Skip to main content
SpringerLink
Log in

Multiple Clocks in the Evolution of Living Organisms

  • Chapter
  • First Online:
Molecular Mechanisms of Microbial Evolution

Part of the book series: Grand Challenges in Biology and Biotechnology ((GCBB))

Abstract

Looking for a common origin of all things is pervasive. This is reflected in the idea of a common clock ticking in parallel with evolution. Yet, two stages mark any form of life, multiplication and being alive without multiplying. Also, constructing more biomass puts together at least three space dimensions: the cell volume, its membranes and its genome. This creates a massive selection pressure on the linear structure of DNA, which must to be synthesised in parallel with the cell’s volume, tending to increase the length of DNA and to decrease the availability of its building blocks while fitting with the core metabolism of the cell. The increase of genome length favours ingress of horizontally transferred genes. The limitation of deoxyribonucleotide synthesis is ensured by using nucleoside diphosphates, not triphosphate, as precursors. Furthermore this synthesis is metabolically tied up with gene expression and membrane synthesis. Evolution trees are built up according to the evolution of multiplication, forgetting that ageing organisms can still produce a progeny. Taken together these processes imply that there is no common clock ticking at the same rate for all the functions essential for the evolution of life.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 249.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Acevedo-Rocha CG, Fang G et al (2013) From essential to persistent genes: a functional approach to constructing synthetic life. Trends Genet 29(5):273–279

    Article  CAS  Google Scholar 

  • Adebali O, Chiou Y-Y et al (2017) Genome-wide transcription-coupled repair in Escherichia coli is mediated by the Mfd translocase. Proc Natl Acad Sci USA 114(11):E2116–E2125

    Article  CAS  Google Scholar 

  • Afshordi N, Magueijo J (2016) Critical geometry of a thermal big bang. Phys Rev D 94(10):101301

    Article  Google Scholar 

  • Alacevic M (1963) Interspecific recombination in Streptomyces. Nature 197(4874):1323–1323

    Article  CAS  Google Scholar 

  • Belda E, Sekowska A et al (2013) An updated metabolic view of the Bacillus subtilis 168 genome. Microbiology 159(Pt 4):757–770

    Article  CAS  Google Scholar 

  • Bennett C (1988) Notes on the history of reversible computation. IBM J Res Dev 44:270–277

    Article  Google Scholar 

  • Binder PM, Danchin A (2011) Life's demons: information and order in biology. What subcellular machines gather and process the information necessary to sustain life? EMBO Rep 12(6):495–499

    Article  CAS  Google Scholar 

  • Bittner L-M, Arends J et al (2016) Mini review: ATP-dependent proteases in bacteria. Biopolymers 105(8):505–517

    Article  CAS  Google Scholar 

  • Bittner L-M, Arends J et al (2017) When, how and why? Regulated proteolysis by the essential FtsH protease in Escherichia coli. Biol Chem 398(5–6):625–635

    CAS  PubMed  Google Scholar 

  • Budovsky A, Fraifeld VE et al (2010) Linking cell polarity, aging and rejuvenation. Biogerontology 12(2):167–175

    Article  Google Scholar 

  • Cao B, Chen C et al (2014) Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences. Nat Commun 5:3951

    Article  CAS  Google Scholar 

  • Cockburn DW, Koropatkin NM (2016) Polysaccharide degradation by the intestinal microbiota and its influence on human health and disease. J Mol Biol 428(16):3230–3252

    Article  CAS  Google Scholar 

  • Cole EL Jr (1998) Functional analysis: a system conceptual design tool [and application to ATC system]. IEEE Trans Aerosp Electron Syst 34(2):354–365

    Article  Google Scholar 

  • Danchin A (1997) Comparison between the Escherichia coli and Bacillus subtilis genomes suggests that a major function of polynucleotide phosphorylase is to synthesize CDP. DNA Res 4(1):9–18

    Article  CAS  Google Scholar 

  • Danchin A (2003) The Delphic boat. What genomes tell us. Harvard University Press, Cambridge

    Google Scholar 

  • Danchin A (2009a) Bacteria as computers making computers. FEMS Microbiol Rev 33:3–26

