Myopic selection of novel information drives evolution

Current Opinion in Biotechnology

Volumn 20, Issue 4, 2009, Pages 504-508

  Danchin, Antoine ^a  

^a CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DEGRADATION PROCESS; NOVEL INFORMATION; PROGRAM CODE; SYNTHETIC BIOLOGY;

BIOLOGY; CELL MEMBRANES; DEGRADATION;

GENES;

BACTERIAL GENOME; BACTERIOPHAGE T7; BIOTECHNOLOGY; DIRECTED MOLECULAR EVOLUTION; ESSENTIAL GENE; GENE CONSTRUCT; GENE SEQUENCE; GENE TRANSFER; GENETIC ENGINEERING; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; REVIEW;

DIRECTED MOLECULAR EVOLUTION; HUMANS; INFORMATION SERVICES;

EID: 70349779542     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2009.07.004     Document Type: Review

References (50)

1. Beardsley T. Biotechnology: Cohen-Boyer patent finally confirmed. Nature 311 (1984) 3
2. McAdams H.H., and Shapiro L. Circuit simulation of genetic networks. Science 269 (1995) 650-656
3. Thomas R. Boolean formalization of genetic control circuits. J Theor Biol 42 (1973) 563-585
4. Endy D., You L., Yin J., and Molineux I.J. Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes. Proc Natl Acad Sci U S A 97 (2000) 5375-5380
5. Goodman C. Engineering ingenuity at iGEM. Nat Chem Biol 4 (2008) 13. The iGEM competition plays an extraordinarily positive role in the teaching of Biology, with considerable cohorts of young students attracted to the domain.
6. Katsnelson A. Brick by brick. The Scientist 22 (2009) 42. The engineering view of SB is fairly naïve, as it assumes robustness in biobricks, a feature that is not apparent from what we already possess in the domain.
7. Endy D. Foundations for engineering biology. Nature 438 (2005) 449-453
8. Heinemann M., and Panke S. Synthetic biology - putting engineering into biology. Bioinformatics 22 (2006) 2790-2799
9. Lartigue C., Glass J.I., Alperovich N., Pieper R., Parmar P.P., Hutchison III C.A., Smith H.O., and Venter J.C. Genome transplantation in bacteria: changing one species to another. Science 317 (2007) 632-638. This work demonstrates the feasibility of genome transplantation from one species to another one. Conceptually this is the proof that, as in computers, the program is separated from the living cell machine. It becomes essential that the work is reproduced to make it practical as a tool for SB.
10. Gibson D.G., Benders G.A., Andrews-Pfannkoch C., Denisova E.A., Baden-Tillson H., Zaveri J., Stockwell T.B., Brownley A., Thomas D.W., Algire M.A., et al. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319 (2008) 1215-1220
11. de Lorenzo V., and Danchin A. Synthetic biology: discovering new worlds and new words. EMBO Rep 9 (2008) 822-827
12. Chan L.Y., Kosuri S., and Endy D. Refactoring bacteriophage T7. Mol Syst Biol 1 (2005) 2005.0018
13. Baba T., Ara T., Hasegawa M., Takai Y., Okumura Y., Baba M., Datsenko K.A., Tomita M., Wanner B.L., and Mori H. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2 (2006) 2006.0008
14. Kobayashi K., Ehrlich S.D., Albertini A., Amati G., Andersen K.K., Arnaud M., Asai K., Ashikaga S., Aymerich S., Bessieres P., et al. Essential Bacillus subtilis genes. Proc Natl Acad Sci U S A 100 (2003) 4678-4683
15. Thomaides H.B., Davison E.J., Burston L., Johnson H., Brown D.R., Hunt A.C., Errington J., and Czaplewski L. Essential bacterial functions encoded by gene pairs. J Bacteriol 189 (2007) 591-602
16. Glass J.I., Assad-Garcia N., Alperovich N., Yooseph S., Lewis M.R., Maruf M., Hutchison III C.A., Smith H.O., and Venter J.C. Essential genes of a minimal bacterium. Proc Natl Acad Sci U S A 103 (2006) 425-430
17. Kobayashi I. Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res 29 (2001) 3742-3756
18. Gerdes K., and Wagner E.G. RNA antitoxins. Curr Opin Microbiol 10 (2007) 117-124
