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How does innovation arise in biological systems?

How does innovation arise in biological systems? | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

How does innovation arise in biological systems? A typical example is the emergence of novel catalytic functions in enzymes.

Hereafter I report two studies that come to contradicting conclusions.

Axe and Gauger suggest that the number of simultaneous mutations required to convert a 2-amino-3-ketobutyrate CoA ligase (Kbl2) to 8-amino-7-oxononanoate synthase (BioF2) are so many changes that it becomes probable only “on timescales much longer than the age of life on earth”.

Conversely, Jez and Penning showed that a single mutation changes D4-3-ketosteroid-5b-reductase to 3a-HSD; where Sommerville and coworkers have proved that six substitutions are sufficient to convert a hydroxylase to a desaturase.

How do we account for such contradicting results?

Does evolvability inversely correlate with specificity and catalytic proficiency?

Shall an enzyme be suboptimal adapted to its function in order to evolve new functions?

Does this apply to whole organism?

 

By Davide De Lucrezia

 

Source:

Gauger AK and Axe DD. The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway. BIO-Complexity, Vol 2011

 

Jez JM and Penning TM. Engineering steroid 5b-reductase activity into rat liver 3a-hydroxysteroid ehydrogenase. Biochemistry 1998, 37:9695-9705.

 

Broun P, Shanklin J, Whittle E and Somerville C. Catalytic plasticity of fatty acid modification enzymes underlying chemical diversity of plant lipids. Science 1998, 282:1315-1317.

 

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Origin of Life: Emergence, Self-organization and Evolution
A system-centered perspective on the origin and evolution of Life on Earth
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Simplified protein design biased for prebiotic amino acids yields a foldable, halophilic protein

Simplified protein design biased for prebiotic amino acids yields a foldable, halophilic protein | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

Source:

Longo et al., Simplified protein design biased for prebiotic amino acids yields a foldable, halophilic protein. PNAS, vol. 110 no. 6, 2013.

Davide De Lucrezia's insight:

Longo and coworkers identified a consensus set of 10 “prebiotic” α-amino acids and used this set to reconstitute an extant protein fold (the β-trefoil) to tackle the question of whether and what exent plausible prebiotic aminoacids "contain sufficient chemical information to permit cooperatively folding polypeptides".

The results suggest that the prebiotic amino acids do comprise a foldable set within the halophile environment.

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Who said that size matters? Dipeptide catalyzes RNA oligomerization

Who said that size matters? Dipeptide catalyzes RNA oligomerization | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

A new scenario for prebiotic formation of nucleic acid oligomers
is presented by Wieczorek  et al in CHEMBIOCHEM. Peptide catalysis is applied to achieve condensation of activated RNA monomers into short RNA chains. Reactions were carried out in selforganised environment, a water-ice eutectic phase, with low concentrations of reactants. Because peptides are much more likely products of spontaneous condensation than nucleotide chains, their potential as catalysts for the formation of RNA is interesting from
the origin-of-life perspective.

 

Source:

Formation of RNA Phosphodiester Bond by Histidine-Containing Dipeptides

CHEMBIOCHEM, 2013

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ComplexInsight's curator insight, February 12, 2013 12:15 PM

I seem to recall Staurt Kauffman talking about the theoretical possiblilty of this quite some time ago. Interesing research

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On Prebiotic Ecology, Supramolecular Selection and Autopoiesis

On Prebiotic Ecology, Supramolecular Selection and Autopoiesis | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it
Davide De Lucrezia's insight:

Wieczorek highlights the importance of ecology and systems chemistry in the origin of Life over one-molecule-does-it-all theories: "Let us begin with an introduction of the notion of prebiotic ecology. In the prebiotic soup thousands of different molecular species where interacting with each other forming all sorts of aggregates, polymers, and amphiphilic assemblies (Hunding et al. 2006) which interacted in various ways with one another. We can say that prebiotic ecology is a situation of systems chemistry from an early Earth, and we make the assumption that what would emerge from such a milieu is supramolecular selection—a situation in which certain assemblies of molecules are selected by the environment over others".

NIce work, highly recomended.