    Article  CAS  Google Scholar 

  • Danchin A (2009b) Natural selection and immortality. Biogerontology 10(4):503–516

    Article  Google Scholar 

  • Danchin A (2012) Scaling up synthetic biology: do not forget the chassis. FEBS Lett 586(15):2129–2137

    Article  CAS  Google Scholar 

  • Danchin A (2014) The emergence of the first cells. Rev Cell Biol Mol Med:https://doi.org/10.1002/3527600906.mcb.20130025

    Google Scholar 

  • Danchin A (2017a) Coping with inevitable accidents in metabolism. Microb Biotechnol 10(1):57–72

    Article  Google Scholar 

  • Danchin A (2017b) From chemical metabolism to life: the origin of the genetic coding process. Beilstein J Org Chem 13:1119–1135

    Article  CAS  Google Scholar 

  • Danchin A, Fang G (2016) Unknown unknowns: essential genes in quest for function. Microb Biotechnol 9(5):530–540

    Article  Google Scholar 

  • Danchin A, Guerdoux-Jamet P et al (2000) Mapping the bacterial cell architecture into the chromosome. Philos Trans R Soc Lond Ser B Biol Sci 355(1394):179–190

    Article  CAS  Google Scholar 

  • Danchin A, Binder PM et al (2011) Antifragility and tinkering in biology (and in business); flexibility provides an efficient epigenetic way to manage risk. Genes 2(4):998–1016

    Article  CAS  Google Scholar 

  • Danchin A, Ouzounis C et al (2018) No wisdom in the crowd: genome annotation in the era of big data - current status and future prospects. Microb Biotechnol 11(4):588–605

    Article  Google Scholar 

  • Dyson FJ (1985) Origins of life. Cambridge University Press, Cambridge

    Google Scholar 

  • Elnatan D, Betegon M, et al (2017) Symmetry broken and rebroken during the ATP hydrolysis cycle of the mitochondrial Hsp90 TRAP1. Elife 6

    Google Scholar 

  • Fang G, Rocha EPC et al (2008) Persistence drives gene clustering in bacterial genomes. BMC Genomics 9:4

    Article  Google Scholar 

  • Flemming H-C, Wingender J et al (2016) Biofilms: an emergent form of bacterial life. Nat Rev Microbiol 14(9):563–575

    Article  CAS  Google Scholar 

  • Gaillard H, Aguilera A (2016) Transcription as a threat to genome integrity. Annu Rev Biochem 85(1):291–317

    Article  CAS  Google Scholar 

  • Glaeser SP, Kämpfer P (2015) Multilocus sequence analysis (MLSA) in prokaryotic taxonomy. Syst Appl Microbiol 38(4):237–245

    Article  CAS  Google Scholar 

  • Goujon P (2001) From biotechnology to genomes: the meaning of the double helix. World Scientific, Singapore

    Book  Google Scholar 

  • Harish A, Kurland CG (2017) Akaryotes and Eukaryotes are independent descendants of a universal common ancestor. Biochimie 138:168–183

    Article  CAS  Google Scholar 

  • Harish A, Tunlid A et al (2013) Rooted phylogeny of the three superkingdoms. Biochimie 95(8):1593–1604

    Article  CAS  Google Scholar 

  • Hashimoto M, Ichimura T et al (2005) Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome. Mol Microbiol 55(1):137–149

    Article  CAS  Google Scholar 

  • Huerta-Sanchez E, Casey FP (2015) Archaic inheritance: supporting high-altitude life in Tibet. J Appl Physiol 119(10):1129

    Article  CAS  Google Scholar 

  • Hug LA, Baker BJ et al (2016) A new view of the tree of life. Nat Microbiol 1:16048

    Article  CAS  Google Scholar 

  • Huntley S, Hamann N et al (2010) Comparative genomic analysis of fruiting body formation in Myxococcales. Mol Biol Evol 28(2):1083–1097

    Article  Google Scholar 

  • Hutchison CA 3rd, Chuang RY et al (2016) Design and synthesis of a minimal bacterial genome. Science 351(6280):aad6253

