Flashcards in Chapter 3: Comparing eukaryotic genomes Deck (16):
Synonymous Nonsynonymous change
S: change that ends in same a.a NS: change that ends with dif a.a
Is the proportion of synonymous substitutions (dS) higher, equal or lower than nonsynonymous changes (dN)?
dN< dSConservation of protein sequence and function
dN= dSChanges are accumulated randomly.
dN> dSProteins differ drastically in sequence and perhaps function.
For most genes, synonymous is ____ than nonsynonymous
For most genes, synonymous is higher than nonsynonymous (reflects mutation rates) The higher variation among genes in nonsynonymousrelates to differences in selective constraints
Positive selected genes were enriched for roles in:
Defense/immunity, Sensory perception Reproduction
MHC. Class I/II
MHC genes code for cell surface glycoproteins that present peptides to T cells. Class I expression is on virtually all cells of the body. Class II: Restricted to immune system cells
What happens during infection?
Protein antigens from the infection are degraded within the cell into a series of peptides. MHC molecules with bound peptides are transported to the cell membrane. The cells presenting MHC-peptide complex are recognized as infected by T cells
Human immunodeficiency virus 1-envelope gene
Encodes the envelope glycoproteins gp120 and gp41 (processed envproteins). 5 hyper-variable regions were identified in gp120 (V1 -V5)
What is the basis of selection for gp120-V3?
Hyper variable regions (particularly V3) have been identified as targets for antibodies against the virus. Selecting agent is the patient antibodies. Once the antibodies become efficient against a particular V3 allele, new viral alleles are at an advantage because they can escape antibodies
Genes involved in fertilization (sperm surface genes)
Sperm lysin of abalone: Species selectivity is very important in most marine invertebrates with external fertilization. When lysin is examined between species dN is higher than dS. The selection is related to the establishment of barriers to interspecies fertilization. An example from mammals The ADAM gene family
Distribution of functionally diverged codon sites
Only sperm surface ADAMs (1,2,3,4,5,32) show signals within the adhesion domain (dis,cys) of the protein (black bars).
Differences in Gastric lysozymes: Colobines are primates capable of foregut-fermentation
Caution about dN/dS ratios
Protamines are small, DNA-binding proteins found in sperm surface in mammals.The proportion of arginine residues is about 50% in mammals. The positions of arginine residues have changed considerably among mammals…but a high proportion of arginine is maintained! Selection allows Amino acid replacements as long as the proportion of Arginine residues stays the same, so this is purifying selection, even though Dn/Ds ratios identify positive selection.
What is selectively different? In humans.
Enzymes for amino acid breakdown (diet) Olfaction genes (perception)
Gene under selection in dogs grouped, based on function, into 4 main categories.The most conspicuous group was nervous system development. (also: Sperm-egg recognition (fertilization).; Regulation of metabolism; Digestion (particularly as it relates to starch-rich diet).) The genes belonging to this category are genes that affect developmental signaling and synaptic strength and plasticity. This finding supports the hypothesis that selection for altered behaviour was important during dog domestication and that mutations affecting developmental genes may underlie these changes.
Ten genes with key roles in starch digestion and fat metabolism also show signals of selection. Support for an increased starch digestion in dogs relative to wolves. Results indicate that novel adaptations allowing the early ancestors of modern dogs to thrive on a diet rich in starch, relative to the carnivorous diet of wolves. This constituted a crucial step in the early domestication of dogs. so amalayze in the saliva, also higher maltose