Mutation, DNA repair, and Evolution (with references to disease, including aging and cancer) Objectives: 1. Define the nature of genetic variation 2. Provide a context for understanding mutation (disease and aging) 3. Define evolutionary principles, such as natural selection, mutation rate, molecular clocks 4. Explain why rates of mutation/variation differ between genes, and between different regions of the same gene Reading: Krane and Raymer, pp. 57-65 What is implied here? 1995 statement by the National Association of Biology Teachers: “Evolution is an unsupervised, impersonal, unpredictable, and natural process of temporal descent with gradual modification” How Do We Explain Adaptation? • Divine creation; intelligent design • Inheritance of acquired characteristics (Lamarck) • Natural selection (Darwin) What is the keyboard upon which Natural Selection plays? --- and --- What is the ultimate source of genetic variation? --- or --- What is the pool of raw materials from which new variants are selected? Why is everyone different? What are the three sources of genetic variation? A human karyotype, or chromosome spread 2N = 4 So, is it possible that no genetic information was inherited from the paternal grandfather (F1) and none from the maternal grandmother (M2)? 1. Meiosis in humans creates tremendous variety: 223 combinations of 23 chromosomes via meiosis = 8.4 million ways to assort 23 pairs of chromosomes Then,… 8.4 million (sperm) x 8.4 million (egg) = Every conception is one among 70 trillion unique possibilities 2. Crossing over between homologous chromosomes during meiosis adds even more variation Meiosis animation showing random assortment + crossing over 3. Mutation: a change in the sequence of DNA “The Dwarf Francisco Lezcano” Normal DNA sequence 5’…A G C T A C G G G G T G G G C…3’ 5’…A G C T A C A G G G T G G G C…3’ Achondroplasia painted by Diego Velazquez c. 1642 How do gene mutations affect the structure of proteins? Point mutations can affect protein structure and function Type of point mutations: - substitutions (missense and nonsense mutations) - insertions and deletions (frameshift mutations) Wild-type sequence Categorize three different types of point mutations 1 GAA … ATA TAC GTA CAT … … ile tyr val his … glu 2 3 TGC TAG … AAA GAA TGG GTT … … lys glu trp val … cys … TCG CCA TGG CCA … … ser pro trp pro… X (stop) Chemical type: Transversion Transversion Transition Informational type: Missense Missense Nonsense Functional type: Deleterious Non-synonymous Nondegenerate site Deleterious Non-synonymous Nondegenerate site Deleterious Non-synonymous Nondegenerate site Categorize three more types of point mutations 4 5 GTC … ATA TAC GTA CAT … … ile tyr val his … 6 TGC A … AAA GAA TGT GTT … … lys glu cys val … val cys … TCG CCA TGG CCA … … ser pro trp pro … … TCG CAC ATG GCC A … … ser his met gly … Chemical type: Transversion Transition Indel (insertion) Informational type: Missense Missense Frameshift Functional type: Neutral (silent) Synonymous (4-fold degenerate site) Neutral Synonymous (2-fold degenerate site) Deleterious Non-synonymous Is a 4-fold degenerate site ever functionally constrained? What is natural selection? “It may be said that natural selection is daily and hourly scrutinising, throughout the world, every variation, even the slightest; rejecting that which is bad, preserving and adding up all that is good; silently and insensibly working, whenever and wherever opportunity offers, at the improvement of each organic being in relation to its organic and inorganic conditions of life.” -The Origin of Species Charles Darwin Darwin’s concept of Natural Selection provided a mechanism by which species could adapt, become stronger, faster…..fitter Ironically, natural selection alone did not explain how species originate, i.e., How Natural Selection can create a new species from a pre-existing one For Natural Selection to work, a new mechanism was required Enter Gregor Mendel The monk,…and physicist,…and mathematician 7 pea traits, or characters, studied by Mendel Gregor Mendel: 1866 - first described a set of mathematical rules by which the appearance of an organism (its PHENOTYPE) could be related to its inherited genetic makeup (GENOTYPE) Dominant versus Recessive traits How does natural selection occur? • Variation exists within populations • These variations are heritable • More are born than can survive (“the struggle for existence”) • Some variations are “better adapted” to their environment and, therefore, survive to produce more offspring