997), Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res. Mar 15;25(6):1203-10.
11. Martinez-Morales F, Borges AC, Martinez A, Shanmaugam KT, Ingram LO (1999), Chromosomal Integration of Heterologous DNA in Escherichia coli with Precise Removal of Markers and Replicons Used during Construction. Journal of Bacteriology, Vol. 181, No. 22, November, p. 7143–7148.
12. Posfai G, Koob MD, Kirkpatrick HA, Blattner FR (1997), Versatile Insertion Plasmids for Targeted Genome Manipulations in Bacteria: Isolation, Deletion, and Rescue of the Pathogenicity Island LEE of the Escherichia coli O157:H7 Genome. Journal of Bacteriology, Vol. 179, No. 13July, p. 4426–4428.
13. Shetty R, Endy D, Knight T (2008), Engineering BioBrick vectors from BioBrick parts. Journal of Biological Engineering, 2:5.

Integrative standard vector for yeast

1. De Antoni A, Gallwitz D (2000), A novel multi-purpose cassette for repeated integrative epitope tagging of genes in Saccharomyces cerevisiae. Gene 246, 179–185.
2. Giaever G et al. (2002), Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387-391.
3. Guldener U, Heck S, Fiedler T, Beinhauer J, Hegemann JH (1996), A new efficient gene disruption cassette for repeated use in budding yeast. Nucleic Acids Research, Vol. 24, No. 13 2519–2524.
4. Gueldener U, Heinisch J, Koehler GJ, Voss D, Hegemann JH (2002), A second set of loxP marker cassettes for Cre-mediated multiple gene knockouts in budding yeast. Nucleic Acids Res. Mar 15;30(6):e23.
5. Kim KS, Pfeifer K, Powell L, Guarente L (1990), Internal deletions in the yeast transcriptional activator HAP1 have opposite effects at two sequence elements. Proc. Nad. Acad. Sci. USA Vol. 87, pp. 4524-4528, June, Genetics.
6. Kim MD, Lee TH, Lim HK, Seo JH (2004), Production of antithrombotic hirudin in GAL1-disrupted Saccharomyces cerevisiae. Applied Microbiology and Biotechnology Volume 65, Number 3 / August.
7. Mortimer RK, Johnston JR (1986), Genealogy of principal strains of the yeast genetic stock center. Genetics 113(1):35-43.
8. Nevoigt E, Kohnke J, Fischer CR, Alper H, Stahl U, Stephanopoulos G (2006), Engineering of Promoter Replacement Cassettes for Fine-Tuning of Gene Expression in Saccharomyces cerevisiae. Applied and Environmental Microbiology, August, Vol. 72, No. 8, 5266–5273.
9. Rohde JR, Trinh J, Sadowski I (2000), Multiple Signals Regulate GAL Transcription in Yeast. Molecular and Cellular Biology, June, p. 3880–3886 Vol. 20, No. 11.
10. Sauer B (1987), Functional expression of the cre-lox site-specific recombination system in the yeast Saccharomyces cerevisiae. Mol. Cell. Biol., 7, 2087–2096.
11. Sherman F (1998), An Introduction to the Genetics and Molecular Biology of the Yeast Saccharomyces cerevisiae. University of Rochester Medical School, Rochester.
12. Sliwa P, Korona R (2005), Loss of dispensable genes is not adaptive in yeast. PNAS, December 6, vol. 102, no.49, 17670–17674.
13. West RW Jr, R. Rogers Yocum R, Ptashne M (1984), Saccharomyces cerevisiae GAL1-GAL1O Divergent Promoter Region: Location and Function of the Upstream Activating Sequence UASG. Molecular and Cellular Biology, November, P.2467-2478, Vol. 4. No. 11.
14. Winzeler EA et al. (1999), Functional Characterization of the S. cerevisiae Genome by Gene Deletion and Parallel Analysis. Science 285, 901.

Self-cleaving affinity tags to easily purify proteins

1. Banki M, Gerngross T, Wood D (2005), Novel and economical purification of recombinant proteins: Intein-mediated protein purification using in vivo polyhydroxybutyrate (PHB) matrix association. Protein Science, 14(6):1387–1395.
2. Barnard GC, McCool JD, Wood DW, Gerngross TU (2005), Integrated Recombinant Protein Expression and Purification Platform Based on Ralstonia eutropha. Applied and Environmental Microbiology, Oct., Vol. 71, No. 10, p.5735–5742.
3. Georgiou G, Jeong KJ (2005), Proteins from PHB granules. Protein Sci. 2005 June; 14(6): 1385–1386.
4. Neumann L, Spinozzi F, Sinibaldi R, Rustichelli F, Potter M, Alexander Steinbuchel A (2008), Binding of the Major Phasin, PhaP1, from Ralstonia eutropha H16 to Poly(3-Hydroxybutyrate) Granules. Journal of Bacteriology, Apr., Vol. 190, No. 8, p.2911–2919.
5. Potter M, Madkour M, Mayer F, Steinbuchel A (2002), Regulation of phasin expression and polyhydroxyalkanoate (PHA) granule formation in ralstonia eutropha h16. Microbiology, 148(8):2413.
6. Spiekermann P, Rehm B, Kalscheuer K, Baumeister D, Steinbuchel A (1999). A sensitive, viable-colony staining method using nile red for direct screening of bacteria that accumulate polyhydroxyalkanoic acids and other lipid storage compounds. Archives of microbiology, 171(2):73–80.
7. Sudan Black staining protocol for PHB: http://santacruzproductions.com/PHBStain.aspx
8. Valentin HE, Dennis D (1997). Production of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) in recombinant Escherichia coli grown on glucose. Journal of Biotechnology, Volume 58, Issue 1, 2 Oct., p.33-38.
9. Wood DW, Wu W, Belfort G, Derbyshire V, Belfort M (1999), A genetic system yields self-cleaving inteins for bioseparations. Nature Biotechnology, Vol. 17, September, 889-892.