2013 , an extension of the concept of vitamin

2014 , bringing the engineer's logic into play

	CM Chan, A Danchin, P Marlière, A Sekowska Paralogous metabolism: S-alkyl-cysteine degradation in Bacillus subtilis Environ Microbiol (2014) 16: 101-117
	A Danchin, A Sekowska The logic of metabolism and its fuzzy consequences Environ Microbiol (2014) 16: 19-28

A Danchin
Comment effacer la mémoire de sa mère, ou pourquoi les bébés naissent-ils très jeunes ?
L'Archicube (2014) 16: 55-61

A Danchin
The emergence of the first cells
Encyclopedia of Molecular Cell Biology and Molecular Medicine (2014) doi: 10.1002/3527600906.mcb.20130025
Abstract The scenario proposed here builds on the critical need for compartmentalisation at the origin of life. In a first step, the surface of minerals compartmentalised and selected the reactive compounds that formed primitive metabolism. Subsequently, RNA molecules replaced mineral surfaces after the discovery of nitrogen fixation and the emergence of ribonucleotides, in parallel with a machinery for synthesis of peptides, coenzymes and lipids. Then, the RNA-metabolism world developed into an RNA-genome world based on RNA as informational templates rather than substrates. Bordered by lipids, the first cells were phagocytes, Protokarya, which put together two compartments stemming from the RNA-metabolism world (the cytoplasm) and the RNA-genome world (the nucleus). Emergence of stable deoxyribonucleotides allowed the clustering together of genes into chromosomes. Phagocytosis created the opportunity for an escape based on an alternative metabolism of membrane lipids and conquest of extreme environments, with the Archaea, and on the emergence of a robust and phagocyte-resistant envelope, with the Bacteria. Reductive evolution allowed bacteria with a modified enveloped to be phagocyted again as symbionts of Protokarya, leading to the final generation of the Eukarya. Continuation of horizontal transfer of the genetic material initially resulting from phagocytosis was carried on with the emergence of gene transfer via specialised conjugation machineries and viruses.

Kyrpides, NC, Hugenholtz, P, Eisen, JA, Woyke, T, Goker, M, Parker, CT, Amann, R, Beck, BJ, Chain, PSG, Chun, J, Colwell, RR, Danchin, A, Dawyndt, P, Dedeurwaerdere, T, DeLong, EF; Detter, JC, De Vos, P, Donohue, TJ, Dong, X-Z, Ehrlich, DS, Fraser, C, Gibbs, R, Gilbert, J, Gilna, P, Glockner, FO, Jansson, JK, Keasling, JD, Knight, R, Labeda, D, Lapidus, Al, Lee, J-S, Li, W-J, Ma, J, Markowitz, V, Moore, ERB, Morrison, M, Meyer, F, Nelson, KE, Ohkuma, M, Ouzounis, CA, Pace, N, Parkhill, J, Qin, N, Rossello-Mora, R, Sikorski, J, Smith, D, Sogin, M, Stevens, R, Stingl, U, Suzuki, K-I, Taylor, D, Tiedje, JM, Tindall, B, Wagner, M, Weinstock, G, Weissenbach, J, White, O, Wang, J, Zhang, L, Zhou, Y-G, Field, D, Whitman, WB, Garrity, GM, Klenk, H-P Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strain PLoS Biology (2014) 12: e1001920

BoOks (en français)

Icarie, l'Ile radieuse

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Risk Engineering A Danchin The cellular chassis as the basis for new functionalities: Shortcomings and requirements In: Synthetic Biology. Character and Impact (Editors B.M. Giese, C. Pade, H. Wigger, A. von Gleich), Springer, Berlin (2015)

M Porcar, A Danchin, V de Lorenzo Confidence, tolerance, and allowance in biological engineering: The nuts and bolts of living things BioEssays (2015) 37: 95-102 Abstract The emphasis of systems and synthetic biology on quantitative understanding of biological objects and their eventual re-design has raised the question of whether description and construction standards that are commonplace in electric and mechanical engineering are applicable to live systems. The tuning of genetic devices to deliver a given activity is generally context-dependent, thereby undermining the re-usability of parts, and predictability of function, necessary for manufacturing new biological objects. Tolerance (acceptable limits within the unavoidable divergence of a nominal value) and allowance (deviation introduced on purpose for the sake of flexibility and hence modularity, i.e. fitting together with a variety of other components) are key aspects of standardization that need to be brought to biological design. These should endow functional building blocks with a pre-specified level of confidence for bespoke biosystems engineering. However, in the absence of more fundamental knowledge, fine-tuning necessarily relies on evolutionary/combinatorial gravitation toward a fixed objective