 

Source:

Origins of Life and Evolution of BiospheresPublished online: 7 November 2012

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Life and fuzziness

Life and fuzziness | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

Many scientists have devoted time to try to find a definition for life, in spite of the differences the large majority of life definitions rely on the dichotomy living vs. non-living. Bruylants and colleagues argue that “it is indeed impossible to define a natural frontier between non-living and living systems and therefore also impossible to define dichotomic criteria which could be used in order to classify systems in one of these two classes (living or non-living)”. Thus authors conclude that “fuzzy logic provides a natural way to deal with problems where class membership lacks sharply defined criteria”, proposing a paradigmatic shift…a truly needed one. Great piece of work, highly raccommended.

 

Source:

Gilles Bruylants, Kristin Bartik and Jacques Reisse

Is it Useful to Have a Clear-cut Definition of Life? On the Use of Fuzzy Logic in Prebiotic Chemistry

Origins of Life and Evolution of Biospheres. Volume 40, Number 2 (2010), 137-143

 

Acknowledgements:

I would like to thank Dr. Fabrizio Anella for bringing this paper to my attention

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The frailty of adaptive hypotheses for the origins of organismal complexity

The frailty of adaptive hypotheses for the origins of organismal complexity | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

"The vast majority of biologists engaged in evolutionary studies interpret virtually every aspect of biodiversity in adaptive terms", conversely Lynch proposes that "numerous aspects of genomic architecture, gene structure, and developmental pathways are difficult to explain without invoking the nonadaptive forces of genetic drift and mutation"

 

Source:

Lynch Michael

The frailty of adaptive hypotheses for the origins of organismal complexity.

PNAS May 15, 2007 vol. 104 no. Suppl 1 8597-8604

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Evolution of biological complexity

Evolution of biological complexity | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

An old paper from Adami and co-workers where researchers investigate the possibility that natural selection forces genomes to behave as a natural “Maxwell Demon”, thus, within a fixed environment, genomic complexity is forced to increase.

 

Source:

Christoph Adami,Charles Ofria, and Travis C. Collier

Evolution of biological complexity

PNAS April 25, 2000 vol. 97

 

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Evolutionary shift dynamics on a cycle

Evolutionary shift dynamics on a cycle | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

Allen and Nowak present a new model of evolutionary dynamics in one-dimensional space. Individuals are arranged on a cycle. When a new offspring is born, another individual dies and the rest shift around the cycle to make room. This rule, which is inspired by spatial evolution in somatic tissue and microbial colonies, has the remarkable property that, in the limit of large population size, evolution acts to maximize the payoff of the whole population.

 

Source:

Allen B, Nowak MA.

Evolutionary shift dynamics on a cycle.

J Theor Biol. 2012 Jul 16;311C:28-39


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Testing the co-evolution theory

Testing the co-evolution theory | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

The coevolution theory (CET) of the genetic code postulates that the genetic code and codon assignment to amino acid coevolved with amino acid biosynthesis. In particular, the coevolution theory proposes that primordial proteins consisted only of those amino acids readily obtainable from the prebiotic environment, representing about half the twenty encoded amino acids of today, and the missing amino acids entered the system as the code expanded along with pathways of amino acid biosynthesis. Namely, as primordial organisms succeeded to synthetize new amino acids, codon were re-assigned and genetic was reshaped accordingly. The isolation of genetic code mutants, and the antiquity of pretran synthesis revealed by the comparative genomics of tRNAs and aminoacyl-tRNA synthetases, have combined to provide a rigorous proof of the fundamental tenets of the theory.

Recently, Fournier and co-workers casted new doubts on CET investigating Aminoacyl-tRNA synthetases (aaRS) which are universally distributed across cellular life. In particular, sequence reconstructions of the paralog ancestors of isoleucyl- and valyl- RS provide strong empirical evidence that at least for this divergence, the genetic code did not co-evolve with the aaRSs; rather, both amino acids were already part of the genetic code before their cognate aaRSs diverged from their common ancestor.

 

Source:

Wong JT

A co-evolution theory of the genetic code.

Proc Natl Acad Sci USA 1975, 72:1909-1912.

 

Gregory P. Fournier, Cheryl P. Andam, Eric J. Alm and J. Peter Gogarten

Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life

Origins of Life and Evolution of Biospheres. Volume 41, Number 6 (2011), 621-632

 

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The Tides of Titan

The Tides of Titan | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

Iess and coworkers detected in Cassini data the signature of the periodic tidal stresses within Titan. The large response to the tidal field requires that Titan’s interior is deformable over time scales of the orbital period, in a way that is consistent with a global ocean at depth.

