title: Hyperstructures, genome analysis and I-cells.
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.
authors.affiliation: Laboratoire de Méthodes Informatiques, CNRS UMR 8042, Université d'Evry, 91025 Evry, France.
authors.forename: Patrick
authors.initials: P
authors.lastname: Amar
authors.forename: Pascal
authors.initials: P
authors.lastname: Ballet
authors.forename: Georgia
authors.initials: G
authors.lastname: Barlovatz-Meimon
authors.forename: Arndt
authors.initials: A
authors.lastname: Benecke
authors.forename: Gilles
authors.initials: G
authors.lastname: Bernot
authors.forename: Yves
authors.initials: Y
authors.lastname: Bouligand
authors.forename: Paul
authors.initials: P
authors.lastname: Bourguine
authors.forename: Franck
authors.initials: F
authors.lastname: Delaplace
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Delosme
authors.forename: Maurice
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authors.lastname: Demarty
authors.forename: Itzhak
authors.initials: I
authors.lastname: Fishov
authors.forename: Jean
authors.initials: J
authors.lastname: Fourmentin-Guilbert
authors.forename: Joe
authors.initials: J
authors.lastname: Fralick
authors.forename: Jean-Louis
authors.initials: JL
authors.lastname: Giavitto
authors.forename: Bernard
authors.initials: B
authors.lastname: Gleyse
authors.forename: Christophe
authors.initials: C
authors.lastname: Godin
authors.forename: Roberto
authors.initials: R
authors.lastname: Incitti
authors.forename: François
authors.initials: F
authors.lastname: Képès
authors.forename: Catherine
authors.initials: C
authors.lastname: Lange
authors.forename: Lois
authors.initials: L
authors.lastname: Le Sceller
authors.forename: Corinne
authors.initials: C
authors.lastname: Loutellier
authors.forename: Olivier
authors.initials: O
authors.lastname: Michel
authors.forename: Franck
authors.initials: F
authors.lastname: Molina
authors.forename: Chantal
authors.initials: C
authors.lastname: Monnier
authors.forename: René
authors.initials: R
authors.lastname: Natowicz
authors.forename: Vic
authors.initials: V
authors.lastname: Norris
authors.forename: Nicole
authors.initials: N
authors.lastname: Orange
authors.forename: Helene
authors.initials: H
authors.lastname: Pollard
authors.forename: Derek
authors.initials: D
authors.lastname: Raine
authors.forename: Camille
authors.initials: C
authors.lastname: Ripoll
authors.forename: Josette
authors.initials: J
authors.lastname: Rouviere-Yaniv
authors.forename: Milton
authors.initials: M
authors.lastname: Saier
authors.forename: Paul
authors.initials: P
authors.lastname: Soler
authors.forename: Pierre
authors.initials: P
authors.lastname: Tambourin
authors.forename: Michel
authors.initials: M
authors.lastname: Thellier
authors.forename: Philippe
authors.initials: P
authors.lastname: Tracqui
authors.forename: Dave
authors.initials: D
authors.lastname: Ussery
authors.forename: Jean-Claude
authors.initials: JC
authors.lastname: Vincent
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Vannier
authors.forename: Philippa
authors.initials: P
authors.lastname: Wiggins
authors.forename: Abdallah
authors.initials: A
authors.lastname: Zemirline
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000166:cytology* / Q000235:genetics* / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D002453:Cell Cycle / Q000502:physiology; D003198:Computer Simulation; D004261:DNA Replication; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism; D005798:Genes, Bacterial / Q000502:physiology*; D046911:Macromolecular Substances; D008954:Models, Biological
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D046911:Macromolecular Substances