1. EVOLUTION OF NEW GENES How do complex organisms acquire extra genes (for new functions)? … and extra forms of regulation? 1. Gene duplication - one copy can perform original function and second one may evolve new function Tandem arrays Dispersed copies Multi-gene families – sets of genes derived by duplication of ancestral gene Pseudogene – non-functional member of gene family chr 1 chr 5 (or degenerate into pseudogene)

2. Homologous genes - share common evolutionary origin Orthologous genes - descendants of an ancestral gene that was present in the last common ancestor of two or more species Paralogous genes - arose by gene duplication within a lineage ancestor Species 1 Species 2 Species 3

3. Fig. 6.11 GLOBIN GENE EVOLUTION Lodish Fig. 3.11

4. Evolution of  – globin gene cluster in mammals Hoffmann Mol Biol Evol 25:591, 2008

5. Unprocessed globin pseudogenes What features might a “processed” globin pseudogene have?

6. Fig. 6.12 Globin superfamily - estimating time of gene duplication events Fig. 6.9

7. - calculate rates of nt sub (r  and r   for genes  and  in species 1 and 2 r  = k  / 2T S r  = k  / 2T S - assume T S is known from geological record - score number of nt sub per site for each gene (that is,  and  ) in the 2 species to determine k  and k  - average rate r = (r  + r  ) / 2 - then to estimate T D (where T D = k  / 2 r), need to know k , the number of sub per site between genes  and  To determine T D

8. - to determine average k , carry out 4 pairwise comparisons 1. Gene  from species 1 and gene  from species 2 2. Gene  from specieis 2 and gene  from species 1 3. Both genes from species 1 4. Both genes from species 2 - depending on degree of divergence may choose to use only synonymous or only non-synonmyous sites… - if rate constancy holds, the 4 pairwise comparisons should be approximately equal T D = k  / 2 r

9. 2. Internal domain duplication - repeated sequence may correspond to functional or structural domain within protein - eg. ovomucoid gene in chickens - enzyme which inhibits trypsin and has 3 domains (as a result of duplication events), each of which can bind one molecule of trypsin

10. Order of duplication events? Fig. 6.5

11. Fig. 6.6 Trypsinogen gene Antifreeze gene in Antarctic cod

12. 3. Exon (or domain) shuffling - exon duplication & incorporation into another gene - functional or structural modules form mosaic proteins - may be mediated by intron recombination Gene 1: 1 2 3 4 Duplication of exon 3 & flanking region 3exon a exon b Gene 2: 3

13. .... CCG|GAA| ACG|GGT|.... 1 2 3 GT AG.... CCG|G AA|ACG|GGT|.... 1 2 3 GT AG.... CCG|GA A|ACG|GGT|.... 1 2 3 GT AG Phase limitations on exon shuffling: If intron lies between 2 codons = “phase 0” If intron between 1 st and 2 nd nt of codon = “phase 1” If intron between 2 nd and 3 rd nt of codon = “phase 2” see Fig. 6.17

14. Do exons correspond to functional (or structural) domains at protein level? In some cases, yes F1 = fibronectin module KR = kringle domain EG = EGF finger module Fig. 6.14 Stryer Fig. 10.35

15. EVOLUTION OF NEW FUNCTION (without duplication) 1. Alternative splicing pathways - single gene can give rise to different mRNAs (and different proteins) pre-mRNA mRNA 1 mRNA 2

16. Fig. 6.21 Some possible types of alternative splicing Example of sex determination pathway in Drosophila see Fig. 6.22

17. eg. mitochondrial-type rps14 gene located within intron of sdh2 gene sdh2 ex1 sdh2 ex2 rps14 Figueroa BBRC 271: 380, 2000 Example of “hitch-hiking” through alternative splicing - organellar genes which move to nucleus during evolution, can only be functional if properly expressed - protein imported back into mitochondria (and N-terminal extension removed) - transferred rps14 gene exploits transcription/translation signals & protein targeting (N-terminal) signals of host sdh2 gene

18. 2. RNA editing - modification of RNA so that message is changed eg. certain C’s in pre-mRNA changed to U’s Lodish Fig. 12-57 eg. apolipoprotein B in mammals In liver: lipid transport in circulation, LDL receptor binding domain In intestine: truncated protein, role in dietary lipid absorption

19. Fig. 6.20 3. Overlapping genes - DNA region codes for more than one protein - different reading frames or complementary strand used - in viruses, bacteriophages… (compact genomes) - rate of evolution expected to be slower for such regions Bacterophage  X174 genome

20. A proteinC protein K protein Fig. 6.20

21. 4. Gene sharing - gene acquires new function without duplication or loss of original function - eg. eye lens crystallin (usually mixture of various structural proteins) - in different animals, different proteins have been recruited (eg. LDH, enolase, heat shock proteins…) in response to changing visual environments aquatic – optically dense, high refractive index terrestrial – lens softer, low RI, focus at distance nocturnal vs. diurnal verebrates… “molecular opportunism”

22. Wistow TIBS 1993 Recruitment of various eye lens crystallins during vertebrate evolution  = lactate dehydrogenase  = enolase  = NADPH-dependent reductase

23. Differences in eye lens proteins between octopus & squid Tomarev J Biol Chem 266:24266, 1991

24. Steps in eye lens gene recruitment 1. Change in regulation so that “housekeeping” gene “up-expressed” in lens multi-functional protein 2. Subsequent aa changes may be favourable for one role, but not other adaptive conflict 3. Resolved by duplication event or reversion back to original function only … and a different gene then recruited for eye lens protein