This findings makes Titan the closest planet within the solar system to what primeval Earth might have been and an unmatched opportunity to study origin of life scenario by the Cassini space probe.

 

Source

Iess L, Jacobson RA, Ducci M, Stevenson DJ, Lunine JI, Armstrong JW, Asmar SW, Racioppa P, Rappaport NJ, Tortora P.

The Tides of Titan.

Science. 2012 Jun 28.

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Again about selection: interspecific competition

Again about selection: interspecific competition | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

The evolutionary landscape is not exhaustively accessible, in particular epistatic interactions between genes in the genome constrain the accessible evolutionary paths of lineages. Nakajimaa investigates the evolution and interspecific competition of 5 enteric bacterial populations grown in medium containing a single limiting resource. The data in this study demonstrate epistatic interactions may prevent a population from evolving through crossing fitness valleys or adaptive ridges if it requires many generations to achieve peak shifts.

 

Source:

Toshiyuki Nakajimaa.

The impact of interspecific competition on lineage evolution and a rapid peak shift by interdemic genetic mixing in experimental bacterial populations.

Volume 108, Issues 1–3, April–June 2012, Pages 34–44

 

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Are certain types of mutations fixed preferentially during adaptive evolution?

Are certain types of mutations fixed preferentially during adaptive evolution? | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

Although there has been much discussion, no quantitative framework currently exists to test for these biases. Streisfeld and Rausher describe a method to examine the type and magnitude of adaptive biases during evolutionary transitions across multiple scales

 

Source:

Streisfeld MA, Rausher MD.

Population genetics, pleiotropy, and the preferential fixation of mutations during adaptive evolution.

Evolution. 2011 Mar;65(3):629-42.
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Between exploration and fixation III: From cells to molecules

Between exploration and fixation III: From cells to molecules | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

How long does it take to an RNA pool to find a particular structure through mutation and selection? In this computational study, Manrubia and Stich relate properties of the sequence-structure map, in particular the abundance of a given secondary structure in a random pool, with the number of replicative events that an initially random population of sequences needs to find that structure through mutation and selection. Search and fixation processes are more efficient in a wider range of mutation rates for common structures, thus indicating that evolvability of RNA populations is not simply determined by abundance.

 

Source

Stich M, Manrubia SC.

Motif frequency and evolutionary search times in RNA populations.

J Theor Biol. 2011 Jul 7;280(1):117-26. Epub 2011 Mar 21.

 

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Between exploration and fixation I

Between exploration and fixation I | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

Evolution is a tricky game between exploration and fixation. Extremely high mutation rates (MRs) lead to error catastrophe. Conversely, unusually low MRs inhibit adaptation to changing environments.

Montero and co-workers investigate the time a phenotype takes to reach fitness peak as function of both fitness landscape and its mutation rate. Researchers evaluate the average time that the system takes to reach a final steady state of simple models of populations formed by self-replicative sequences (quasispecie).

 

Source:

Arturo Marína, Héctor Tejeroa, Juan Carlos Nuñob, Francisco Monteroa.

Characteristic time in quasispecies evolution

Journal of Theoretical Biology Volume 303, 21 June 2012, Pages 25–32

 

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Multicellularity: A key event in the evolution of life

Multicellularity: A key event in the evolution of life | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

(Phys.org)—Multicellularity in cyanobacteria originated before 2.4 billion years ago and is associated with the accumulation of atmospheric oxygen, subsequently enabling the evolution of aerobic life, as we know it today.

Davide De Lucrezia's insight:

...in turn the necessity to handle oxygen and its potentially toxic derivates such as radicals may have led to the evolution of aerobic respiration...Life is a network of unpredictable responses

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We are all a bit stochastic after all...The Importance of Stochastic Transitions for the Origin of Life

We are all a bit stochastic after all...The Importance of Stochastic Transitions for the Origin of Life | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it
Davide De Lucrezia's insight:

Higgs and Wu discuss the origin of life in terms of "a rare stochastic event that occurs due to spatially localized concentration fluctuations". Authors investigate stochastic fluctuaction in the RNA World scenarioto illustrate that life arises from simple chemical systems jumping to a living state by means of localized concentration fluctuations that are subsequently "spread deterministically through the rest of the system". 

