Revisiting Evolutionin the 21st Century

James A. ShapiroUniversity of Chicago

Oxford, March 16, 2010

Why revisit now?• May 8, 2009, debate with Lynn Margulis and RichardDawkins at Balliol Collegeftp://eclogite.geo.umass.edu/pub/gaia/Homage_to_Darwin_part1.mp3• No real discussion of last 50 years research: cellrepair, sensory and regulatory networks; signaltransduction; natural genetic engineering; epigeneticinterfaces with life history events; results of genomesequencing (major roles for cell fusions, horizontaltransfer, whole genome doublings) - empirical resultsthat have transformed the conceptual landscape

Disentangling basic issues in evolutionarydebates

• Origin of life & the first cells- still on the fringes of serious scientific discussion

• Descent with modification of all related livingorganisms- more convincing with each new technologicaladvance (e.g. detailed protein and genomephylogenies)

• The actual processes of evolutionary change overtime- an ever growing number of documented events andmolecular possibilities as we learn more about howcells control genome structure

Outstanding Questions Still at Issuein 21st Century Evolutionary Theory

• Descent with modification: tree/web of life,branching/merging topology, how many cell types inthe beginning, role of virosphere?

• Nature of heredity: vertical/horizontal transmission,passive/active variations, micro/macromutations,isolated/interactive germ plasm, influence of lifehistory events, Central Dogma still valid?

• Role of selection: positive/neutral/purifying?• Relationship of evolutionary change to planetary,

environmental & ecological events?

Molecules involved in cellular information transfer- revisiting the Central Dogma (Shapiro, 2009)

1970:• (DNA --> 2X DNA) --> RNA --> Protein --> Phenotype

(Crick, Central dogma of molecular biology. Nature 1970, 227:561-563) 2010:

• DNA + 0 --> 0• DNA + Protein + ncRNA --> chromatin/epigenetic markings (epigenotype)• Chromatin + Protein + ncRNA --> DNA replication, chromatin maintenance/reconstitution• Protein + RNA + lipids + small molecules --> signal transduction• Signals + Chromatin + Protein --> RNA (primary transcript)• RNA + Protein + ncRNA --> RNA (processed transcript)• RNA + Protein + ncRNA --> Protein (primary translation product)• Protein + nucleotides + Ac-CoA + SAM + sugars + lipids --> Processed and decorated

protein• DNA + Protein --> New DNA sequence (mutator polymerases, terminal transferases)• Chromatin + Protein --> New DNA structure (DNA-based rearrangements)• RNA + Protein + chromatin --> New DNA structure and sequence (retrotransposition,

retroduction, retrohoming, diversity-generating retroelements)• Signals + chromatin + proteins + ncRNA + lipids --> nuclear/nucleoid localization• Protein + ncRNA + chromatin + signals + other molecules + structures <-->

Phenotype & Genotype & Epigenotype

Major Points1. Evolution does not have to proceed by small

changes – and we know from the DNA record thatmajor steps did occur rapidly.

2. DNA change is a cell-regulated, biological process,not a series of infrequent, random, independentaccidents. (Genome as RW memory system)

3. We already know of numerous molecularprocesses that allow us to deal scientifically withcomplex evolutionary events – and with the rapidevolution of complex, multi-componentadaptations.

Darwin’s 1859 gradualist view

Origin of Species, p. 194

Darwin’s later acknowledgment of otherpossibilities:"...variations which seem to us in our ignorance to arisespontaneously. It appears that I formerly underrated the frequency andvalue of these latter forms of variation, as leading to permanentmodifications of structure independently of natural selection."

(Origin of Species, 6th edition, Chapter XV, p. 395).

Four kinds of rapid, multi-characterchanges Darwin could not have imagined

• Multiple cell types and cell fusions in evolution;• Horizontal DNA transfer in evolution;• Genome doublings at key steps of eukaryotic

evolution;• Built-in mechanisms ofgenetic change = naturalgenetic engineering

Barbara McClintock, 1951

Carl Woese,molecularphylogeny,

and three cellkingdoms

(1977)

Rampanthorizontal transferwithin & between

kingdoms

Mitochondria andchloroplasts areendosymbioticbacteria inside

eukaryotic cells

Whatgenomes

teach: cellfusions at

key places ineukaryoticevolution

T. M. Embley and W. Martin. 2006.Eukaryotic evolution, changes andchallenges. Nature 440, 623-630.

diatoms

Evolution in real time using horizontal DNAtransfer: Bacterial antibiotic resistance

• experimentallyconfirmed mutationtheory of resistance(1950s)

• clinically resistantbacteria carrytransmissible plasmids(Watanabe, 1963)

Transmissible Antibiotic Resistance

Also transposons, integrons, integrative conjugating elements,genomic islands

GenomeDuplications in

AngiospermEvolution (“That

abominablemystery”)

Haibao Tang, John E. Bowers,Xiyin Wang, Ray Ming, MaqsudulAlam, and Andrew H. Paterson.Synteny and Collinearity in PlantGenomes. Science 25 April 2008320: 486-488

Genomicduplications in

vertebrateevolution

•Jurg Spring. Genome duplication strikesback. Nature Genetics †31, 128 - 129 (2002)doi:10.1038/ng0602-128

What genomes teach: whole genomeduplications at the root of vertebrate evolution

The 2R hypothesis: an update. Kasahara, M. 2007 CurrentOpinion in Immunology 19 (5), pp. 547-552

NetworkEvolution by

Whole GenomeDuplication

A. S. Veron, K. Kaufmann, and E.Bornberg-Bauer. Evidence ofInteraction Network Evolution byWhole-Genome Duplications: A CaseStudy in MADS-Box Proteins. MolBiol Evol March 1, 2007 24:670-678.

