microme
Everything works by spirit on spirit, therefore the spirit of the medicine works on the spirit of the disease. Certain diseases are combatable by certain spirits in certain herbs. Other diseases are caused by spirits not amenable to herb-dwelling spirits ; they must be tackled by spirits of a more powerful grade.

West African Studies
Mary H. KINGSLEY


Table of Contents

microme

Other Programmes

A microbial metabolic pathways knowledge base

The European Union supports research via grants which permit development of research activities associating several european partners, according to the principle of subsidiarity. The Microme programme has been meant to foster construction of a platform for automatic and expert annotation of bacterial metabolic pathways. The effort presented here corresponds to our contribution via grant FP7-2009-222886-2.

This page aims at informing the general public (in particular members of european countries which steer the European Union) about the ultimate developments of this research.

The acetate switch

It has long been known that bacteria such as E. coli, when grown on a carbon-rich food supply in the presence of oxygen would respond in a biphasic fashion, by first growing exponentially, while accumulating acetate in the growth medium to compensate for an overflow of carbon, to abruptly shift to an acetate consuming stage when entering into the stationary phase. This process, named the "acetate switch" is the only known metabolic process that parallels entry into stationary phase of growth. It is fairly universal, and matches the function of the enzymes in the TCA « cycle »: during exponential growth, the pathway does not cycle, but produces metabolites essentially via oxaloacetate and 2-ketoglutarate production; subsequently, in the respiratory stage, it cycles in the textbook presentation of the TCA cycle to produce protons permitting ATP synthesis and accumulation of energy for future difficult times (often as polyphosphates).

acetate

An arsenic/sulfur connection?

After discussion with the geochemist Raoul-Marie Couture we wrote an article proposing a detailed scenario whereby some bacteria could synthesise monothioarsenate, a fairly innocuous derivative of arsenic. The metabolic scenario is hypothetical and fairly wild, of course, but showing that we should explore many biochemical hypotheses before trying to challenge our standard knowledge of the constraints of the law of physics on atoms. This paper is published in Environmental Microbiology. More about the arsenic nightmare.

Features of the paleome

Among the various metabolic functions we have to characterise for Microme are unknown, or unrecognised important functions. We have further identified nanoRNase families that are meant to supply for the degradation of the short leftovers of processive RNases. We also note that these enzymes interfere with the regulation of sulfur metabolism (via control of the reduction of sulfate), as well as lipid metabolism (via formation of 4-phosphopantetheine from Coenzyme A).

AGM april 2012 pdf

This is also an important knowledge for the construction of synthetic cells.

We note that this type of function deals with generic molecules (oligonucleotides) of a type that is not explicitly identified in metabolic databases, but that Microme aims at taking into account.

Publications


CM Chan, A Danchin, P Marlière, A Sekowska
Paralogous metabolism: S-alkyl-cysteine degradation in Bacillus subtilis
Environ Microbiol (2014) 16: 101-117 pubmed

A Danchin, A Sekowska
The logic of metabolism and its fuzzy consequences
Environ Microbiol (2014) 16: 19-28 pubmed

CG Acevedo-Rocha, G Fang, M Schmidt, DW Ussery, A Danchin
From essential to persistent genes: a functional approach to constructing synthetic life
Trends Genet. (2013) 29: 273-279. doi: 10.1016/j.tig.2012.11.001 pubmed

E Belda, A Sekowska, F Le Fèvre, A Morgat, D Mornico, C Ouzounis, D Vallenet, C Médigue, A Danchin
An updated metabolic view of the Bacillus subtilis 168 genome
Microbiology (2013) 159: 757-770. doi: 10.1099/mic.0.064691-0 pubmed

A Danchin, A Sekowska
Constraints in the design of the synthetic bacterial chassis
Methods in Microbiology (2013) 40: 39-68

RM Couture , A Sekowska, G Fang, A Danchin
Linking selenium biogeochemistry to the sulfur-dependent biological detoxification of arsenic
Environ Microbiol (2012) 14: 1612-1623. doi: 10.1111/j.1462-2920.2012.02758.x. PubMed

A Danchin
A path from predation to mutualism
Molecular Microbiology (2010) 77: 1346-1350

