Chemical approaches to synthetic biology.

The term chemical synthetic biology defines that part of the field that, instead of assuming an engineering approach based on genome manipulation, is oriented towards the synthesis of chemical structures alternative to those present in nature. Several different literature projects will be illustrated, including the two of our group. One is concerned with the 'Never Born Proteins' (NBPs), namely polypeptide sequences that are not present in nature, the other is concerned with the notion of 'minimal cells', semi-synthetic compartments (usually liposomes) containing the minimal and sufficient number of components to perform the basic function of a biological cell.

[1]  Andrés Moya,et al.  Extreme genome reduction in Buchnera spp.: Toward the minimal genome needed for symbiotic life , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[2]  Timothy B. Stockwell,et al.  Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome , 2008, Science.

[3]  D. Endy.  Foundations for engineering biology , 2005, Nature.

[4]  J. Szostak,et al.  Template-directed synthesis of a genetic polymer in a model protocell , 2008, Nature.

[5]  M. Kula,et al.  Improving the carboligase activity of benzoylformate decarboxylase from Pseudomonas putida by a combination of directed evolution and site-directed mutagenesis. , 2002, Protein engineering.

[6]  Tetsuya Yomo,et al.  Expression of a cascading genetic network within liposomes , 2004, FEBS letters.

[7]  High solubility of random-sequence proteins consisting of five kinds of primitive amino acids. , 2005, Protein engineering, design & selection : PEDS.

[8]  Takuya Ueda,et al.  Cell-free translation reconstituted with purified components , 2001, Nature Biotechnology.

[9]  R C Ladner.  Phage display and pharmacogenomics. , 2000, Pharmacogenomics.

[10]  P. Luisi,et al.  Enzymatic RNA replication in self-reproducing vesicles: an approach to a minimal cell. , 1995, Biochemical and biophysical research communications.

[11]  Fabio Polticelli,et al.  Investigation of de novo Totally Random Biosequences, Part II , 2006, Chemistry & biodiversity.

[12]  Pier Luigi Luisi,et al.  Autocatalytic self-replicating micelles as models for prebiotic structures , 1992, Nature.

[13]  S. Akanuma,et al.  Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[14]  Pier Luigi Luisi,et al.  OPARIN'S REACTIONS REVISITED : ENZYMATIC SYNTHESIS OF POLY(ADENYLIC ACID) IN MICELLES AND SELF-REPRODUCING VESICLES , 1994 .

[15]  O. Olsen,et al.  Rational design of coagulation factor VIIa variants with substantially increased intrinsic activity , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[16]  M Wakabayashi,et al.  Synthesis of functional protein in liposome. , 2001, Journal of bioscience and bioengineering.

[17]  E. Andrianantoandro,et al.  Synthetic biology: new engineering rules for an emerging discipline , 2006, Molecular systems biology.

[18]  Pasquale Stano,et al.  Approaches to semi-synthetic minimal cells: a review , 2005, Naturwissenschaften.

[19]  Sung-Hun Nam,et al.  Design and Evolution of New Catalytic Activity with an Existing Protein Scaffold , 2006, Science.

[20]  Yoichiro Ito,et al.  Evolution of an Arbitrary Sequence in Solubility , 2004, Journal of Molecular Evolution.

[21]  P. Luisi.  About Various Definitions of Life , 1998, Origins of life and evolution of the biosphere.

[22]  Christian de Duve,et al.  Life Evolving: Molecules, Mind, and Meaning , 2002 .

[23]  Pasquale Stano,et al.  The Minimal Size of Liposome‐Based Model Cells Brings about a Remarkably Enhanced Entrapment and Protein Synthesis , 2009, Chembiochem : a European journal of chemical biology.

[24]  Kenichi Yoshikawa,et al.  Gene Expression within Cell‐Sized Lipid Vesicles , 2003, ChemBioChem.

[25]  Alberto Diaspro,et al.  Protein synthesis in liposomes with a minimal set of enzymes. , 2007, Biochemical and biophysical research communications.

[26]  L. H. Bradley,et al.  De novo proteins from designed combinatorial libraries , 2004, Protein science : a publication of the Protein Society.

[27]  Robert T. Sauer,et al.  Cooperatively folded proteins in random sequence libraries , 1995, Nature Structural Biology.

