Hyperstructures, genome analysis and I-cells.
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.
Amar
Patrick
P
Laboratoire de Méthodes Informatiques, CNRS UMR 8042, Université d'Evry, 91025 Evry, France.
Ballet
Pascal
P
Barlovatz-Meimon
Georgia
G
Benecke
Arndt
A
Bernot
Gilles
G
Bouligand
Yves
Y
Bourguine
Paul
P
Delaplace
Franck
F
Delosme
Jean-Marc
JM
Demarty
Maurice
M
Fishov
Itzhak
I
Fourmentin-Guilbert
Jean
J
Fralick
Joe
J
Giavitto
Jean-Louis
JL
Gleyse
Bernard
B
Godin
Christophe
C
Incitti
Roberto
R
Képès
François
F
Lange
Catherine
C
Le Sceller
Lois
L
Loutellier
Corinne
C
Michel
Olivier
O
Molina
Franck
F
Monnier
Chantal
C
Natowicz
René
R
Norris
Vic
V
Orange
Nicole
N
Pollard
Helene
H
Raine
Derek
D
Ripoll
Camille
C
Rouviere-Yaniv
Josette
J
Saier
Milton
M
Soler
Paul
P
Tambourin
Pierre
P
Thellier
Michel
M
Tracqui
Philippe
P
Ussery
Dave
D
Vincent
Jean-Claude
JC
Vannier
Jean-Pierre
JP
Wiggins
Philippa
P
Zemirline
Abdallah
A
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
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D046911:Macromolecular Substances