AGR2451 Lecture 5 - Notes (M. Raizada) •complete last week’s lecture

1. AGR2451 Lecture 5 - Notes (M. Raizada) •complete last week’s lecture •this lecture’s handout at the front •please pick up a questionnaire at the front •No Reading for this lecture: •Did you review your notes on Tuesday night???!!! ------------------------------------------------------------------- Lecture 5 - Change I- “New Plant Traits from DNA Mutations”

2. Change:Evolution of Land Plant Phenotypes (see Labs) •Plants, unlike animals came onto land only once -- all land plants related •there are >250,00 species of land plants, most flowering plants Corn Arabidopsis Wind pollen Roots Stomates Surface wax Model Research Species For Plant Geneticists Land ecosystems, human civilization Slide 5.2

3. 1. By mutating ancestral genes, single-celled eukaryotes have created multicellular organisms with novel, divergent traits. However, all organisms share a common set of genes. Why?? Functions of genes in Arabidopsis (weed, Mustard) -Transcription 16.9% 3,018 genes -Protein synthesis 4.1% 730 -Protein fate (modifications, 9.9% 1,766 Folding, compartment targeting) -Signalling 10.4% 1,855 (incl coordination of multiple cell types) -Intracellular transport 8.3% 1,472 (between compartments) -Metabolism 22.5% 4,009 -Plant defence 11.5% 2,055 -Growth 11.7% 2,079 -Transport 4.8% 849 ---------- Source: TAGI (2000) Nature 408, 796-814 assigned 17,833 total 25,498 Why?? Because all cells must carry out basic functions such as transcription, protein synthesis and making plasma membranes. These are called “housekeeping genes”. Slide 1 Slide 5.3

4. • Despite dramatic phenotype changes, a key concept is that all organisms are remarkably related at the molecular level in the protein coding regions: •this may be thegreatest discovery in Biology in the last 50 years!! eg. >30% of human genes may have a functional counterpart in yeast (fungus) after 1.4 billion years of evolution •Obvious related proteins between species pairs: Human -Fruit fly 61% Human-Worm 43% Human-Yeast (fungus) 46% •~52% of Arabidopsis (plant) genes have a recognizable DNA/protein sequence to genes of fruit flies, worms, fungus and humans Source: IHGSC (2001) Nature 409, 860-921 •out of 289 human disease genes, 48% were signficantly related to Arabidopsis genes!! •17 human disease genes are more similar to Arabidopsis genes than yeast, fruit fly or worm eg. Hereditary deafness, MYO15 Cystic fibrosis, ABCC7 Source: TAGI (2000) Nature 408, 796-814 •The genetic codes of different plants are very related to one another. Why is relatedness advantageous to research in agriculture? Slide 5.4

5. Conservation of DNA (Genotype) During Evolution •sometimes, DNA/amino acid sequences have diverged, but when the 3-dimensional shapes of proteins from distant organisms are compared, they have the same shape and perform a related function •natural selection selects for protein shape and function regardless of the encoding DNA sequence •not only are DNA/protein sequences related, but the linear order of genes may be shared between more closely related species (=chromosomal synteny): demo eg.mouse-cat-human eg. rice-corn-wheat-barley-oat-sorghum (cereals) eg. tomato-potato-tobacco-canola-Arabidopsis •this suggests that during evolution, not only genes, but entire chromosomal segments were conserved: Moore, Devos, Wang and Gale (1995) Current Biology 5, 737-739 Current Biology Publishing Group, (UK) Grass synteny chromosome map Slide 5.5

6. 2. If proteins are so highly conserved across species, then why are there such dramatic differences between species even closely-related species (humans to chimpanzees or turfgrass to corn)? Asked another way, are all mutations equal in their effect? To breed each of the following new traits, in what type of gene and location within that gene should mutations be selected for? -to recognize a new pathogen? -to make a leaf bigger in size? -to create a plant with 5 fewer leaves? -to cause 1000 new genes (responsible for drought tolerance) to be induced by a new stimulus such as heat? -to change the amount of starch in a seed? -to add a sugar group (-OH) onto a plant toxin to detoxify it for human consumption? Slide 5.6

7. To answer the previous questions posed: •Though proteins and thus DNA coding regions may be conserved, the regulatory regions are not. Small changes in regulatory regions can lead to dramatic changes in phenotype quickly. This is important in plant breeding. •Small changes in signalling molecules (transcription factor binding sites, receptor-ligand recognition, hormone dose) can also lead to dramatic changes in phenotype. Case Study: Maize evolved from its wild relative, Teosinte. The two plants can interbreed (same species), yet their shoot architecture is dramatically different. Mutations in only 1 major gene, Tb1, is responsible for this change. Slide 5.7

