Dynamical modules in metabolism, cell and developmental biology.
activity-function
dynamical systems
metabolic control
modularity
regulatory networks
systems biology
Journal
Interface focus
ISSN: 2042-8898
Titre abrégé: Interface Focus
Pays: England
ID NLM: 101531990
Informations de publication
Date de publication:
06 Jun 2021
06 Jun 2021
Historique:
accepted:
10
03
2021
entrez:
31
5
2021
pubmed:
1
6
2021
medline:
1
6
2021
Statut:
epublish
Résumé
Modularity is an essential feature of any adaptive complex system. Phenotypic traits are modules in the sense that they have a distinguishable structure or function, which can vary (quasi-)independently from its context. Since all phenotypic traits are the product of some underlying regulatory dynamics, the generative processes that constitute the genotype-phenotype map must also be functionally modular. Traditionally, modular processes have been identified as structural modules in regulatory networks. However, structure only constrains, but does not determine, the dynamics of a process. Here, we propose an alternative approach that decomposes the behaviour of a complex regulatory system into elementary activity-functions. Modular activities can occur in networks that show no structural modularity, making dynamical modularity more widely applicable than structural decomposition. Furthermore, the behaviour of a regulatory system closely mirrors its functional contribution to the outcome of a process, which makes dynamical modularity particularly suited for functional decomposition. We illustrate our approach with numerous examples from the study of metabolism, cellular processes, as well as development and pattern formation. We argue that dynamical modules provide a shared conceptual foundation for developmental and evolutionary biology, and serve as the foundation for a new account of process homology, which is presented in a separate contribution by DiFrisco and Jaeger to this focus issue.
Identifiants
pubmed: 34055307
doi: 10.1098/rsfs.2021.0011
pii: rsfs20210011
pmc: PMC8086940
doi:
Types de publication
Journal Article
Langues
eng
Pagination
20210011Informations de copyright
© 2021 The Authors.
Références
Interface Focus. 2021 Apr 16;11(3):20210007
pubmed: 34055306
J Mol Biol. 2005 Jun 10;349(3):501-14
pubmed: 15890368
PLoS Comput Biol. 2017 Feb 3;13(2):e1005285
pubmed: 28158178
Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):11980-5
pubmed: 14530388
Nature. 1999 Dec 2;402(6761 Suppl):C47-52
pubmed: 10591225
Cell Cycle. 2017 Oct 18;16(20):1885-1892
pubmed: 28902568
Bioinformatics. 2008 Aug 15;24(16):i213-9
pubmed: 18689828
J R Soc Interface. 2012 Dec 12;10(79):20120826
pubmed: 23235261
Mol Syst Biol. 2017 Apr 27;13(4):925
pubmed: 28455348
Bioessays. 2020 Jun;42(6):e1900226
pubmed: 32449193
J R Soc Interface. 2018 Dec 21;15(149):20180595
pubmed: 30958230
Dev Biol. 1996 Feb 1;173(2):357-72
pubmed: 8605997
BMC Genomics. 2006 May 05;7:108
pubmed: 16677373
PLoS Comput Biol. 2009 Mar;5(3):e1000303
pubmed: 19282965
Curr Top Dev Biol. 2020;137:219-246
pubmed: 32143744
Development. 1987 Sep;101(1):1-22
pubmed: 2896587
BMC Syst Biol. 2017 Feb 28;11(1):30
pubmed: 28241833
J Theor Biol. 1982 Jul 7;97(1):43-55
pubmed: 7132385
Bioessays. 2000 Aug;22(8):753-60
pubmed: 10918306
Development. 2021 Feb 25;148(4):
pubmed: 33547135
Cell Syst. 2015 Oct 28;1(4):257-69
pubmed: 27136055
Curr Opin Genet Dev. 2012 Dec;22(6):578-84
pubmed: 23276682
Nature. 2005 Jun 9;435(7043):814-8
pubmed: 15944704
Nat Rev Genet. 2008 Jan;9(1):75-82
pubmed: 18059367
Curr Opin Genet Dev. 2020 Aug;63:61-70
pubmed: 32505051
Science. 2014 Aug 1;345(6196):566-70
pubmed: 25082703
Genetica. 2007 Jan;129(1):83-103
pubmed: 16897451
Nat Rev Genet. 2007 Jun;8(6):450-61
pubmed: 17510665
Methods Mol Biol. 2014;1170:29-40
pubmed: 24906307
