Plant Speciation & Evolution (PBIO 475/575)

1. Plant Speciation & Evolution (PBIO 475/575) Molecular Components of Heredity

2. DNA Double Helix • Sugar-phosphate backbone • Base-pair "rungs" of ladder • Nucleotides attached to S-P molecules • Strands antiparallel (run in opposite directions, 5'-->3') Raven et al. (1992)

3. DNA Double Helix • Each base-pair "rung" has a purine (A or G) and pyrimidine (C or T) • Strands held together by hydrogen bonds between nucleotides • Chemical structures of nucleotides discourage "incorrect" pairing • G-C pair has 3 hydrogen bonds, A-T only 2-->former is stronger

4. DNA Replication • Semiconservative--replication results in two strands, one original and one new • Sequence of events • Helix unwinds • Both strands replicate simultaneously, during unwinding process Raven et al. (1992)

5. DNA Replication • Sequence of events (cont.) • "Leading" strand replicates continuously from 3' end • newest end of forming strand oriented toward replication fork • "Lagging" strand replicates by a series of fragments placed end-to-end, facing away from fork; fragments with newest ends of fragments later "ligated" • 2 polymerases "proofread" for mismatched bases

6. Physical Structure of Genes • Segments of chromatin that yield proteins through transcription, translation • Typically separated by stretches of inactive chromatin (intergenic spacers) • Commonly encompasses short stretches of inactive chromatin that get cut out during translation (introns) • Can experience recombination in whole or in part! (contrary to original theories)

7. Physical Structure of Genes • Fundamental components • Promoter region "upstream" of initiation site • Necessary binding site for RNA polymerase to accomplish translation • Bears recognition sequences for enzyme (e.g., TTTA) • Initiation site for transcription--yields ribosomal binding site in mRNA Suzuki et al. (1989)

8. Gene Structure and Function • Fundamental components (cont.) • Coding region (exon) of structural gene • Composed of codons (triplets) of nucleotides • Begins with start codon (e.g., TAA) • Ends with stop codon • Codons complementary to mRNA codons --> amino acids in ultimate protein chain • Termination region--halts polymerase from transcribing

9. Transcription • Transcription from DNA strand in nucleus • Takes place in three areas of DNA strand • One site codes for large & small subunits of rRNA • Second site downstream codes for tRNAs • Third site further downstream codes for proteins • Nucleotides assembled parallel to DNA • Complementary nucleotides used: A<-->U, C<-->G Suzuki et al. (1989)

10. Post-transcriptional Processes • Processing of primary RNA transcript from protein-coding DNA • 5' cap and 3' poly-A tail stuck on • introns spliced out in several stages, bringing exons into proximity • Processing in different organs eliminates different portions of transcript --> different mRNA products from initial transcript Suzuki et al. (1989)

11. Post-transcriptional Processes • rRNA and tRNAs move into cytoplasm through nuclear pores immediately • Mature mRNA moves into cytoplasm after processing completed • Genes of mature mRNA translated to proteins • Ribosomal subunits attach to mRNA (usually several at different points) • tRNAs bring amino acids corresponding to mRNA codons into proximity of ribosomal complex • Amino acids joined by peptide bonds to form protein chain • No "proofreading" functions by RNA polymerases

12. Post-transcriptional Processes • MicroRNAs (miRNAs)—newly discovered, very small RNAs that bind to trancripts and render them non-functional (Griffiths et al. [2008]) • play potentially huge role in accomplishing heterochronic (time-shifting) or tissue-specific gene expression • Hundreds of loci found in typical genomes, appear to be produced from “junk” DNA regions • miRNA abundance and diversity influenced by environmental conditions • Heritable in the next generation—hence “Lamarckian” in behavior!

