Basic considerations in formulating a 21st Century theory of the genome and genome evolution

1. Basic considerations in formulating a 21st Century theory of the genome and genome evolution James A. Shapiro University of Chicago jsha@uchicago.edu, http:shapiro.bsd.uchicago.edu • • 40 years of molecular deconstruction ==> no units, only systems • • Contact with physicists ==> emphasis on basic principles • • Experience with transposable elements ==> genetic change not stochastic

2. What are the Basic Functions of Cells? • Transport • Metabolism • Growth (includes RNA, protein synthesis, DNA replication, membrane biogenesis, etc.) • Division (includes distribution of essential cell structures & molecules) • Movement (includes tropisms and motility) • Communication with other cells (multicellularity, symbiosis & pathogenesis) • Cognition, signal transduction & information processing (all the above) Fraser et al. 1997. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature 390: 580-586.

3. Signal Transduction in Yeast Mating Pheromone Response Frank van Drogen et al. MAP kinase dynamics in response to pheromones in budding yeast. Nature Cell Biology 3, 1051 - 1059 (2001). Mary J. Cismowski et al. Genetic screens in yeast to identify mammalian nonreceptor modulators of G-protein signaling. Nature Biotechnology 17, 878 - 883 (1999).

4. What are basic properties of biological macromolecules? • Stereospecificity • Structural flexibility • Multivalency (multiple ligands) • Allostery • Reversible covalent modifications (-CH3, ~PO3) • Weak interactions • Cooperativity • Modularity • Combinatorics

5. What functions does the genome fulfill? • Expression (Protein & RNA coding) – transcription, chromatin • Maintenance – replication & repair • Transmission to progeny cells – chromosome movement/segregation at division • Restructuring – natural genetic engineering (genome as RW storage organelle) • NB – all functions involve nucleoprotein complexes, not naked DNA

6. What is the functional organization of the genome? • Formatting by generic signals for compaction, attachment, transcription, replication, transmission, repair • Networking by repeat sequences • Higher order “indexing” by chromatin domains, spatial organization of chromosomes

7. DNA formatting to execute a cognitive algorithm -E. coli discriminates glucose and lactose 1. The algorithm: IF lactose present AND glucose not present AND cell can synthesize active LacZ (beta-galactosidase) and LacY (lactose permease), THEN transcribe lacZYA from lacP 2. The formatted DNA:

8. DNA formatting for chromosome transmission to daughter cells - centromeres B A Sullivan, M D Blower & G H Karpen DETERMINING CENTROMERE IDENTITY: CYCLICAL STORIES AND FORKING PATHS Nature Reviews Genetics 2; 584-596 (2001)

9. What are the sources of novelty in evolution? • New protein functions - domain shuffling and accretion  New adaptive systems (Hox complexes, olfactory sensing, early embryonic functions) – duplication, reverse transcription, multiple transpositions  New species (novel cereals, Muntjac, Drosophila) – hybridization, changes in ploidy, chromosome fusions, inversions  New kinds of cells (e.g. Gram-negative bacteria, eukaryotes, plants) - symbiosis

10. Protein evolution by domain accretion International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860 - 921 (2001)

11. Protein Amplification: Olfactory Receptors Most pairs of similar OR gene clusters (labeled in black) fall into established syntenic chromosomal regions (http://www.ncbi.nlm.nih.gov/Homology/index.html), but some (labeled in red) do not. Young, J. M. et al. Different evolutionary processes shaped the mouse and human olfactory receptor gene families. Hum. Mol. Genet. 11, 535-546 (2002)

12. Segmental Duplications in Arabidopsis Segmentally duplicated regions in the Arabidopsis genome. Individual chromosomes are depicted as horizontal grey bars (with chromosome 1 at the top), centromeres are marked black. Coloured bands connect corresponding duplicated segments. Similarity between the rDNA repeats are excluded. Duplicated segments in reversed orientation are connected with twisted coloured bands. The scale is in megabases. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796 - 815 (2000).

13. Evolution of imprinted heterochromatin by insertions Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, Lavine K, Mittal V, May B, Kasschau KD, Carrington JC, Doerge RW, Colot V, Martienssen R. Role of transposable elements in heterochromatin and epigenetic control. Nature. 2004 Jul 22;430(6998):471-6.

14. How does primary genome structure change? - Natural Genetic Engineering: the cellular toolbox for genome restructuring • Homologous recombination • Non-homologous end-joining • Site-specific recombination • DNA transposons (large-scale rearrangements) • Retrotransposons and reverse transcription (small-scale rearrangements) • Homing and retrohoming introns and inteins • Mutator polymerases

15. The Mammalian Immune System:An Evolved Rapid Evolution System D. C. van Gent, J. H. Hoeijmakers, R. Kanaar, Chromosomal Stability And The DNA Double-Stranded Break Connection 2, 196 (2001) Somatic hypermutation & class switch recombination - transcription directed Tasuko Honjo, Kazuo Kinoshita, and Masamichi Muramatsu. 2001. Molecular Mechanism of Class Switch Recombination: Linkage with Somatic Hypermutation. Annu. Rev. Immunol.;

16. Temporal & metabolic regulation of natural genetic engineering Shapiro, J.A. 1997b. Genome organization, natural genetic engineering, and adaptive mutation. Trends in Genetics13, 98-104

17. Leaf wounding and retrotransposon transcription http://www-biocel.versailles.inra.fr/Anglais/03Transposon.html The expression of the tobacco Tnt1 retrotransposon is induced by wounding : the expression of the LTR-GUS construct is detected by a blue staining surrounding injury points in transgenic tomato (A), tobacco (B) and Arabidopsis (C) plants. M.-A. Grandbastien et al. Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae. Cytogenetic and Genome Research 2005;110:229-241

18. Targeting of natural genetic engineering • Known molecular mechanisms: • Sequence recognition by proteins (yeast mating-type switching, ribosomal LINE elements, homing introns, VDJ joining); • Protein-protein interaction wth transcription factors or chromatin proteins (Ty retrotransposon targeting); • Sequence recognition by RNA (reverse splicing of group II retrohoming introns); • Transcriptional activation of target DNA (somatic hypermutation; class-switch recombination). • Unknown mechanisms: • Telomere targeting of certain LINE elements in insects; • HIV & MLV targeting upstream of transcribed regions; • P factor homing directed by transcription, chromatin signals. Shapiro, JA. 2005. A 21st Century View Of Evolution: Genome System Architecture, Repetitive DNA, And Natural Genetic Engineering. Gene 345: 91-100

19. Yeast Ty5 targeting S. Sandmeyer. Integration by design. PNAS, May 13, 2003; 100(10): 5586 - 5588.

20. Advantages of non-random searches of genome space at evolutionary crises • Genome changes occur under stress or other conditions, when they are most likely to prove beneficial; • Multiple related changes can occur when a particular natural genetic engineering system is activated; • Rearrangement of proven genomic components increases the chance that novel combinations will be functional; • Targeting can increase the probability of functional integration and reduce the risk of system damage; • Rearrangements followed by localized changes provide opportunities for fine tuning once novel function has been achieved.

21. What general principles operate in genome function and genome reorganization? • All genome functions are interactive (no Cartesian dualism, genome always in communication with rest of cell); • Every genome component operates as part of a complex information-processing system (no “one gene-one trait” correlation); • Genome systems are organized and integrated into cell networks by repetitive DNA; • Genome change is a regulated biological function; • Natural genetic engineering processes are subject to biological feedback at multiple levels.