[28]  Tetsuya Yomo,et al.  Can an Arbitrary Sequence Evolve Towards Acquiring a Biological Function? , 2003, Journal of Molecular Evolution.

[29]  P. Luisi,et al.  Polymerase chain reaction in liposomes. , 1995, Chemistry & biology.

[30]  R. Micura,et al.  Pyranosyl-RNA: chiroselective self-assembly of base sequences by ligative oligomerization of tetranucleotide-2',3'-cyclophosphates (with a commentary concerning the origin of biomolecular homochirality). , 1997, Chemistry & biology.

[31]  Patrick C Cirino,et al.  Generating mutant libraries using error-prone PCR. , 2003, Methods in molecular biology.

[32]  Martin M Hanczyc,et al.  Replicating vesicles as models of primitive cell growth and division. , 2004, Current opinion in chemical biology.

[33]  Vincent Noireaux,et al.  A vesicle bioreactor as a step toward an artificial cell assembly. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[34]  Tetsuya Yomo,et al.  Evolvability of random polypeptides through functional selection within a small library. , 2002, Protein engineering.

[35]  Yinan Wei,et al.  Stably folded de novo proteins from a designed combinatorial library , 2003, Protein science : a publication of the Protein Society.

[36]  L. H. Bradley,et al.  Protein design by binary patterning of polar and nonpolar amino acids. , 1993, Methods in molecular biology.

[37]  Hiroshi Murakami,et al.  Random insertion and deletion mutagenesis. , 2003, Methods in molecular biology.

[38]  Y. Shimada,et al.  Positional and fatty acid specificities of Geotrichum candidum lipases. , 1994, Protein engineering.

[39]  Cameron Neylon,et al.  Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: library construction methods for directed evolution. , 2004, Nucleic acids research.

[40]  P. Luisi,et al.  Protein expression in liposomes. , 1999, Biochemical and biophysical research communications.

[41]  Ronald R. Breaker,et al.  Production of RNA by a polymerase protein encapsulated within phospholipid vesicles , 1994, Journal of Molecular Evolution.

[42]  H. Maturana,et al.  Autopoiesis: the organization of living systems, its characterization and a model. , 1974, Currents in modern biology.

[43]  A. Paul,et al.  Chemical Synthesis of Poliovirus cDNA: Generation of Infectious Virus in the Absence of Natural Template , 2002, Science.

[44]  D. Bartel,et al.  Synthesizing life : Paths to unforeseeable science & technology , 2001 .

[45]  Yutetsu Kuruma,et al.  A synthetic biology approach to the construction of membrane proteins in semi-synthetic minimal cells. , 2009, Biochimica et biophysica acta.

[46]  Kazufumi Hosoda,et al.  Quantitative study of the structure of multilamellar giant liposomes as a container of protein synthesis reaction. , 2008, Langmuir : the ACS journal of surfaces and colloids.

[47]  Pasquale Stano,et al.  From Never Born Proteins to Minimal Living Cells: Two Projects in Synthetic Biology , 2007, Origins of Life and Evolution of Biospheres.

[48]  P. Luisi,et al.  Autopoiesis with or without cognition: defining life at its edge , 2004, Journal of The Royal Society Interface.

[49]  G. Winter,et al.  Proteolytic selection for protein folding using filamentous bacteriophages. , 1998, Folding & design.

[50]  Burckhard Seelig,et al.  Selection and evolution of enzymes from a partially randomized non-catalytic scaffold , 2007, Nature.

[51]  Frances Arnold,et al.  Staggered extension process (StEP) in vitro recombination. , 2002, Methods in molecular biology.

[52]  Peter E. Nielsen,et al.  PNA hybridizes to complementary oligonucleotides obeying the Watson–Crick hydrogen-bonding rules , 1993, Nature.

[53]  Kazufumi Hosoda,et al.  Replication of Genetic Information with Self‐Encoded Replicase in Liposomes , 2008, ChemBioChem.

[54]  Pier Luigi Luisi,et al.  Chemical Aspects of Synthetic Biology , 2007, Chemistry & biodiversity.

[55]  P. Luisi.  The Emergence of Life: Autopoiesis: the logic of cellular life , 2006 .