13. The Genetic Code • Degeneracy of the code • 4 nucleotides, organized into triplets, yield 64 possible combinations • 20 commonly employed amino acids • Multiple "synonymous" codons for many amino acids Raven et al. (1992)

14. The Genetic Code • Codon-anticodon pairing • Third position "wobble"--sloppy pairing for last nucleotide in codon • mRNA codons with G or U in third position will recognize and accept more than one tRNA anticodon

15. Regulatory Genes • Determine or influence timing, placement or extent of structural gene (enzyme-producing gene) action • Regulation most common at the transcriptional level • Effects most far-reaching (especially morphologically) of all possible regulatory types • Results from "switching" on and off of gene transcription for particular genes • Simple system—encompasses some but not all genetic systems

16. Regulatory Genes • "Multiple" systems—may represent multiple genes, promoters, regulators or combos of these • Originate from duplications, can diverge later Langridge (1991)

17. Enzyme Architecture • Primary--linear sequence of amino acids • Secondary--side-group interactions • alpha-helix • beta-pleated sheet Computer-simulated folding of rubisco Kellogg & Juliano (1997)

18. Enzyme Architecture • Tertiary--folding of secondary components • Quaternary--multimeric associations among tertiary elements • Protein structure at any or all levels can impact or determine enzymatic function

19. Enzymatic Pathways • One gene-one enzyme hypothesis • One gene controls production of a single enzyme • A biochemical reaction is catalyzed by one enzyme • Processes occur as a series of catalyzed reactions each ultimately regulated by a different gene Suzuki et al. (1989)

20. Enzymatic Pathways • Metabolic cycles • e.g., photosynthesis • e.g., flavonoids • Usually slow to evolve • Would have been important early on in evolution of land plants • Increased complexity, integration-->now largely regulatory adjustments, at least among closely related species

21. Enzymatic Pathways • Development/morphology • e.g., pollination mechanisms in orchids • May evolve very rapidly • Slight changes by many different genes yield major cumulative changes-->new adaptive complexes in a radiating lineage • Slight individual (developmental) modifications to morphology accompanied by biochemical adjustments

22. Regulatory vs. Structural Genetic Change • Example 1--Studies of duplicate gene expression in catastomid fishes • Family originated from polyploidy ca. 50 million years ago • 15 species now extant • Half of duplicated genes in polyploids have lost expression

23. Regulatory vs. Structural Genetic Change • Example 1--Studies of duplicate gene expression in catastomid fishes (cont.) • Remainder have altered in expression in 60% of tissues studied • Most changes in duplicate gene expression relate to different organ and tissue locations, not to cell type or developmental stage • Only 12/84 divergent tissue expressions traceable to enzyme-coding gene mutations • Most tissue-characteristic enzyme patterns have therefore resulted from mutations in transcriptional or processing stages of RNAregulatory elements

24. Regulatory vs. Structural Genetic Change • Example 2--Surveys of tryptophan biosynthetic pathways in protists and fungi • Regulation mechanisms are at least as easily modified as gene locations (=chromosome structural changes) • Much more readily altered than primary structure of active enzymesmore evidence of rapid changes in regulatory mechanism

25. Regulatory vs. Structural Genetic Change • Example 3--Hybrids between morphologically very similar taxa of fish • Express ontogenetic disturbances, e.g., increases in morphological abnormalities, lethality • Species very closely related, probably only recently diverged (not sufficient time for extensive genetic differentiation of structural genes • Species divergence must be in the molecular regulation of genes underlying morphological traits

26. Organization of Genetic Material • Hierarchical arrangement • DNA strands paired in a double helix • Chromatin "beads on a string"--double helix wound helically around 8-part histone molecule, as chain of "nucleosomes" • Nucleosomes packed into a tight "solenoid" ("supercoiling") • Packed stretches of nucleosomes for part of condensed chromosomes Raven et al. (1992)

27. Organization of Genetic Material • Multiple-copy DNA • Dispersed repetitive DNA • Scattered throughout genome • Minisatellites--complicated motifs, dozens/hundreds of bp long • Microsatellites--simple repeat motifs, usually <30 bp long • Considered "junk" DNA—but may accidentally become involved in transcription through accidents of replication • Gene families • Copies in different locations, i.e., on different chromosomes • e.g., ribosomal genes, histone genes • “concerted evolution” in some families homogenizes sequence across all loci—but is random in direction, can proceed with different “templates” across populations

28. Mendelian Principles • Alleles--different phenotypic expressions of the same genetic trait • Dominance relationships • Complete dominance • Dominant allele--expresses phenotype if only one copy is present • Recessive allele--only expresses phenotype if both copies are present Raven et al. (1992)