Nat Rev Genet. 2009 Feb;10(2):141-8
pubmed: 19139764
Nature. 2009 Dec 3;462(7273):587-94
pubmed: 19956253
BMC Bioinformatics. 2007 Oct 25;8:413
pubmed: 17961242
Nature. 2004 Jul 15;430(6997):368-71
pubmed: 15254541
Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):7821-6
pubmed: 12060727
Biosystems. 2010 Oct;102(1):11-5
pubmed: 20655358
Nature. 1980 Oct 30;287(5785):795-801
pubmed: 6776413
Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2658-63
pubmed: 14981240
Annu Rev Ecol Evol Syst. 2016;47:463-486
pubmed: 28966564
Nat Genet. 2003 Jun;34(2):166-76
pubmed: 12740579
Nat Biotechnol. 2003 Nov;21(11):1337-42
pubmed: 14555958
Proc Natl Acad Sci U S A. 2006 Jun 6;103(23):8577-82
pubmed: 16723398
Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):5862-5869
pubmed: 28584110
Nat Rev Mol Cell Biol. 2008 Dec;9(12):981-91
pubmed: 18971947
Sci Rep. 2015 Aug 20;5:13015
pubmed: 26290154
Science. 2016 Jul 8;353(6295):163-6
pubmed: 27387949
J Exp Zool. 1999 Dec 15;285(4):307-25
pubmed: 10578108
J Exp Zool B Mol Dev Evol. 2011 Jun 15;316(4):241-53
pubmed: 21259417
Nat Rev Genet. 2007 Dec;8(12):921-31
pubmed: 18007649
Development. 2008 Oct;135(19):3175-83
pubmed: 18776142
Evolution. 1996 Jun;50(3):967-976
pubmed: 28565291
Nature. 1988 Sep 1;335(6185):25-34
pubmed: 2901040
J Theor Biol. 1993 Jul 7;163(1):135-44
pubmed: 8412239
PLoS Biol. 2018 Feb 16;16(2):e2003174
pubmed: 29451884
J Physiol. 2014 Jun 1;592(11):2267-81
pubmed: 24882812
Nat Commun. 2016 May 23;7:11582
pubmed: 27211489
Science. 2010 Sep 24;329(5999):1616-20
pubmed: 20929839
Development. 2012 Feb;139(4):625-39
pubmed: 22274695
J R Soc Interface. 2018 May;15(142):
pubmed: 29743273
Dev Cell. 2019 Feb 11;48(3):361-370.e3
pubmed: 30753836
Development. 2008 Aug;135(15):2489-503
pubmed: 18621990
Curr Opin Struct Biol. 2004 Jun;14(3):283-91
pubmed: 15193307
Curr Opin Genet Dev. 1995 Feb;5(1):5-11
pubmed: 7749325
Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14863-8
pubmed: 9843981
Dev Cell. 2016 Feb 22;36(4):401-14
pubmed: 26906736
J Exp Zool. 2001 Apr 15;291(1):1-12
pubmed: 11335912
Nat Rev Genet. 2008 Nov;9(11):868-82
pubmed: 18927580
J Theor Biol. 2008 Jun 7;252(3):546-54
pubmed: 18068730
Adv Exp Med Biol. 2012;751:93-119
pubmed: 22821455
Mol Syst Biol. 2008;4:161
pubmed: 18277378
Nat Rev Genet. 2007 Jun;8(6):473-9
pubmed: 17486120
Philos Trans R Soc Lond B Biol Sci. 2010 Feb 27;365(1540):557-66
pubmed: 20083632
Nat Genet. 1999 Jul;22(3):281-5
pubmed: 10391217
Cell Syst. 2018 Apr 25;6(4):521-530.e3
pubmed: 29574056
Evolution. 1982 May;36(3):444-459
pubmed: 28568040
Elife. 2019 Jun 06;8:
pubmed: 31169494
Trends Biotechnol. 2002 Oct;20(10):407-10; discussion 410
pubmed: 12220896
Cell. 2012 Jan 20;148(1-2):273-84
pubmed: 22265416
J Exp Zool B Mol Dev Evol. 2012 Dec;318(8):591-612
pubmed: 23060018
Science. 2017 Jun 30;356(6345):1379-1383
pubmed: 28663499
Science. 2003 Oct 10;302(5643):249-55
pubmed: 12934013
J R Soc Interface. 2016 Jul;13(120):
pubmed: 27440255
PLoS Comput Biol. 2012;8(7):e1002589
pubmed: 22807664
Nat Rev Genet. 2016 Dec;17(12):744-757
pubmed: 27818507
J Exp Zool. 2001 Aug 15;291(2):116-29
pubmed: 11479913
Cell. 2011 Mar 18;144(6):970-85
pubmed: 21414487
Science. 2006 Feb 10;311(5762):796-800
pubmed: 16469913
Genetica. 1991;84(1):5-11
pubmed: 1874440
Sci Signal. 2009 Jul 28;2(81):pe44
pubmed: 19638611
BMC Biol. 2015 Jul 01;13:46
pubmed: 26129844
FEBS Lett. 2000 Jun 30;476(1-2):47-51
pubmed: 10878248
Curr Opin Genet Dev. 2010 Dec;20(6):684-93
pubmed: 20956081
Nature. 2007 Nov 29;450(7170):717-20
pubmed: 18046410
J Theor Biol. 2009 Apr 21;257(4):543-59
pubmed: 19185585
BMC Syst Biol. 2008 Nov 17;2:98
pubmed: 19014692
Cell. 2013 Feb 28;152(5):945-56
pubmed: 23452846
Development. 2015 Apr 1;142(7):1203-11
pubmed: 25804733
Development. 2011 Jul;138(13):2783-92
pubmed: 21652651