19. Zhang R., and Lin Y. DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res 37 (2009) D455-458
20. Tettelin H., Masignani V., Cieslewicz M.J., Donati C., Medini D., Ward N.L., Angiuoli S.V., Crabtree J., Jones A.L., Durkin A.S., et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A 102 (2005) 13950-13955
21. Lapierre P., and Gogarten J.P. Estimating the size of the bacterial pan-genome. Trends Genet 25 (2009) 107-110. Metagenomic studies reveal that the number of genes in the environment is unlimited. Analysis of 573 bacterial genomes shows that while they share a core of common features, there is, in each genome, accretion of genes that belong to clusters evolving along different pathways.
22. Touchon M., Hoede C., Tenaillon O., Barbe V., Baeriswyl S., Bidet P., Bingen E., Bonacorsi S., Bouchier C., Bouvet O., et al. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 5 (2009) e1000344. How far can we go in defining a bacterial species? Comparison of many E. coli genomes with their closest kin, E. fergusonii, permitted identification of a core-genome of some 2000 genes, which can be used to define the species. A set of approximately the same size is collected to make each individual strain, permitting it to adapt to a particular niche.
23. Danchin A. Bacteria as computers making computers. FEMS Microbiol Rev 33 (2009) 3-26
24. Fang G., Rocha E., and Danchin A. How essential are nonessential genes?. Mol Biol Evol 22 (2005) 2147-2156
25. Médigue C., Rouxel T., Vigier P., Hénaut A., and Danchin A. Evidence for horizontal gene transfer in Escherichia coli speciation. J Mol Biol 222 (1991) 851-856
26. Gerdes S., Edwards R., Kubal M., Fonstein M., Stevens R., and Osterman A. Essential genes on metabolic maps. Curr Opin Biotechnol 17 (2006) 448-456
27. Wang Z., and Zhang J. Why is the correlation between gene importance and gene evolutionary rate so weak?. PLoS Genet 5 (2009) e1000329. This analysis demonstrates that, contrary to a widely spread opinion, important genes do not evolve with a speed that differs much from the bulk. However, gene conservation (persistence) is a way to predict the importance of a particular gene.
28. Dyson F.J. Origins of Life (1985), Cambridge University Press, Cambridge, UK
29. Bennett C. Notes on the history of reversible computation. IBM J Res Dev 44 (1988) 270-277
30. Danchin A. Natural selection and immortality. Biogerontology 10 (2009) 503-516. Making a parallel between information theories and biology, this work proposes that information is an authentic category of reality, and that living organisms behave as information traps. An energy-dependent degradative process, using energy to prevent degradation of functional entities is conjectured to make room for the accumulation of information over time.
31. You L., and Yin J. Evolutionary design on a budget: robustness and optimality of bacteriophage T7. Syst Biol (Stevenage) 153 (2006) 46-52
32. Bull J.J., and Molineux I.J. Predicting evolution from genomics: experimental evolution of bacteriophage T7. Heredity 100 (2008) 453-463
33. Nobeli I., Favia A.D., and Thornton J.M. Protein promiscuity and its implications for biotechnology. Nat Biotechnol 27 (2009) 157-167. This review article argues, using published work as well as new reflection, that besides their recognised activity, proteins have much room to display other activities at a low but significant level. In this context there should always be a background level of metabolism in cells, involving most proteins when they have not been altered by ageing or other deleterious processes.
34. Palsson B. Two-dimensional annotation of genomes. Nat Biotechnol 22 (2004) 1218-1219
