Hyperstructures, genome analysis and I-Cells
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Patrick Amar
- Function : Author
- PersonId : 3404
- IdHAL : patrick-amar
- ORCID : 0000-0003-0584-0546
- IdRef : 082846685
Pascal Ballet
- Function : Author
- PersonId : 13209
- IdHAL : pascal-ballet
- IdRef : 125955316
Arndt Benecke
- Function : Author
- PersonId : 748914
- IdHAL : arndt-benecke
- ORCID : 0000-0002-7121-823X
Gilles Bernot
- Function : Author
- PersonId : 1197974
- 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
- PersonId : 172057
- 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.