Hyperstructures, genome analysis and I-cells

Patrick Amar, Pascal Ballet, Georgia Barlovatz-Meimon, Arndt Benecke, Gilles Bernot, Yves Bouligand, Paul Bourguine, Franck Delaplace, Jean Marc Delosme, Maurice Demarty, Itzhak Fishov, Jean Fourmentin-Guilbert, Joe Fralick, Jean Louis Giavitto, Bernard Gleyse, Christophe Godin, Roberto Incitti, François Képès, Catherine Lange, Lois Le ScellerCorinne Loutellier, Olivier Michel, Franck Molina, Chantal Monnier, René Natowicz, Vic Norris*, Nicole Orange, Helene Pollard, Derek Raine, Camille Ripoll, Josette Rouviere-Yaniv, Milton Saier, Paul Soler, Pierre Tambourin, Michel Thellier, Philippe Tracqui, Dave Ussery, Jean Claude Vincent, Jean Pierre Vannier, Philippa Wiggins, Abdallah Zemirline

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

14 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)357-373
Number of pages17
JournalActa Biotheoretica
Volume50
Issue number4
DOIs
StatePublished - Jan 1 2002

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Philosophy
  • Environmental Science(all)
  • Agricultural and Biological Sciences(all)
  • Applied Mathematics

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