35. Nogales J., Palsson B.O., and Thiele I. A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst Biol 2 (2008) 79. Metabolic reconstruction is an essential step in the choice of a particular organism as a chassis for evolving it as a cell factory. This work is rich both in the way it identifies the features that have to be considered in priority and in its methodological approach.
36. Chen Z., Wen F., Sun N., and Zhao H. Directed evolution of homing endonuclease I-SceI with altered sequence specificity. Protein Eng Des Sel 22 (2009) 249-256
37. Bershtein S., and Tawfik D.S. Advances in laboratory evolution of enzymes. Curr Opin Chem Biol 12 (2008) 151-158
38. Gupta R.D., and Tawfik D.S. Directed enzyme evolution via small and effective neutral drift libraries. Nat Methods 5 (2008) 939-942
39. Thomson J.M., Gaucher E.A., Burgan M.F., De Kee D.W., Li T., Aris J.P., and Benner S.A. Resurrecting ancestral alcohol dehydrogenases from yeast. Nat Genet 37 (2005) 630-635. The idea to infer ancestral activities from extant ones has been fully exploited in this work. Generalisation of this approach could help us in evolving novel activities, using as start points enzyme with broad substrate spectra.
40. Bull J.J., Springman R., and Molineux I.J. Compensatory evolution in response to a novel RNA polymerase: orthologous replacement of a central network gene. Mol Biol Evol 24 (2007) 900-908
41. Metzgar D., Bacher J.M., Pezo V., Reader J., Doring V., Schimmel P., Marliere P., and de Crecy-Lagard V. Acinetobacter sp. ADP1: an ideal model organism for genetic analysis and genome engineering. Nucleic Acids Res 32 (2004) 5780-5790
42. Philippe N., Crozat E., Lenski R.E., and Schneider D. Evolution of global regulatory networks during a long-term experiment with Escherichia coli. Bioessays 29 (2007) 846-860. This review article summarises observation of long-term experiments recording evolution of bacterial populations in the laboratory. Adaptation to the experimental protocol is often via shortening the duration of the lag phase before re-commencing growth.
43. Anton J., Llobet-Brossa E., Rodriguez-Valera F., and Amann R. Fluorescence in situ hybridization analysis of the prokaryotic community inhabiting crystallizer ponds. Environ Microbiol 1 (1999) 517-523
44. de Crecy-Lagard V.A., Bellalou J., Mutzel R., and Marliere P. Long term adaptation of a microbial population to a permanent metabolic constraint: overcoming thymineless death by experimental evolution of Escherichia coli. BMC Biotechnol 1 (2001) 10
45. Fussmann G.F., Loreau M., and Abrams P.A. Eco-evolutionary dynamics of communities and ecosystems. Funct Ecol 21 (2007) 465-477
46. Nozawa K., O'Donoghue P., Gundllapalli S., Araiso Y., Ishitani R., Umehara T., Soll D., and Nureki O. Pyrrolysyl-tRNA synthetase-tRNA(Pyl) structure reveals the molecular basis of orthogonality. Nature 457 (2009) 1163-1167
47. Liu C.C., Mack A.V., Tsao M.L., Mills J.H., Lee H.S., Choe H., Farzan M., Schultz P.G., and Smider V.V. Protein evolution with an expanded genetic code. Proc Natl Acad Sci U S A 105 (2008) 17688-17693. An excellent illustration, among many other works of the same type, of the way proteins can be evolved using the genetic code degeneracy.
48. Stern D.L., and Orgogozo V. Is genetic evolution predictable?. Science 323 (2009) 746-751
49. Lindner A.B., Madden R., Demarez A., Stewart E.J., and Taddei F. Asymmetric segregation of protein aggregates is associated with cellular aging and rejuvenation. Proc Natl Acad Sci U S A 105 (2008) 3076-3081. A much awaited demonstration that bacteria, as all living organisms, do age.
50. Bylund F., Castan A., Mikkola R., Veide A., and Larsson G. Influence of scale-up on the quality of recombinant human growth hormone. Biotechnol Bioeng 69 (2000) 119-128