29. Mendelian Principles • Other dominance relationships • Incomplete dominance--intermediate phenotype in heterozygote • Codominance--both phenotypes expressed in heterozygote (e.g., blood types LmLm, LnLn and LmLn)

30. Mendelian Principles • Allelic systems • Classical 2-allele—”traditional” model • Multiple allelic series • Documented for many genes, often with non-simple relationships • e.g., chevron leaf pattern of white clover • e.g., incompatibility systems enforcing outcrossing

31. Mendelian Principles • Genotypes • Homozygote--both alleles are the same • Homozygous dominant (AA)—expresses phenotype coded by the “dominant” allele • Homozygous recessive (aa)—expresses phenotype coded by the “recessive” allele • Heterozygote--alleles are different (Aa); expresses phenotype of dominant allele if dominance relationship is “dominant” type, but something intermediate or divergent where relationship is “incomplete” or “codominant”

32. Mendelian Principles • Mendel's laws • Law of Segregation • Members of a gene pair segregate into separate gametes • One-half of the gametes has one member, the other half, the other • Law of Independent assortment--during gamete formation, segregation in each gene pair is independent of other pairs Suzuki et al. (1989); Raven et al. (1992)

33. Other Genetic Effects • Lethal genes • Death in recessive homozygote harboring lethal alleles • Sometimes skews progeny ratios where heterozygotes are "subvital" • Pleiotropy--one allele affects two or more characters, e.g., coat color and survival in yellow mice • Epistasis--phenotypic expression of one gene dependent on expression of another gene • Suppressor genes • Modifier genes • Duplicate genes • NOTE—many of these are “non-Mendelian” or even “non-Darwinian” in inheritance!

34. Mitotic and Meiotic Products • Mitosis • Occurs in somatic cells • Yields two daughter cells from one • Daughters diploid, same as parent • Daughters typically genotypically identical to each other and to parent • Usually disregarded in terms of heritable variation (but consider somatic mutations affecting flower primordia) Mitosis Meiosis Raven et al. (1992)

35. Mitotic and Meiotic Products • Meiosis • Occurs in generative cells ("sex cells") • Yields, ultimately, four daughter cells from one • Daughters haploid, reduced from diploid parent (meiocyte) • Daughters typically genotypically different from each other and from parent • Primary point where mutations are incorporated as heritable variation

36. Crossing-over • Commonly accompanies meiosis, at the "four-strand" stage • Occurs usually between any two nonsister chromatids • Begins with intertwining of homologous chromosomes ("chiasmata") Suzuki et al. (1989)

37. Crossing-over • Intertwined strands break at chiasmata and reunite, with exchange of chromosome parts • Typically crossing-over is equal-->same-sized fragments broken at same point and swapped, yielding structurally identical chromatids • 50% or fewer progeny are recombinant • Generates huge numbers of new recombinant genotypes, at each sexual reproductive cycle, in each individual, in each population, across the species!

38. Crossing-over • Multiple crossing-over events • Double crossing-over between adjacent sister chromatids yields double recombinants • Crossing-over also takes place among non-adjacent chromatids • Interference • In some areas of chromosomes double crossing-over never occurs • Suggests non-independence of crossing-over in some regions

39. Bibliography • Griffiths, A. J. F., S. R. Wessler, R. C. Lewontin, and S. B. Carroll. 2008. Introduction to genetic analysis, 9th ed. W. H. Freeman and Company, New York, New York. 838 pp. • Kellogg, E. A. and N. D. Juliano. 1997. The structure and function of RuBisCO and their implications for systematic studies. American Journal of Botany 84:413-428. • Langridge, J. 1991. Molecular genetics and comparative evolution. John Wiley & Sons, Inc., New York, New York. 216 pp.

40. Bibliography • Raven, P. H., R. F. Evert, and S. E. Eichhorn. 1992. Biology of plants, 5th ed. Worth Publishers, New York, New York. 791 pp. • Suzuki, D. T., A. J. F. Griffiths, J. H. Miller, and R. C. Lewontin. 1989. An introduction to genetic analysis, 4th ed. W. H. Freeman and Company, New York, New York. 768 pp.