Viral & Prokaryotic Genetics “Simple” Model Systems

Experimental Model Systems for Genetics  characteristics of good model systems  small genome size  E. coli: ~4 million base pairs (bp)  bacteriophage: ~45,000 bp  large population size  E. coli: ~one billion (10 9 ) per liter  bacteriophage: ~100 billion (10 11 ) per liter

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 ]  bacteriophage: ~20 minutes  haploid genome  genotype => phenotype

viruses are small Table 13.1

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

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

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

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

bacteriophage life cycles Figure 13.2

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

bacteriophage lytic life cycle Figure 13.3

mammalian influenza virus Figure 13.4

HIV retrovirus structure Figure 13.5

Laboratory Propagation of Bacteria Figure 13.6

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

bacteria exhibit genetic recombination Figure 13.7 minimal complete minimal + Met, Biotin, Thr, Leu minimal + Met, Biotin minimal + Thr, Leu

genetic recombination in bacteria Figure 13.9

transformation: scavenging DNA Figure 13.10

transduction: viral transfer Figure generalized transduction specialized transduction

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

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

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

of a gene Figure transpositional inactivation

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

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

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

alternate regulatory mechanisms Figure 13.14

Regulation of Gene Expression transcriptional regulation of gene expression –the E. coli lac operon is inducible

enzyme induction in bacteria Figure 13.13

the lac operon of E. coli Figure 13.16

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

a repressor protein blocks transcription lac repressor blocks transcription Figures 13.15, promoter gene

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

lac inducer inactivates the lac repressor Figure 13.17

trp repressor is normally inactive; trp operon is transcribed Figure 13.18

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

trp co-repressor activates trp repressor; trp operon is not transcribed Figure 13.18

positive and negative regulation both lac and trp operons are negatively regulated –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

induced lac operon also requires activation before genes are transcribed induced lac operon also requires activation before genes are transcribed Figure 13.19

positive & negative regulation of the lac operon Table 13.2

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

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

map of the entire Haemophilus influenzae chromosome Figure 13.21

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

How many genes does it take…? Figure 13.22