What genomes teach:dispersed repeats in the human genome

International Human Genome Sequencing Consortium. Initial sequencing and analysis ofthe human genome. Nature 409, 860 - 921 (2001)

Natural Genetic Engineering• Nucleotide substitutions by mutator polymerases• DNA import and export systems• General and localized recombination systems.• Mobile DNA elements and large scale genome rearrangements.• Mobile elements that transpose through RNA intermediates and

mobilize shorter genome/RNA segments.• Direct integration of cellular RNAs into the genome by reverse

splicing.Adaptive use of natural genetic engineering• Protein switching, protein engineering and sex changes by diverse

organisms.• The mammalian immune system as an example of rapid protein

evolution and specialization by natural genetic engineering.

International Human Genome Sequencing Consortium. Initial sequencing and analysis of the humangenome. Nature 409, 860 - 921 (2001)

What genomes teach: protein evolutionby domain shuffling

Natural genetic engineering in evolution:Pack MULEs in the rice genome

Jiang N, Bao Z, ZhangX, Eddy SR, WesslerSR: Pack-MULEtransposable elementsmediate gene evolutionin plants. Nature 2004,431:569-573.

Stimuli that Activate Natural GeneticEngineering and Disrupt Epigenetic

Silencing• Chromosome breaks

(McClintock, 1944)• Pheromones, hormones

& cytokines• Starvation (Shapiro,

1984)• DNA damage

(mutagens)• Telomere erosion• Antibiotics, Phenolics,

Osmolites

• Oxidants• Pressure, Temperature,Wounding• Protoplasting & growth intissue culture• Bacterial or fungal infection& endosymbiosis• Changes in ploidy & DNAcontent (genome doubling)• Hybridization (interspecificmating)

Temporal & metabolic regulation of naturalgenetic engineering

0 10 200

100

200

MCS2 (2 subclones)

MCS1366 (4 subclones)

Days/32

Tota

l fus

ion

colo

nies

lacZaraB

Derepression(42C, starvation)ClpPX, Lon RpoS

MuA, HU, IHF

Strand transfer

Replication (exponential growth)

ClpX

DNA processing(RpoS-, Crp-dependent functions?)

lacZaraB

araB-lacZ fusion

STC = strand transfer complex

araB lacZ

U118

U118

lacZaraBCDC/Target complex

U118araB lacZ

Adjacent inversion (precludes fusion)

U118

Transposasome formation

MuB for replication(Crp-dependent starvation-induced functions inhibitand/or replace MuB?)

ClpX

Shapiro, J.A. 1997b. Genome organization, natural genetic engineering, and adaptive mutation. Trends in Genetics 13, 98-104

Molecular Targeting of Natural GeneticEngineering

• DNA sequence homology - homologous recombination,targeted conversions, cassette exchanges, certaintransposons

• Protein recognition of DNA sequences and secondarystructures (nucleases, recombinases, transposases)

• RNA base-pairing to DNA guide sequences (reversesplicing, diversity-generating retroelements)

• Coupling to transcription– retrotransposon integration (protein-protein tethering)– transcription-dependent DS breaks in B cell CSR– V region somatic hypermutation

• Coupling to chromatin (retrotransposon integration)• P-element “homing” (colocalization in nuclear foci?)

21st Century view of evolutionary change: theimportance of a cognitive systems perspective

• McClintock (1984): “In the future, attention undoubtedlywill be centered on the genome, with greater appreciation ofits significance as a highly sensitive organ of the cell thatmonitors genomic activities and corrects common errors,senses unusual and unexpected events, and responds to them,often by restructuring the genome.”

• Ecological events and subsequent biological challengesactivate natural genetic engineering functions that can act atmultiple genomic locations within one or a few generations

• Molecular basis for rapid genome restructuring affectingmultiple adaptive features at the same time in response toabrupt challenges

Searching Genome Space by Natural GeneticEngineering: More Efficient than a Random

Walk Guided by Gradual Selection• combinatoric search using established functional

modules (e.g. domain accretion and shuffling)• activation when most biologically useful by

“genome shock” (including starvation, infection,hybridization) ==> coordinated changes

• network adaptation after WGD, domain shuffling,establishment of novel interaction patterns

• molecular mechanisms for targeting coincidentchanges to functionally related locations (researchagenda for the coming decades)

21st Century view of evolutionary change:a generalized scenario

• Ecological disruption ==> changes in biota, food sources, adaptiveneeds & organismal behavior;

• Macroevolution triggered by cell fusions & interspecifichybridizations (WGDs) leading to massive episodes of horizontaltransfer, genome rearrangements;

• Establishment of new cellular and genome system architectures;complex novelties arising from WGD and network exaptation;

• Survival and proliferation of organisms with useful adaptive traitsin depleted ecology; elimination of non-functional architectures;selection largely purifying;

• Microevolution by localized natural genetic engineering afterecological niches occupied (immune system model).