Lecture 23. Genetic concepts III: The nature of alleles Muller, H.J. 1932.

1. Lecture 23. Genetic concepts III: The nature of alleles Muller, H.J. 1932. Further studies on the nature and causes of gene mutations. Sixth International Congress of Genetics 1:231-255. Hawley and Walker. Ch. 1. Mutation. pp. 1-14. Also Hartwell Chapter 3, Extensions to Mendel: complexities in relating genotype to phenotype; and Chapter 19 Using Genetics to Study Development, pp. 653-654

2. Mendel's first law was the principle of dominance. In a heterozygote, one allele may conceal the presence of another. In this case, yellow, round and purple are each the dominant trait of a pair.

3. Review. How would you test to see whether a true-breeding (presumably homozygous) mutation in a selfing organism such as Arabidopsis or C. elegans was dominant or recessive (to the wild-type allele)? How would you test to see whether a true-breeding (presumably homozygous) mutation in Drosophila was dominant or recessive? How would you test to see whether a new mutation isolated in a haploid yeast strain was dominant or recessive?

5. Codominance. Codominance requires that the two phenotypes be compatible rather than mutually exclusive. While all dominance relationships are in reference to a particular phenotype, codominance is especially characteristic of the phenotypes rather than the gene or the alleles. Codominance. (semindominant) and would be more accurate

6. Codominance. - Whenever two alleles can be detected independently they will be codominant.

7. The sequence of an allele is a molecular phenotype. The sequence (or any phenotype directly dependent upon it) is a codominant phenotype. Thus, all alleles, even differentwild-type alleles, are co-dominant at the sequence level. If you have a molecular assay (such as allele-specific amplification), the assay will be positive whenever that allele is present.

8. The sequence of an allele is a molecular phenotype. The sequence (or any phenotype directly dependent upon it) is a codominant phenotype. Thus, all alleles, even differentwild-type alleles, are co-dominant at the sequence level. Point: dominance is a relationship among phenotypes, not alleles. For many (all?) recessive mutations, the molecular phenotype is still codominant!

9. Semidominance.

10. Mendel's first law was the principle of dominance. In a heterozygote, one allele may conceal the presence of another. In this case, yellow, round and purple are each the dominant trait of a pair. Complete dominance is very common.

11. How do you explain complete dominance?

12. How do you explain complete dominance? - One dose is sufficient (wild-type is dominant to a null).

13. Drosophila Notch. N / N dead (null phenotype) N / + notched wings (haploinsufficiency) The threshold for the wild-type wing notching phenotype is above 50% of normal activity. Therefore, a haploinsufficient dominant phenotype is observed. The threshold for viability is much lower. Note that the lethality is recessive but the wing-notching is dominant. This example should make it clear that dominance is a property of certain phenotypes, not of the alleles. In this case, both are phenotypes of the same allele.

14. Muller's 'curve of effectiveness.' Types of allele and mechanisms of dominance.

15. 2 x Confluens phenotype None (wild-type phenotype) 1 x Gene activity 0.5 x Notched wings lethality Gene dosage

16. Drosophila Notch. N / N dead N / + notched wings haploinsufficiency amorph, null or nullomorph

17. The ideas of allelic series and thresholds.

19. Types of allele: amorph or null - no activity, a simple concept. haploinsufficiency is when the null is dominant. hypomorph - reduced activity common. neomorph -- a new function antimorph or dominant negative “antimorph” is defined in terms of gene activity; “dominant negative” in terms of molecular basis hypermorphs -- a gain in activity.

20. Phenotype Genotype Red RR White WW R and W are alleles at a single locus.

21. Phenotype Genotype Activity Red RR 2X White WW 0 The simplest assumption is that the R allele has activity and that activity is somehow related to the production of pigment.

22. ADE3 ADE2 A B C red pigment However, your already seen a counterexample: ade2 strains are red, whereas ADE2 strains are white.

