Viral & Prokaryotic Genetics

1. Viral & Prokaryotic Genetics “Simple” Model Systems

2. Experimental Model Systems for Genetics • characteristics of good model systems • small genome size • E. coli: ~4 million base pairs (bp) • l bacteriophage: ~45,000 bp • large population size • E. coli: ~one billion (109) per liter • l bacteriophage: ~100 billion (1011) per liter

3. Experimental Model Systems for Genetics • characteristics of good model systems • short generation time • E. coli:18-20 minutes • O/N: 45 generations [1 => 1.76 x 1013] • l bacteriophage: ~20 minutes • haploid genome • genotype => phenotype

4. viruses are smallTable 13.1

5. Viruses • small • resistant to inactivation by • alcohol • dehydration • infectivity may decrease; can’t increase • reproduction: obligate intracellular parasites • uses host nucleotides, amino acids, enzymes • hosts • animals, plants, fungi, protists, prokaryotes

6. Viruses • virus structure • virion = virus particle • central core = genome: DNA or RNA • capsid = protein coat; determines shape • lipid/protein membrane on some animal viruses

7. Viruses • virus classification • host kingdom • genome type (DNA or RNA) • strandedness (single or double) • virion shape • capsid symmetry • capsid size • +/- membrane

8. Viruses • bacteriophage (“bacteria eater”) • reproduction • lytic cycle: virulent phages • infection, growth, lysis • lysogenic cycle: temperate phages • infection, incorporation, maintenance

9. bacteriophage l life cyclesFigure 13.2

10. Viruses • expression of bacteriophage genes during lytic infection • early genes - immediate • middle genes • depends on early genes • replicates viral DNA • late genes • packages DNA • prepares for lysis

11. bacteriophage lytic life cycleFigure 13.3

12. mammalian influenza virusFigure 13.4

13. HIV retrovirus structureFigure 13.5

14. Laboratory Propagation of BacteriaFigure 13.6

15. Prokaryotes • bacteria reproduce by binary fission • reproduction produces clones of identical cells • research requires growth of pure cultures • auxotrophic bacteria with different requirements can undergo recombination

16. bacteria exhibit genetic recombinationFigure 13.7 minimal minimal + Met, Biotin complete minimal + Met, Biotin, Thr, Leu minimal minimal minimal + Thr, Leu

17. genetic recombination in bacteriaFigure 13.9

18. transformation: scavenging DNAFigure 13.10

19. transduction: viral transferFigure 13.10 generalized transduction specialized transduction

20. Prokaryotes • recombination exchanges new DNA with existing DNA • three mechanisms can provide new DNA • transformation - takes up DNA from the environment • transduction - viral transfer from one cell to another • conjugation - genetically programmed transfer from donor cell to recipient cell

21. conjugation: programmed genetic exchange programmed by the chromosome or by an F (fertility) plasmid Figure 13.11

22. Prokaryotes • Plasmids provide additional genes • small circular DNAs with their own ORIs • most carry a few genes that aid their hosts • metabolic factors carry genes for unusual biochemical functions • F factors carry genes for conjugation • Resistance (R) factors carry genes that inactivate antibiotics and genes for their own transfer

23. of a geneFigure 13.12 transpositional inactivation

24. Transposable Elements • mobile genetic elements • move from one location to another on a DNA molecule • may move into a gene - inactivating it • may move chromosome => plasmid => new cell => chromosome • may transfer an antibiotic resistance gene from one cell to another

25. of a gene transpositional inactivation an additional gene hitchhiking on a Transposon Figure 13.12

26. Regulation of Gene Expression • transcriptional regulation of gene expression • saves energy • constitutive genes are always expressed • regulated genes are expressed only when they are needed

27. alternate regulatory mechanismsFigure 13.14

28. Regulation of Gene Expression • transcriptional regulation of gene expression • the E. colilac operon is inducible

29. enzyme induction in bacteria Figure 13.13

30. the lac operon of E. coliFigure 13.16

31. Regulation of Gene Expression • regulation of lac operon expression • the lac operon encodes catabolic enzymes • the substrate (lactose) comes and goes • the cell does not need a catabolic pathway if there is no substrate • the lac operon is inducible • expressed only when lactose is present • allolactose is the inducer

32. a repressor protein blocks transcriptionlac repressor blocks transcription Figures 13.15, 13.17 promoter gene

33. Regulation of Gene Expression • regulation of lac operon expression • lac repressor (lac I gene product) blocks transcription • lac inducer inactivates lac repressor

34. lac inducer inactivates the lac repressorFigure 13.17

35. trp repressor is normally inactive; trp operon is transcribedFigure 13.18

36. Regulation of Gene Expression • regulation of trp operon expression • the trp operon encodes anabolic enzymes • the product is normally needed • the cell needs an anabolic pathway except when the amount of product is adequate • the trp operon is repressible • trp repressor is normally inactive • trp co-repressor activates trp repressor when the amount of tryptophan is adequate

37. trp co-repressor activates trp repressor; trp operon is not transcribedFigure 13.18

38. positive and negative regulation • both lac and trp operons are negativelyregulated • each is regulated by a repressor • lac operon is also positively regulated • after lac repressor is inactivated by the inducer, transcription must be stimulated by a positive regulator

39. inducedlac operon alsorequiresactivation before genesare transcribedinducedlac operon alsorequiresactivation before genesare transcribed Figure 13.19

40. positive & negative regulation ofthe lac operonTable 13.2

41. positive and negative regulation in  bacteriophage • the “decision” between lysis & lysogeny depends on a competition between two repressors

42. lysis vs. lysogenyFigure 13.20 in a healthy, well-nourished culture in a slow-growing nutrient-poor culture

43. map of the entire Haemophilus influenzae chromosomeFigure 13.21

44. new tools for discovery • genome sequencing reveals previously unknown details about prokaryotic metabolism • functional genomics identifies the genes without a known function • comparative genomics reveals new information by finding similarities and differences among sequenced genomes

45. How many genes does it take…?Figure 13.22