 

Source

The Importance of Stochastic Transitions for the Origin of Life

Origins of Life and Evolution of Biospheres

Published online: 25 October 2012

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The plausibility of RNA-templated peptides

The plausibility of RNA-templated peptides | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

Has thew genetic code evolved on the stereochemical complementarity between aminoacids and correspondent anti-codon? Or is it a frozen accident? Or is it the result of the coevolution of aminoacid anabolism and codon usage?

Check out the altest paper by Yarus and co-workers.

 

Source:

Turk-Macleod RM, Puthenvedu D, Majerfeld I, Yarus M.

The plausibility of RNA-templated peptides: simultaneous RNA affinity for adjacent peptide side chains.

J Mol Evol. 2012 Apr;74(3-4):217-25.

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Biostructural theory of the living systems

Biostructural theory of the living systems | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

The biostrucutral hypothesis is a controversial theory first developed by Eugen Macovschi in 1958. Murariua and Drochioiub reappraise this theory in their latest work published on Biosystems.The biostructural theory is based on a supramolecular description of biological systems, where molecules and matter acquire distinctive properties by means of reciprocal interactions when embedded in highly four-dimensional structured systems.

 

Source:

Manuela Murariua and Gabi Drochioiub,

Biostructural theory of the living systems.

Biosystems, Volume 109, Issue 2, August 2012, Pages 126–132

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Bifurcation under far-from-equilibrium conditions and emergence of Life

Bifurcation under far-from-equilibrium conditions and emergence of Life | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

In his latest work, Kompanichenko reviews the concept of transition from non-living to living suggesting that the transition into primary forms of life might occur only in the microsystems oscillating around the bifurcation point under far-from-equilibrium conditions. The transformation consists in the inversion of the balance “free energy contribution / entropy contribution”, from negative to positive values. At the inversion moment the microsystem radically reorganizes in accordance with the new negentropy (i.e. biological) way of organization. According to this approach, the origin-of-life process on the early Earth took place in the fluctuating hydrothermal medium.

 

Source:

V. N. Kompanichenko

Inversion Concept of the Origin of Life

Origins of Life and Evolution of Biospheres. Volume 42, Numbers 2-3 (2012), 153-178, DOI: 10.1007/s11084-012-9279-0

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Measuring the Complexity of Ultra-Large-Scale Evolutionary Systems

Measuring the Complexity of Ultra-Large-Scale Evolutionary Systems | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

 

Ultra-large scale (ULS) systems are becoming pervasive. They are inherently complex, which makes their design and control a challenge for traditional methods. Amoretti and Gershenson propose the design and analysis of ULS systems using measures of complexity, emergence, self-organization, and homeostasis based on information theory. They evaluate the proposal with a ULS computing system provided with genetic adaptation mechanisms. Researchers show the evolution of the system with stable and also changing workload, using different fitness functions. When the adaptive plan forces the system to converge to a predefined performance level, the nodes may result in highly unstable configurations, that correspond to a high variance in time of the measured complexity. Conversely, if the adaptive plan is less "aggressive", the system may be more stable, but the optimal performance may not be achieved.

 

Source:

Michele Amoretti, Carlos Gershenson

Measuring the Complexity of Ultra-Large-Scale Evolutionary Systems

Neural and Evolutionary Computing. Submitted on 27 Jul 2012

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Geographic Mosaics of Coevolution

Geographic Mosaics of Coevolution | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

Species constantly engage in strong interactions with other species - parasites, predators, prey, and mutualists. As a result, their traits may coevolve and diversify in geographic mosaics. A nice introduction to Co-Evolution on large scale http://www.nature.com/scitable/knowledge/library/geographic-mosaics-of-coevolution-26425

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Evolutionary dynamics of RNA-like replicator systems

Evolutionary dynamics of RNA-like replicator systems | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

RNA-like replicator systems have been central to many speculative theories on the emergence of Life as network of interacting molecules. In this work, Takeuchi and Hogeweg investigate several parameters (e.g. information maintenance, emergence and storage) to review central concepts such as quasi-species, error threshold, genotype–phenotype map, hypercycle and multilevel selection.

