ProteInProgress: a cellular assembly line for protein manufacturing

References

Self-inducible promoters

COS’E’ il QUORUM SENSING:

Jayaraman A, Wood TK (. Bacterial quorum sensing: signals, circuits, and implications for biofilms and disease. Annu Rev Biomed Eng. 2008; 10:145-67.

Miller MB, Bassler BL (2001), Quorum sensing in bacteria, Annu Rev Microbiol. 2001;55:165-99.

GENI LUX VIBRIO FISCHERI:

BRIAN L. HANZELKA, ANN M. STEVENS,† MATTHEW R. PARSEK, TAMMERA J. CRONE, AND E. P. GREENBERG (1997), Mutational Analysis of the Vibrio fischeri LuxI Polypeptide: Critical Regions of an Autoinducer Synthase, JOURNAL OF BACTERIOLOGY, Aug. 1997, p. 4882–4887

ANN M. STEVENS, E. P. GREENBERG (1997), Quorum Sensing in Vibrio fischeri: Essential Elements for Activation of the Luminescence Genes JOURNAL OF BACTERIOLOGY, Jan. 1997, p. 557–562

Weiss R, Knight TF (2000) Engineered communications for microbial robotics. DNA6: Sixth International Meeting on DNA Based Computers, pp 1–55

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

APPLICAZIONI IN BIOLOGIA SINTETICA DI AUTOINDUZIONE DA QUORUM SENSING:

Anderson et al. (2006), Environmental…

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.

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

Canton B, Labno A, Endy D (2008), Refinement and standardization of synthetic biological parts and devices. Nat Biotechnol. Jul;26(7):787-93.

M. Fussenegger (2010), Synthetic biology: Synchronized bacterial clocks, Nature 463, 301-302 (21 January 2010) | doi:10.1038/463301a

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

McMillen D, Kopell N, Hasty J, Collins J (2002). Synchronizing genetic relaxation oscillators by intercell signaling. PNAS, 99(2):679-684.

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