V de Lorenzo, A Sekowska, A Danchin, Chemical reactivity drives spatiotemporal organisation of bacterial metabolism FEMS Microbiology Reviews (2015) 39: 96-119 Abstract We examine how bacterial metabolism is shaped by chemical constraints acting on the material and dynamic layout of enzymatic networks and beyond. These are moulded not only for optimisation of given metabolic objectives (e.g. synthesis of a particular amino acid or nucleotide) but also for curbing the detrimental reactivity of chemical intermediates. Besides substrate channelling, toxicity is avoided by barriers to free diffusion (i.e. compartments) that separate otherwise incompatible reactions, along with ways for distinguishing damaging vs. harmless molecules. On the other hand, enzymes age and their operating lifetime must be tuned to upstream and downstream reactions. This time dependence of metabolic pathways creates time-linked information, learning and memory. These features suggest that the physical structure of existing biosystems, from operon assemblies to multicellular development may ultimately stem from the need to restrain chemical damage and limit the waste inherent to basic metabolic functions. This provides a new twist of our comprehension of fundamental biological processes in live systems as well as practical take-home lessons for the forward DNA-based engineering of novel biological objects

A Danchin, A Sekowska
The logic of metabolism
Perspectives in Science (2015) 6: 15-26

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	M Blaxter, A Danchin, B Savakis, K Fukami-Kobayashi, K Kurokawa, S Sugano, RJ Roberts, SL Salzberg, CI Wu Reminder to deposit DNA sequences Science (2016) 352: 780 doi: 10.1126/science.aaf7672
	E Belda, RG van Heck, MJ Lopez-Sanchez, S Cruveiller, V Barbe, C Fraser, HP Klenk, J Petersen, A Morgat, PI Nikel, D Vallenet, Z Rouy, A Sekowska, VA Martins Dos Santos, V de Lorenzo, A Danchin, C Médigue The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis Environ Microbiol (2016) 18: 3403-3424. doi: 10.1111/1462-2920.13230
	A Danchin From function to structure take the archaeal TRAM Environ Microbiol (2016) 18: 2776-2778 doi: 10.1111/1462-2920.13300
	A Danchin Nature or manufacture: What should we fear most? C R Biol (2016) 339: 329-335. doi: 10.1016/j.crvi.2016.05.001
	A Danchin, G Fang Unknown unknowns: essential genes in quest for function Microb Biotechnol. (2016) 9: 530-540 doi: 10.1111/1751-7915.12384
	PI Nikel, M Chavarría, A Danchin, V de Lorenzo From dirt to industrial applications: Pseudomonas putida as a Synthetic Biology chassis for hosting harsh biochemical reactions Curr Opin Chem Biol (2016) 34: 20-29 doi: 10.1016/j.cbpa.2016.05.011
	A Sekowska, S Wendel, EC Fischer, MH Nørholm, A Danchin Generation of mutation hotspots in ageing bacterial colonies Sci Rep (2016) 6: 2. doi: 10.1038/s41598-016-0005-4
	K Timmis, JL Ramos, W de Vos, S Vlaeminck, A Prieto, A Danchin, W Verstraete, V de Lorenzo Microbial Biotechnology-2020 Microb Biotechnol. (2016) 9: 529 doi: 10.1111/1751-7915.12403
	Y Wang, JM Huang, SL Wang, ZM Gao, AQ Zhang, A Danchin, LS He Genomic characterization of symbiotic mycoplasmas from the stomach of deep-sea isopod Bathynomus sp. Environ Microbiol (2016) 18: 2646-2659 doi: 10.1111/1462-2920.13411

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2017 Bringing the engineer's logic into play
  to explore the human holometabolism