23. Phenotype Genotype Activity Red R 0 ade2 White W 2X ADE2

24. Phenotype Genotype Activity Red R 2X w+ White W 0 white

25. How can you tell the difference between the two?

26. How can you tell the difference between the two? The allele that is dominant is likely to be the active allele (“a little dab’ll do ya”)

27. Semidominance Phenotype Genotype Red RR Pink RW White WW R and W are alleles at a single locus.

28. Phenotype Genotype Activity Red RR 2X Pink RW 1X White WW 0 Again, the simplest assumption is that the R allele has activity and that activity is somehow related to the production of pigment.

29. How can you tell the difference between the two? By knowing the null phenotype.

30. How can you tell the difference between the two? By knowing the null phenotype. "Fortunately X-rays provide us with a new tool which helps to shed light on these questions concerning the character of mutations.... That is, we can induce gene rearrangements and so get fragments of chromosomes carrying normal or mutant genes.... We can then add or subtract such fragments, creating hyperploidy or hypoploidy, and can thus determine what the effects of changing the quantity of a given gene material really are. These known effects of purely quantitative changes may then be compared with the effects that were produced by the mutations themselves." - H. J. Muller. 1932

31. "The first locus which we undertook to study was that of the white eye. We chose first flies containing the moderately pigmented mutant [allele] of white called eosin, in which the color is considerably lighter than the normal red.... By irradiation we produced a deleted X chromosome containing this gene. It was then found that the addition of this fragment ... caused the eye color to become darker, more nearly like the normal red. This shows that the actual effect of the ... gene is not to inhibit color, as might have been thought ... but to produce color, since the addition of more of it results in more color, -- only it does not produce as much color as the normal [allele] does.... That the above observed results were not to be explained as effects of the excess dosage of other genes than eosin in the extra fragment was shown by producing a slightly smaller deleted X chromosome, not containing the locus of eosin, and repeating the same tests with it. It was found to have no effect upon the eye color." - H. J. Muller. 1932

32. Types of allele: amorph or null - no activity, a simple concept. haploinsufficiency is when the null is dominant. hypomorph - reduced activity common. neomorph -- a new function antimorph or dominant negative “antimorph” is defined in terms of gene activity; “dominant negative” in terms of molecular basis hypermorphs -- a gain in activity.

37. "Tests thus far indicate that most mutant genes (both spontaneous and induced) are hypomorphs, inasmuch as they show "exaggeration" with deficiencies ... or at least give a form having about the same degree of abnormality as the homozygous mutant. The latter relation would be expected in cases like white eye, where the mutant gene had nearly reached the bottom of the scale of effectiveness and hence itself had almost as little normal effect as the deficiency had. This latter type of mutant may, descriptively, be called 'amorphic.'" - H. J. Muller. 1932 w / Df w / w wild-type wa wa / Df

38. Muller's test of hypomorphs. "for a hypomorph, m/Df is expected to be more severe in phenotype than an m/m homozygote." hypo/ + < hypo/hypo < hypo/null < null/null

39. Muller's test of neomorphs. The normal allelomorph ... acts like an amorph so far as its detectable effect on the character under consideration is concerned. neo/ + = neo/+/+

40. Types of allele: amorph or null - no activity, a simple concept. haploinsufficiency is when the null is dominant. hypomorph - reduced activity common. neomorph -- a new function antimorph or dominant negative “antimorph” is defined in terms of gene activity; “dominant negative” in terms of molecular basis hypermorphs -- a gain in activity.

41. Inhibitory regulation by truncated HLH proteins. (note that heterodimerization can also alter their DNA-binding specificity) (Alberts et al. Fig 9-21). The Hairy-wing mutation is a dominant negative HLH protein; it behaves as a neomorph and was Muller’s example in his 1936 article.

42. Muller's test of antimorphs. Anti/Anti > Anti/Df > Anti/+ > Anti/+/+ >> +/Df = +/+

43. A dominant negative effect of a protein. Here a gene is engineered to produce a mutant protein that prevents the normal copies of the same protein from performing their function. (Alberts et al. Fig 9-21). (also see Fig. 7.27b of Hartwell)

44. Review. What type of allele was created by the Arabidopsis etr1-1 dominant ethylene-insensitive mutation?