Hyperstructures, genome analysis and I-Cells
Patrick Amar
(1)
,
Pascal Ballet
(2)
,
Georgia Barlovatz-Meimon
(3)
,
Arndt Benecke
(4)
,
Gilles Bernot
(2)
,
Yves Bouligand
(5)
,
Paul Bourguine
(6)
,
Franck Delaplace
(2)
,
Jean-Marc Delosme
(2)
,
Maurice Demarty
(7)
,
Itzhak Fishov
(8)
,
Jean Fourmentin-Guilbert
(9)
,
Joe Fralick
(10)
,
Jean-Louis Giavitto
(2)
,
Bernard Gleyse
(11)
,
Christophe Godin
(12)
,
Roberto. Incitti
(2)
,
François Képès
(13)
,
Catherine Lange
(14)
,
Lois Le Sceller
(7)
,
Corinne Loutellier
(14)
,
Franck Molina
(15)
,
Chantal Monnier
(7)
,
René Natowicz
(16)
,
Vic Norris
(7)
,
Nicole Orange
(17)
,
Hélène Pollard
(18)
,
Derek Raine
(19)
,
Camille Ripoll
(7)
,
Josette Rouviere-Yaniv
(20)
,
Milton Saier
(21)
,
Paul Soler
(18)
,
Pierre Tambourin
(18)
,
Michel Thellier
(7)
,
Philippe Tracqui
(22)
,
Dave Ussery
(23)
,
Jean-Claude Vincent
(24)
,
Jean-Pierre Vannier
(25)
,
Philippa Wiggins
(26)
,
Abdallah Zemirline
(27)
,
Olivier Michel
(2)
1
LRI -
Laboratoire de Recherche en Informatique
2 LaMI - Laboratoire de Méthodes Informatiques
3 DYNAMIC - Dynamic Microbiology - EA 7380
4 IHES - Institut des Hautes Études Scientifiques
5 Histophysique
6 CREA - Centre de recherche en épistémologie appliquée
7 GTCV - Glycobiologie et transports chez les végétaux
8 BGU - Ben-Gurion University of the Negev
9 Fondation Scientifique Fourmentin-Guilbert
10 University of Texas Health Science Center
11 IMAG - Institut d'Informatique et de Mathématiques Appliquées de Grenoble
12 UMR AMAP - Botanique et Modélisation de l'Architecture des Plantes et des Végétations
13 Atelier de Génomique Cognitive [Evry]
14 Spectrométrie de Masse Bio-organique [Rouen]
15 Institut de Biotechnologie-Pharmacologie
16 Computer Sciences Department
17 LMDF-SME - Laboratoire de Microbiologie du Froid – Signaux et Micro-Environnement
18 Genopole Research
19 Department of Physics and Astronomy [Leicester]
20 IBPC (FR_550) - Institut de biologie physico-chimique
21 Division of Biology [La Jolla]
22 DynaCell
23 Center for Biological Sequence Analysis [Lyngby]
24 PBM - Polymères, biopolymères, membranes
25 Hématologie-Oncologie Pédiatrique
26 Genesis Research and Development Corporation Limited
27 Département d'Informatique [Brest]
2 LaMI - Laboratoire de Méthodes Informatiques
3 DYNAMIC - Dynamic Microbiology - EA 7380
4 IHES - Institut des Hautes Études Scientifiques
5 Histophysique
6 CREA - Centre de recherche en épistémologie appliquée
7 GTCV - Glycobiologie et transports chez les végétaux
8 BGU - Ben-Gurion University of the Negev
9 Fondation Scientifique Fourmentin-Guilbert
10 University of Texas Health Science Center
11 IMAG - Institut d'Informatique et de Mathématiques Appliquées de Grenoble
12 UMR AMAP - Botanique et Modélisation de l'Architecture des Plantes et des Végétations
13 Atelier de Génomique Cognitive [Evry]
14 Spectrométrie de Masse Bio-organique [Rouen]
15 Institut de Biotechnologie-Pharmacologie
16 Computer Sciences Department
17 LMDF-SME - Laboratoire de Microbiologie du Froid – Signaux et Micro-Environnement
18 Genopole Research
19 Department of Physics and Astronomy [Leicester]
20 IBPC (FR_550) - Institut de biologie physico-chimique
21 Division of Biology [La Jolla]
22 DynaCell
23 Center for Biological Sequence Analysis [Lyngby]
24 PBM - Polymères, biopolymères, membranes
25 Hématologie-Oncologie Pédiatrique
26 Genesis Research and Development Corporation Limited
27 Département d'Informatique [Brest]
Patrick Amar
- Function : Author
- PersonId : 3404
- IdHAL : patrick-amar
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- IdRef : 082846685
Pascal Ballet
- Function : Author
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Arndt Benecke
- Function : Author
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- IdHAL : arndt-benecke
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Gilles Bernot
- Function : Author
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- IdHAL : bernot
Jean-Louis Giavitto
- Function : Author
- PersonId : 2943
- IdHAL : jean-louis-giavitto
- ORCID : 0000-0002-3964-9080
- IdRef : 059912979
Christophe Godin
- Function : Author
- PersonId : 1509
- IdHAL : christophe-godin
- ORCID : 0000-0002-1202-8460
- IdRef : 100750958
Franck Molina
- Function : Author
- PersonId : 757999
- ORCID : 0000-0003-4181-0854
René Natowicz
- Function : Author
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- IdHAL : rene-natowicz
- ORCID : 0000-0003-2281-354X
- IdRef : 033044872
Olivier Michel
- Function : Author
- PersonId : 5915
- IdHAL : olivier-michel2
Abstract
New concepts may prove necessary to profit from the avalanche of sequence data on the genome, transcriptome, proteome and interactome and to relate this information to cell physiology. Here, we focus on the concept of large activity-based structures, or hyperstructures, in which a variety of types of molecules are brought together to perform a function. We review the evidence for the existence of hyperstructures responsible for the initiation of DNA replication, the sequestration of newly replicated origins of replication, cell division and for metabolism. The processes responsible for hyperstructure formation include changes in enzyme affinities due to metabolite-induction, lipid-protein affinities, elevated local concentrations of proteins and their binding sites on DNA and RNA, and transertion. Experimental techniques exist that can be used to study hyperstructures and we review some of the ones less familiar to biologists. Finally, we speculate on how a variety of in silico approaches involving cellular automata and multi-agent systems could be combined to develop new concepts in the form of an Integrated cell (I-cell) which would undergo selection for growth and survival in a world of artificial microbiology.