than those “less well adapted.” • The frequency of these successful variations, therefore, increases over time • As the environment changes, different variations are favored. Light and dark morphs of the moth Biston betularia dd = peppered (light colored) Dd and DD = melanic (dark colored) 100 90 80 70 60 50 40 30 20 10 0 d allele D allele Soot on lichens due to industrialization At the genetic level, evolution is simply a change in the gene pool of a population over time. Let’s look at the following example of two genetic diseases caused by mutations in the pathway for tyrosine metabolism, Alkaptonuria (AKU) and Phenylketonuria (PKU) Review of terms: - Homozygous - Heterozygous - Recessive - Dominant - Allele - Haplotype - Pedigree - Functional constraint - Heterozygote advantage Relationship between genes and proteins Example of a monogenic, or single-gene disorder What is wrong with the mouse on the right? Alkaptonuria, aka Black Urine disease, in humans Symptoms: - urine and ear wax turns black as ink shortly after exposure to air -ochronosis: musculoskeletal effects, including progressive degenerative arthritis of the large joints, esp. hip and shoulder - signs of ochronosis: -black deposits in the sclerae (white of eye) -blue colored auricles (ear lobes) Inheritance pattern of Alkaptonuria, i.e., genetic basis of the disease A simple pedigree Incidence: rare, ~1/150,000 births Highly toxic: Phenylketonuria (PKU) Mildly toxic: Alkaptonuria Highly toxic: Type 1 tyrosinemia What is the gene defect, or molecular genetic basis, in alkaptonuria? - four point mutations occur in the human HGO gene - Blastp comparison of HGO gene from human and fungus RVTLPDGPVRGYICELYQGHYQLPELGPIGSNGLANARDFQA PVAAFDDEEGPTE 247 + + + RGYI E+Y H++LP+LGPIG+NGLAN RDFP+A ++D + P SIDVFE-ETRGYILEVYGVHFELPDLGPIGANGLANPRDFLI PIAWYEDRQVPGG 242 T196fs (frameshift) P230S (missense) KFNNHLFSARQDHTPFDIVAWHGNYYPYKYDLGRFNTMGSVSFDHPDPSIYT VLT 307 K+ LF+A+QD +PF++VAWHGNY PYKY+L F + SV+FDHDPSI+ VLTT KYQGKLFAAKQDVSPFNVVAWHGNYTPYKYNLKNFMVINSVAFDHADPSIFT VLT 302 (missense) V300G VGTAIADFVIFPP RWLVAEKTFRPPWYHRNTMSEFMGLITGNYDAKTGGGFQPAG 367 G AIADFVIFPP RW VA+KTFRPP+YHRN MSEFMGLI G+Y+AK GGF P G PGVAIADFVIFPP RWGVADKTFRPPYYHRNCMSEFMGLIRGHYEAKQ-GGFLPGG 361 R321X (nonsense) Are any of the sites in these proteins functionally constrained? Molecular basis of Alkaptonuria, 1898-1998 Mutations: Proline230Serine and Valine300Glycine account for most cases of the disorder Haplotypes: each of these two mutant alleles constitutes a haplotype, i.e., one haploid type. Progeny inherit one haplotype from each parent. But wait: are all mutations deleterious or neutral? Can a mutation rarely be advantageous? And,….can a “deleterious” mutation ever be advantageous? Let’s examine the strange example of the PKU gene, defects in which cause a deadly disease, phenylketonuria Postnatal testing for a common inherited disorder ……phenylketonuria (PKU) Phenylketonuria (PKU) PKU is an inherited error of metabolism caused by a deficiency in the enzyme phenylalanine hydroxylase (PAH). Symptoms: Loss of the PAH enzyme results in mental retardation, organ damage, unusual posture and can, in cases of maternal PKU, severely compromise pregnancy. Inheritance: autosomal recessive disorder, caused by mutations in both alleles of the gene for phenylalanine hydroxylase (PAH), found on chromosome 12. Biochemical basis of PKU: Mutations in both copies of the gene for PAH means that the enzyme is inactive or is less efficient, and the concentration of phenylalanine and phenylpyruvate in the body can build up to toxic levels. http:// willroberts .com/pku/ What is the incidence of Alkaptonuria and Phenylketonuria? AKU: relatively mild, non-fatal & rare, ~1/100,000 to 1/200,000 PKU: severe and rapidly fatal* and common in some groups Caucasians: 1/10,000 Turks: 1/2600 Irish: 1/4500 Japanese 1/143,000 How many caucasians carry the defective trait? 1. 