    Article  Google Scholar 

  • Hutinet G, Swarjo MA et al (2017) Deazaguanine derivatives, examples of crosstalk between RNA and DNA modification pathways. RNA Biol 14(9):1175–1184

    Article  Google Scholar 

  • Jannasch H (1967) Growth of marine bacteria at limiting concentrations of organic carbon in seawater. Limnol Oceanogr 12(2):264–271

    Article  CAS  Google Scholar 

  • Jinks-Robertson S, Bhagwat AS (2014) Transcription-associated mutagenesis. Annu Rev Genet 48(1):341–359

    Article  CAS  Google Scholar 

  • Karas BJ, Jablanovic J et al (2013) Direct transfer of whole genomes from bacteria to yeast. Nat Methods 10(5):410–412

    Article  CAS  Google Scholar 

  • Kumar S (2005) Molecular clocks: four decades of evolution. Nat Rev Genet 6(8):654–662

    Article  CAS  Google Scholar 

  • Kysela DT, Randich AM et al (2016) Diversity takes shape: understanding the mechanistic and adaptive basis of bacterial morphology. PLoS Biol 14(10):e1002565

    Article  Google Scholar 

  • Landan G, Cohen G et al (1990) Evolution of isopenicillin N synthase genes may have involved horizontal gene transfer. Mol Biol Evol 7(5):399–406

    CAS  PubMed  Google Scholar 

  • Landauer R (1961) Irreversibility and heat generation in the computing process. IBM J Res Dev 3:184–191

    Google Scholar 

  • Lartigue C, Glass JI et al (2007) Genome transplantation in bacteria: changing one species to another. Science 317(5838):632–638

    Article  CAS  Google Scholar 

  • Li S, Ou XH et al (2012) Septin 7 is required for orderly meiosis in mouse oocytes. Cell Cycle 11(17):3211–3218

    Article  CAS  Google Scholar 

  • Longacre A, Reimers JM et al (1999) Specificity of transcription-enhanced mutations. Ann N Y Acad Sci 870:383–385

    Article  CAS  Google Scholar 

  • McCormick JR, Flärdh K (2012) Signals and regulators that govern Streptomyces development. FEMS Microbiol Rev 36(1):206–231

    Article  CAS  Google Scholar 

  • Médigue C, Rouxel T et al (1991a) Evidence for horizontal gene transfer in Escherichia coli speciation. J Mol Biol 222(4):851–856

    Article  Google Scholar 

  • Médigue C, Viari A et al (1991b) Escherichia coli molecular genetic map (1500 kbp): update II. Mol Microbiol 5(11):2629–2640

    Article  Google Scholar 

  • Médigue C, Krin E et al (2005) Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. Genome Res 15(10):1325–1335

    Article  Google Scholar 

  • Monod J (1972) Chance and necessity: an essay on the natural philosophy of modern biology. Vintage Books, New York

    Google Scholar 

  • Moonens K, Remaut H (2017) Evolution and structural dynamics of bacterial glycan binding adhesins. Curr Opin Struct Biol 44:48–58

    Article  CAS  Google Scholar 

  • Muro-Pastor AM, Hess WR (2012) Heterocyst differentiation: from single mutants to global approaches. Trends Microbiol 20(11):548–557

    Article  CAS  Google Scholar 

  • Nongkhlaw FMW (2014) Epiphytic and endophytic bacteria that promote growth of ethnomedicinal plants in the subtropical forests of Meghalaya, India. Universidad de Costa Rica

    Google Scholar 

  • Ohama T, Inagaki Y et al (2008) Evolving genetic code. Proc Jpn Acad Ser B Phys Biol Sci 84(2):58–74

    Article  CAS  Google Scholar 

  • Ohno S (1987) Repetition as the essence of life on this Earth: music and genes. Modern trends in human Leukemia VII: new results in clinical and biological research including pediatric oncology. Springer, Berlin, pp 511–519

    Google Scholar 

  • Ouzounis C, Kyrpides N (1996) The emergence of major cellular processes in evolution. FEBS Lett 390(2):119–123