A Danchin
Scaling up synthetic biology: Do not forget the chassis
FEBS Letters (2012)586: 2129-2137. PubMed

A Danchin, PM Binder, S Noria
Antifragility and tinkering in biology (and in business): Flexibility provides an efficient epigenetic way to manage risk
Genes (2011), 2: 998-1016; doi:10.3390/genes2040998

S Engelen, D Vallenet, C Médigue, A Danchin
Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC
BMC Genomics (2012) 13: 69. PubMed

M Porcar, A Danchin, V de Lorenzo, VA dos Santos, N Krasnogor, S Rasmussen, A Moya
The ten grand challenges of synthetic life
Systems and Synthetic Biology (2011) 5: 1-9 PubMed

G Postic, A Danchin, U Mechold
Characterization of NrnA homologs from Mycobacterium tuberculosis and Mycoplasma pneumoniae
Symplectic Biology (2010) 1: c390t9c12uxx.1

G Postic, A Danchin, U Mechold
Characterization of NrnA homologs from Mycobacterium tuberculosis and Mycoplasma pneumoniae
RNA (2012) 18: 155-165

H Rohde, J Qin, Y Cui, D Li, NJ Loman, M Hentschke, W Chen, Fei Pu, Y Peng, J Li, F Xi, S Li, Y Li, Z Zhang, X Yang, M Zhao, Peng Wang, Y Guan, Z Cen, X Zhao, M Christner, R Kobbe, S Loos, J Oh, L Yang, A Danchin, GF Gao, Y Song, Y Li, H Yang, J Wang, J Xu, the E. coli O104:H4 Genome Analysis Crowd-sourcing consortium, MJ Pallen, J Wang, M Aepfelbacher, R Yang
Open-source genomics of an isolate from a german family outbreak of Shiga-toxin-producing Escherichia coli O104:H4
New England Journal of Medicine (2011) 365: 718-724 PubMed IF 53,484

Conferences

COST Workshop on Whitefly Metagenomics–Synthetic Biology & Symbiosis
Cavanilles Institute on Biodiversity and Evolutionary Biology
University of Valencia
Valencia , Spain

27-28 february 2012
« Functional Analysis for Synthetic Biology. Metabolic Frustration is Driving Compartmentalisation »

Presentation bageco11

Frontiers in Systems Biology II
Baptist University
The Croucher Foundation
1 - 2 December 2011

Hong Kong, SAR Hong Kong, China
« Ageing vs senescence: the fate of the cell factory »

Synthetic Biology (SB) puts together two separate entities, a program and a chassis. The majority of SB-related work deals with the program, not the chassis. We will deal with the chassis and ask the quetion: will scaling up synthetic processes be possible, and to what extent? Indeed, scaling up implies reproduction of the chassis, i.e. making similar copies. As in all systems this implies progressive ageing. Living cells have a knack to make that ageing differs from senescence. We will explore how rhis is possible, and why this has important consequences in terms of SB.

Working Seminar in Conceptual Biology
Department of Mathematics
The University of Hong Kong
30 November 2011
Hong Kong, SAR Hong Kong , China
« Update on antifragility: a concept used in banking that may be relevant to (synthetic) biology »

Bageco11
Bacterial Genetics and Ecology

Kerkyra, Greece
29 may - 2 June 2011
« Antifragility: a concept used in banking that may be relevant to (synthetic) biology »

Exploratory Round Table Conference of 2010 - Synthetic Biology
Shanghai, october 20th, 2010
« Natural selection and Maxwell's demon »

TARPOL summer school on synthetic biology
Basel, september 27th, 2010
« Metabolic and spatial frustration as a constraint for synthetic biology »

EMBO Meeting 2010
Barcelona, september 6th, 2010
« Metabolic frustration as a constraint for synthetic biology »

International workshop on synthetic biology
Interfacing biology, technology and society
Molecular traffic jams and the reproduction vs replication dilemma
25-27 august 2010
Copenhagen, Denmark

Piotr Slonimski: from mitochondria to genomes
Gif sur Yvette, july 8th, 2010
A Danchin : « From EEC genes to Maxwell’s demon’s genes »

accueil