 

Source

Nobuto Takeuchi and Paulien Hogeweg

Evolutionary dynamics of RNA-like replicator systems: A bioinformatic approach to the origin of life

Physics of Life Reviews,12 June 2012

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Emergence of Self-Reproduction in Cooperative Chemical Evolution

Emergence of Self-Reproduction in Cooperative Chemical Evolution | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

Fishkis presents a model of coevolution of short peptides (P) and short oligonucleotides (N) at an early stage of chemical evolution leading to the origin of life. The model describes polymerization of both P and N types of molecules on mineral surfaces in aqueous solution at moderate temperatures. It is assumed that amino acid and nucleotide monomers were available in a prebiotic milieu, that periodic variation in environmental conditions between dry/warm and wet/cool took place and that energy sources were available for the polymerization. An artificial chemistry approach in combination with agent-based modeling was used to explore chemical evolution from an initially random mixture of monomers. It was assumed that the oligonucleotides could serve as templates for self-replication and for translation of peptide compositional sequences, and that certain peptides could serve as weak catalysts. The result of the simulation was the emergence of self-replicating molecular systems consisting of peptide catalysts and oligonucleotide templates.

 

Source:

Maya Fishkis

Emergence of Self-Reproduction in Cooperative Chemical Evolution of Prebiological Molecules

Origins of Life and Evolution of Biospheres. Volume 41, Number 3 (2011), 261-275.

 

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Weak selection: Just slightly better

Weak selection: Just slightly better | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

What happen to evolving biosystems when all phenotypes perform approximately equally well? Weak selection is an important limiting case in evolutionary biology and it occurs when a phenotype is slightly advantageous over another. Traulsen and co-workers investigate the influence of weak selection on the stochastic dynamics in finite populations both unstructured and structured populations.

 

Source

Wu B, Altrock PM, Wang L, Traulsen A.

Universality of weak selection.

Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Oct;82

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Why this and not that? Never Born Proteins are back...

Why this and not that? Never Born Proteins are back... | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

My professor Pierluigi Luisi used to say: “Why this and not that?” [1] when speaking about proteins. The underlining question was about the emergence and fixation of protein sequences in extant organisms. There might be some 10^14 different protein sequences in the biosphere today, yet this apparently huge number represents only an infinitesimal fraction of all theoretically possible proteins. Just to give an example, there are some 10^65 theoretically different proteins 50 amino acids long. The number of extant proteins represents a “grain of sand in the Sahara” [1] when compare to the number of possible ones.

Do extant proteins have any particular features that make them eligible for selection? Or are they the sheer outcome of chance? Are extant proteins the exquisite result of natural selection or are they random sequences slightly edited by evolution?

In our latest work [2], we address this question by comparing a set of 762 natural proteins with an average length of 70 amino acids and an equal number of completely random ones of comparable length on the basis of their structural features. Our results suggest that random proteins are significantly different from extant ones, yet they display inherent conformational order which derives from chemico-physical constrains rather than from natural selection. This intrinsic order represents a “free-ticket” to start the adaptation process to specific functions and environments.

 

Source:

1. Pier Luigi Luisi The Emergence of Life. From Chemical Origins to Synthetic Biology. Cambridge University Press. 2006

2. De Lucrezia D, Slanzi D, Poli I, Polticelli F, Minervini G. Do Natural Proteins Differ from Random Sequences Polypeptides? Natural vs. Random Proteins Classification Using an evolutionary Neural Network. PLoS ONE, 2012. 7(5)

 

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Between exploration and fixation II: When you cannot stop

Between exploration and fixation II: When you cannot stop | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

Evolution is a tricky game between exploration and fixation, we said. True, if you do not need to win the evolutionary arms race against your opponent (predator/parasite).

Yomo and Kashiwagi report about the phenotypic and genomic changes in experimental coevolution of RNA bacteriophage Qβ and Escherichia coli. They observed how the phenotypes and genotypes of coevolving parasite-host pairs change through the arms race. Copropagation experiments with Escherichia coli and the lytic RNA bacteriophage Qβ in a spatially unstructured environment revealed continuous adaptation and counter-adaptation: “E. coli first adapted by developing partial resistance to infection and later increasing specific growth rate. The phage counter-adapted by improving release efficiency with a change in host specificity and decrease in virulence. Whole-genome analysis indicated that the phage accumulated 7.5 mutations, mainly in the A2 gene, 3.4-fold faster than in Qβ propagated alone. E. coli showed fixation of two mutations (in traQ and csdA) faster than in sole E. coli experimental evolution.”

 

Source:

Kashiwagi A, Yomo T.

Ongoing phenotypic and genomic changes in experimental coevolution of RNA bacteriophage Qβ and Escherichia coli.

PLoS Genet. 2011 Aug;7(8):e1002188. Epub 2011 Aug 4.

 

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