    Article  CAS  Google Scholar 

  • Paixão-Cortes VR, Viscardi LH et al (2012) Homo sapiens, Homo neanderthalensis and the Denisova specimen: new insights on their evolutionary histories using whole-genome comparisons. Genet Mol Biol 35(4 Suppl):904–911

    Article  Google Scholar 

  • Pearl LH (2016) Review: the HSP90 molecular chaperone – an enigmatic ATPase. Biopolymers 105(8):594–607

    Article  CAS  Google Scholar 

  • Ragan MA, McInerney JO et al (2009) The network of life: genome beginnings and evolution. Introduction. Philos Trans R Soc Lond B Biol Sci 364(1527):2169–2175

    Article  CAS  Google Scholar 

  • Robinson N, Robinson A (2004) Molecular clocks deamidation of asparaginyl and glutaminyl residues in peptides and proteins. Althouse Press, Cave Junction, OR

    Google Scholar 

  • Roszak DB, Colwell RR (1987) Survival strategies of bacteria in the natural environment. Microbiol Rev 51(3):365–379

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rusconi R, Garren M et al (2014) Microfluidics expanding the frontiers of microbial ecology. Annu Rev Biophys 43:65–91

    Article  CAS  Google Scholar 

  • Sakofsky CJ, Grogan DW (2013) Endogenous mutagenesis in recombinant Sulfolobus plasmids. J Bacteriol 195(12):2776–2785

    Article  CAS  Google Scholar 

  • Sekowska A, Wendel S et al (2016) Generation of mutation hotspots in ageing bacterial colonies. Sci Rep 6(1):2

    Article  Google Scholar 

  • Staley JT, Fuerst JA (2017) Ancient, highly conserved proteins from a LUCA with complex cell biology provide evidence in support of the nuclear compartment commonality (NuCom) hypothesis. Res Microbiol 168(5):395–412

    Article  CAS  Google Scholar 

  • Stankiewicz P (2016) One pedigree we all may have come from – did Adam and Eve have the chromosome 2 fusion? Mol Cytogenet 9:72

    Article  Google Scholar 

  • Stringer C (2016) The origin and evolution of Homo sapiens. Philos Trans R Soc B Biol Sci 371(1698)

    Article  Google Scholar 

  • Sukhodolets VV (1988) Organization and evolution of the bacterial genome. Microbiol Sci 5(7):202–206

    CAS  PubMed  Google Scholar 

  • Taheri-Araghi S, Brown SD et al (2015) Single-cell physiology. Annu Rev Biophys 44(1):123–142

    Article  CAS  Google Scholar 

  • Watanabe S, Shiwa Y et al (2012) Complete sequence of the first chimera genome constructed by cloning the hwole genome of Synechocystis strain PCC6803 into the Bacillus subtilis 168 genome. J Bacteriol 194(24):7007–7007

    Article  CAS  Google Scholar 

  • Woese CR (2002) On the evolution of cells. Proc Natl Acad Sci USA 99(13):8742–8747

    Article  CAS  Google Scholar 

  • Wright BE (2004) Stress-directed adaptive mutations and evolution. Mol Microbiol 52(3):643–650

    Article  CAS  Google Scholar 

  • Wu T, Huang Q et al (2017) Mechanistic investigation on ROS resistance of phosphorothioated DNA. Sci Rep 7:42823

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work benefited from discussions held in the E-seminar Stanislas Noria.

Author information

Authors and Affiliations

  1. Institute of Cardiometabolism and Nutrition, Paris, France

    Antoine Danchin

  2. School of Biological Sciences, Li KaShing Faculty of Medicine, Hong Kong University, Pokfulam, SAR Hong Kong, China

    Antoine Danchin

Authors
  1. Antoine Danchin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Antoine Danchin .

Editor information

Editors and Affiliations

  1. Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil

    Pabulo H. Rampelotto

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer International Publishing AG, part of Springer Nature

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Danchin, A. (2018). Multiple Clocks in the Evolution of Living Organisms. In: Rampelotto, P. (eds) Molecular Mechanisms of Microbial Evolution. Grand Challenges in Biology and Biotechnology. Springer, Cham. https://doi.org/10.1007/978-3-319-69078-0_4

Download citation

Publish with us

Policies and ethics

Search

Navigation