8. Teosinte vs. Maize Tb1 gene TB1 is a signalling protein, which regulates the number of vegetative branches produced by a plant. Comparing the Tb1 gene between teosinte and maize,most of the mutations are in the regulatory region (as well as in the intron), not the exons. Changes in the regulation and dose of the mRNA likely explain the differences in plant architecture. Indigenous people in Mexico selected for mutations in the regulatory region of Tb1 over a period of >300 years. In addition to mutations in the regulatory regions, small amino acid changes at the binding sites of proteins (eg. enzyme-substrate binding site,or transcription factor binding site) can lead to dramatic changes in phenotype. Slide 5.8

9. 3. Do mutations happen randomly or are they targetted to certain genes or certain parts of genes? In the case of Tb1, if mutations occur randomly, why are there so few mutations between Teosinte and modern maize in the exons of Tb1? Natural Selection is the “filter” that the environment places on a phenotype, thus selecting for or against mutations in the genotype. demo example-Dubautia (sunflower family) includes 28 species in Hawaii and California -Rainfall diversity 40cm-1230 cm/year -Result: natural selection on leaf size -Is natural selection active or passive? Most mutations have no effect (neutral) and hence they simply build-up over generations (eg. in introns and in the DNA between genes on a chromosome) From Biology of Plants p.164 P. Raven, R. Evert and S.Eichhorn Worth Publishers, New York, 1992 Slide 1 Slide 5.9

10. 4. Natural Selection vs. Human Selection •Natural selection took place over 1.4-1.6 billion years for plants in complex ecosystems, with competition from predators, struggle over resources with other plants. Plants were not selected for to serve humans, but rather to deter animals or use them for seed dispersal. •Human selection on plants has been the exact opposite: It has taken place only for >10,000 years, for the benefit of the human herbivore, in a monoculture ecosystem with much less competition. What are the consequences of these differences? Slide 5.10 From Raven

11. •Mutations selected by human selection by farmers are a much more valuable resource for crop breeding than random mutations,or arguably, mutations selected by natural selection. Hundreds of thousands of these varieties exist in seedbanks around the world and are used in breeding programs to introduce new traits. •Many of these farmer-selected mutations are likely in regulatory regions of genes, signalling proteins and enzyme binding sites. International Seed Banks The Seedbank at The International Maize and Wheat Improvement Center (CIMMYT), Mexico •novel alleles caused drought tolerance, cold resistance, disease resistance, pest tolerance Raizada Slide 5.11

12. 5. What causes the (random) DNA mutations? i) Point mutations, short insertions and deletions. eg. G to A. These are caused by mistakes during DNA replication. ii). Parasitic DNA -- DNA parasites that duplicate themselves and “jump” into genes and between genes (called transposons, retroelements, or mobile elements) Walbot and Petrov (2001) PNAS 98, 8163-8164 National Academy Sci. Press, USA, Washington, DC gene gene gene •ancient jumping genes may have given rise to introns •highly repeated blocks of mobile elements are called heterochromatin (gene-rich blocks = euchromatin) •examples of mobile elements in humans: SINEs 1.6 million copies LINEs 868,000 copies Source IHGSC (2001) Nature 409, 860-921 •in humans and corn, 80-90% of genome consists of mobile element parasites (“junk DNA”) •mobile elements can carry new regulatory information or jump into gene switches (very important in plant evolution), and hence have created new alleles for plant evolution Slide 5.12

13. Consequences of Parasitic DNA (Mobile Genes) •dilemma: corn, rice, wheat have highly related genes, similar # of genes (50-60,000) but the total amount of DNA in their genomes is very different: Rice 450 million base pairs Corn 2,600 million bp Wheat 12,200 million bp (all haploid) Why?? •these genomes vary in the amount of “junk DNA” they have due to a high copy number DNA parasites •therefore, mobile DNA is responsible for genome expansion by creating blocks intergenic “junk DNA” blocks. **DNA quantity does not correlate with complexity in multicellular organisms.** Example of a corn jumping gene jumping in and out: demo Source: M.Raizada Slide 5.13

14. Lecture 5 - Concept Summary 1. Proteins are conserved across evolution, especially “housekeeping proteins”. Most important concept!! 2. Even between non-housekeeping genes, the proteins they encode maintain their 3-D structures (only 1000 unique folds). 3. Though proteins and thus DNA coding regions may be conserved, the regulatory regions are not. Small changes in regulatory regions can lead to dramatic changes in phenotype quickly. This is important in plant breeding. 4. Small changes in signalling molecules (transcription factor binding sites, receptor-ligand recognition, hormone dose) can also lead to dramatic changes in phenotype. 5. Small amino acid changes at the binding sites of proteins (eg. enzyme-substrate binding site,or transcription factor binding site) can lead to dramatic changes in phenotype. 6. DNA mutations occur randomly. Mutations with no effect can accumulate. Mutations with phenotypic effects can be selected by natural selection or human (breeding) selection and these new mutations can spread through the population. 7. Two mechanisms responsible for creating DNA mutations are spontaneous nucleotide “point mutations” and the insertion and excision of parasitic mobile DNA elements (“jumping genes”) Slide 5.14