	A Danchin Coping with inevitable accidents of metabolism Microb Biotechnol. (2017) 10: 57-72 doi: 10.1111/1751-7915.12461
	K Bastard, A Perret, A Mariage, T Bessonnet, A Pinet-Turpault, J-L Petit, E Darii, P Bazire, C Vergne-Vaxelaire, C Brewee, A Debard, V Pellouin, M Besnard-Gonnet, F Artiguenave, C Médigue, D Vallenet, A Danchin, A Zaparucha, J Weissenbach, M Salanoubat, V de Berardinis Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis Nat Chem Biol. (2017)13: 858-866 doi:10.1038/nchembio.2397
	A Danchin From chemical metabolism to life: the origin of the genetic coding process Beilstein J Org Chem. (2017) 13: 1119-1135 doi:10.3762/bjoc.13.111
	A Danchin, S Braham Coenzyme B12 synthesis as a baseline to study metabolite contribution of animal microbiota Microb Biotechnol. (2017) 10: 688-701 doi:10.1111/1751-7915.12722
	Timmis K, de Vos WM, Ramos JL, Vlaeminck SE, Prieto A, Danchin A, Verstraete W, de Lorenzo V, Lee SY, Brüssow H, Timmis JK, Singh BK The contribution of microbial biotechnology to sustainable development goals Microb Biotechnol. (2017) 10: 984-987 doi: 10.1111/1751-7915.12818
	Timmis K, de Lorenzo V, Verstraete W, Ramos JL, Danchin A, Brüssow H, Singh BK, Timmis JK The contribution of microbial biotechnology to economic growth and employment creation Microb Biotechnol. (2017) 10: 1137-1144 doi: 10.1111/1751-7915.12845
	He LS, Zhang PW, Huang JM, Zhu FC, Danchin A, Wang Y The enigmatic genome of an obligate ancient Spiroplasma symbiont in a hadal holothurian. Appl Environ Microbiol. (2017) 84:  e01965-17 doi: 10.1128/AEM.01965-17

A Danchin
CRISPR-Cas, accélérateur de la recherche génétique du XXIe siècle
L'Humanité Dimanche 2 novembre 2017

A. Danchin Produit de l'écriture, la science fait l'humanité de l'homme Qu'est-ce que la science pour vous ? (2017) pp. 71-75    Éditions matériologiques, Paris
A Danchin The holy grail of genetic engineering Project Syndicate 14 december 2017

2018  Bringing the engineer's logic into play
  to explore the human holometabolism 

	R Borriss, A Danchin, CR Harwood, C Médigue, EPC Rocha, A Sekowska, D Vallenet Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement Microb Biotechnol. (2018) 11: 3-17 doi: 10.1111/1751-7915.12461
	Y Wang, FC Zhu, LS He, A Danchin Unique tRNA gene profile suggests paucity of nucleotide modifications in anticodons of a deep-sea symbiotic Spiroplasma Nucleic Acids Res. (2018) 46: 2197-2203 doi:10.1111/1751-7915.12461
	A Danchin Bacteria in the ageing gut: Did the taming of fire promote a long human lifespan? Environ Microbiol. (2018) 20: 1066-1087 doi:10.1111/1462-2920.14255
	A Danchin, C Ouzounis, T Tokuyasu, JD Zucker No wisdom in the crowd: genome annotation in the era of big data - current status and future prospects Microb Biotechnol. (2018) 11: 588-605 doi:10.1111/1751-7915.13284
	A Danchin Retour sur les origines de la vie: De l'atome aux molécules, reproduction, réplication Med Sci (Paris) (2018) 34: 857-864 doi:10.1051/medsci/2018212
	A Danchin Retour sur les origines de la vie: Des métabolites aux cellules Med Sci (Paris) (2018) 34: 984-899 doi:10.1051/medsci/2018234
	A Danchin, A Sekowska, S Noria Chapter 5. Functional requirements in the program and the cell chassis for next-generation synthetic biology pp. 81-108 In: Synthetic Biology: Parts, Devices and Applications (2018) Christina Smolke (Editor) Sang Yup Lee (Series Editor), Jens Nielsen (Series Editor), Gregory Stephanopoulos (Series Editor), Wiley doi:10.1002/9783527688104.ch5           ISBN: 978-3-527-68808-1
	A Danchin Multiple clocks in the evolution of living organisms pp. 101-118 In: Molecular Mechanisms of Microbial Evolution (2018) edited by Pabulo H. Rampelotto, Springer ISBN: 978-3-319-69078-0