1/10,000 live births x 1/4 chance of homozygous offspring with disease when each parent is a carrier = 1/2500 marriages are between parents who are both carriers; and… 2. Square root of 1/2500 = 1/50 caucasians is heterozygous, i.e., carries one defective allele and one normal allele. Gene Histories: PKU A unique PKU alle le originate d in San’a and s pre ad am ong Ye m e nite Je w s . Mutations in the PAH gene have occurred independently in many human populations and spread due to evolutionary forces nsm1.utdallas.edu/bio/Yasbin/H umanGenetics/ Population2W.ppt A deleterious mutation should be eliminated from the gene pool, but the deadly PKU allele has instead survived and spread widely…..WHY? pku frequency +/pku Parents 1/4 Progeny +/+ x +/pku 1/2 +/pku 50% 1/4 +/pku X pku/pku dies 33% Why is PKU, a devastating disease, common? And why is AKU, a milder disease, rare? - the answer is probably rooted in evolution (ultimate causes): - two fungi, Aspergillus ochraceus and Penicillium viridicatum Ochratoxin A Gene dosage determines how much phenylalanine will be present in the body PKU genotype: Phenylalanine levels: +/+ +/pku pku/pku PHE PHE PHE TYR TYR TYR “The dose makes the poison” Does evolution explain the high incidence of PKU in humans? 1. Carriers of PKU (+/pku heterozygotes) have elevated phenylalanine levels --- BUT they do not develop PKU symptoms 2. Women who are PKU carriers have a much lower-than-average incidence of miscarriage 3. Ochratoxin A is a fungal poison known to cause spontaneous abortion. The fungi that produce this toxin grow on grains (wheat, barley, rye, etc.). Hypothesis: Excess phenylalanine inactivates the fungal poison Rationale: If PKU carriers were more likely to have children than non-carriers because of the protective effects of the PKU gene, then over time, the disease-causing allele would increase and spread through the population. Genes are selected for their reproductive fitness, even if the consequences for some individuals is disastrous pku frequency +/pku Parents x 1/4 Progeny X +/+ +/pku 1/2 +/pku 50% 1/4 +/pku X pku/pku dies Susceptibility to miscarriage reduces reproductive success “Natural Selection, the blind, unconscious, automatic process which Darwin discovered, and which we now know is the explanation for the existence and apparently purposeful form of all life, has no purpose… ….It is the blind watchmaker” ---Richard Dawkins, The Blind Watchmaker Arms Race without End The Red Queen hypothesis explains how antibiotic resistant bacteria, and new diseases, emerge "...in our country," said Alice, still panting a little, "you'd generally get to somewhere else -- if you ran very fast for a long time as we've been doing." "A slow sort of country!" said the Queen. "Now here, you see, it takes all the running you can do to keep in the same place. If you want to get somewhere else, you must run at least twice as fast as that." Antibiotics Antibiotics on filter disc Emergence of antibiotic-resistance coincides with the appearance of antibiotics http://www.sumanasinc.com/scienceinfocus/sif_antibiotics.html http://www.fda.gov/cvm/Documents/01_Selection_Pressure.wmv http://www.pbs.org/wgbh/evolution/educators/lessons/lesson6/act1notes.html “Nothing in biology can be understood except in the light of evolution” -- Theodosius Dobzhansky Where can you find resources for the basics of heredity and genetics? 1. http://www.mun.ca/biology/desmid/brian/BIOL2250/Ghome01.html: -- a brief online genetics primer, taken from the following text: 2. Introduction to Genetic Analysis, 8th ed. 2005. -- this is the text for Bio 211 - Genetics Assignment for Monday, 10/11: 1. 2. Online reading: read Introduction + Part One “Patterns of Inheritance” Online problems: “Homework Assignment 1” and “HA2” in Pt. One above 3. Analyze the following two pedigrees, and do the following: A B a. Deduce the pattern of inheritance, i.e., dominant or recessive b. Deduce the genotype for each progeny individual, and write it out for each one, e.g., AA, Aa, or aa Assignment: Compare the homogentisic acid oxidase genes between Aspergillus nidulans (aka Emericella nidulans), flies, and human 1. Find the A. nidulans, Drosophila melanogaster, human genes, and make a MSWord file showing the protein sequences of each. Terms to search: Homogentisate 1,2-dioxygenase, hmgA, HGO, homogentisic acid oxidase, AKU 2. Using the fly protein as a query sequence, perform a Blastp search. Copy the alignments for fly - fungus and fly - human into a MSWord file. Use Courier 10 or 11 font, and make sure you preserve the properly formatted alignments. Record the following information in a separate table: a. b. 3. % identity and % similarity for each alignment. Gene regions that are excluded from the alignment. If absent, these will be at the N- or C-terminus, and at exon-intron boundaries. Identify regions or blocks of sequence that are functionally constrained in all three of the genes. This may be an approximate, rather than precise, undertaking. Identify these regions by using a color highlighter. What is the evolutionary significance of these functionally constrained regions.