Chapter 18

1. Chapter 18 The Genetics of Virusesand Bacteria

2. 0.5 m Figure 18.1 • Overview: Microbial Model Systems • Viruses called bacteriophages • Can infect and set in motion a genetic takeover of bacteria, such as Escherichia coli

3. E. coli and its viruses • Are called model systems because of their frequent use by researchers in studies that reveal broad biological principles • Beyond their value as model systems • Viruses and bacteria have unique genetic mechanisms that are interesting in their own right

4. Virus Bacterium Animalcell 0.25 m Animal cell nucleus Figure 18.2 • Recall that bacteria are prokaryotes • With cells much smaller and more simply organized than those of eukaryotes • Viruses • Are smaller and simpler still

5. Concept 18.1: A virus has a genome but can reproduce only within a host cell • Scientists were able to detect viruses indirectly • Long before they were actually able to see them

6. Figure 18.3 The Discovery of Viruses: Scientific Inquiry • Tobacco mosaic disease • Stunts the growth of tobacco plants and gives their leaves a mosaic coloration

7. In the late 1800s • Researchers hypothesized that a particle smaller than bacteria caused tobacco mosaic disease • In 1935, Wendell Stanley • Confirmed this hypothesis when he crystallized the infectious particle, now known as tobacco mosaic virus (TMV)

8. Structure of Viruses • Viruses • Are very small infectious particles consisting of nucleic acid enclosed in a protein coat and, in some cases, a membranous envelope

9. Viral Genomes • Viral genomes may consist of • Double- or single-stranded DNA • Double- or single-stranded RNA

10. Capsomereof capsid RNA DNA Capsomere Glycoprotein 18  250 mm 70–90 nm (diameter) 20 nm 50 nm (b) Adenoviruses Figure 18.4a, b (a) Tobacco mosaic virus Capsids and Envelopes • A capsid • Is the protein shell that encloses the viral genome • Can have various structures

11. Membranousenvelope Capsid RNA Glycoprotein 80–200 nm (diameter) 50 nm (c) Influenza viruses Figure 18.4c • Some viruses have envelopes • Which are membranous coverings derived from the membrane of the host cell

12. Head DNA Tail sheath Tail fiber 80  225 nm 50 nm (d) Bacteriophage T4 Figure 18.4d • Bacteriophages, also called phages • Have the most complex capsids found among viruses

13. General Features of Viral Reproductive Cycles • Viruses are obligate intracellular parasites • They can reproduce only within a host cell • Each virus has a host range • A limited number of host cells that it can infect

14. VIRUS DNA Entry into cell and uncoating of DNA Capsid Transcription Replication HOST CELL Viral DNA mRNA Viral DNA Capsid proteins Self-assembly of new virus particles and their exit from cell Figure 18.5 • Viruses use enzymes, ribosomes, and small molecules of host cells • To synthesize progeny viruses

15. Reproductive Cycles of Phages • Phages • Are the best understood of all viruses • Go through two alternative reproductive mechanisms: the lytic cycle and the lysogenic cycle

16. The Lytic Cycle • The lytic cycle • Is a phage reproductive cycle that culminates in the death of the host • Produces new phages and digests the host’s cell wall, releasing the progeny viruses

17. 1 Attachment. The T4 phage usesits tail fibers to bind to specificreceptor sites on the outer surface of an E. coli cell. 2 Entry of phage DNA and degradation of host DNA.The sheath of the tail contracts,injecting the phage DNA intothe cell and leaving an emptycapsid outside. The cell’sDNA is hydrolyzed. 5 Release. The phage directs productionof an enzyme that damages the bacterialcell wall, allowing fluid to enter. The cellswells and finally bursts, releasing 100 to 200 phage particles. Phage assembly 3 Synthesis of viral genomes and proteins. The phage DNAdirects production of phageproteins and copies of the phagegenome by host enzymes, usingcomponents within the cell. 4 Assembly. Three separate sets of proteinsself-assemble to form phage heads, tails,and tail fibers. The phage genome ispackaged inside the capsid as the head forms. Head Tail fibers Figure 18.6 Tails • The lytic cycle of phage T4, a virulent phage

18. The Lysogenic Cycle • The lysogenic cycle • Replicates the phage genome without destroying the host • Temperate phages • Are capable of using both the lytic and lysogenic cycles of reproduction

19. Phage DNA The phage attaches to a host cell and injects its DNA. Many cell divisions produce a large population of bacteria infected with the prophage. Phage DNA circularizes Phage Occasionally, a prophage exits the bacterial chromosome, initiating a lytic cycle. Bacterial chromosome Lytic cycle Lysogenic cycle Certain factors determine whether The bacterium reproduces normally, copying the prophage and transmitting it to daughter cells. The cell lyses, releasing phages. Prophage Lytic cycle is induced Lysogenic cycle is entered or New phage DNA and proteins are synthesized and assembled into phages. Phage DNA integrates into the bacterial chromosome,becoming a prophage. Figure 18.7 • The lytic and lysogenic cycles of phage , a temperate phage

20. Reproductive Cycles of Animal Viruses • The nature of the genome • Is the basis for the common classification of animal viruses

21. Viral Envelopes • Many animal viruses • Have a membranous envelope • Viral glycoproteins on the envelope • Bind to specific receptor molecules on the surface of a host cell

22. Glycoproteins on the viral envelope bind to specific receptor molecules(not shown) on the host cell, promoting viral entry into the cell. Capsid RNA 2 1 Envelope (with glycoproteins) Capsid and viral genome enter cell 3 HOST CELL The viral genome (red) functions as a template forsynthesis of complementary RNA strands (pink) by a viral enzyme. Viral genome (RNA) Template 5 mRNA Complementary RNA strands also function as mRNA, which is translated into both capsid proteins (in the cytosol)and glycoproteins for the viral envelope (in the ER). New copies of viral genome RNA are made using complementary RNA strands as templates. 4 Capsid proteins ER Copy of genome (RNA) Glyco- proteins 6 Vesicles transport envelope glycoproteins to the plasma membrane. 7 New virus 8 A capsid assembles around each viral genome molecule. Figure 18.8 • The reproductive cycle of an enveloped RNA virus

23. RNA as Viral Genetic Material • The broadest variety of RNA genomes • Is found among the viruses that infect animals

24. Glycoprotein Viral envelope Capsid RNA(two identicalstrands) Reversetranscriptase Figure 18.9 • Retroviruses, such as HIV, use the enzyme reverse transcriptase • To copy their RNA genome into DNA, which can then be integrated into the host genome as a provirus

25. 1 Reverse transcriptase catalyzes the synthesis of a DNA strand complementary to the viral RNA. 2 The virus fuses with the cell’s plasma membrane. The capsid proteins are removed, releasing the viral proteins and RNA. Membrane of white blood cell HIV Reverse transcriptase catalyzes the synthesis ofa second DNA strand complementary to the first. 3 Reverse transcriptase HOST CELL Viral RNA 4 The double-stranded DNA is incorporated as a provirus into the cell’s DNA. RNA-DNAhybrid 0.25 µm HIV entering a cell DNA ChromosomalDNA NUCLEUS Provirus 5 Proviral genes are transcribed into RNA molecules, which serve as genomes for the next viral generation and as mRNAs for translation into viral proteins. RNA genomefor the nextviral generation mRNA 6 The viral proteins include capsid proteins and reverse transcriptase (made in the cytosol) and envelope glycoproteins (made in the ER). 7 Capsids are assembled around viral genomes and reverse transcriptase molecules. Vesicles transport the glycoproteins from the ER to the cell’s plasma membrane. 8 9 New viruses bud off from the host cell. Figure 18.10 New HIV leaving a cell • The reproductive cycle of HIV, a retrovirus

26. Evolution of Viruses • Viruses do not really fit our definition of living organisms • Since viruses can reproduce only within cells • They probably evolved after the first cells appeared, perhaps packaged as fragments of cellular nucleic acid

27. Concept 18.3: Rapid reproduction, mutation, and genetic recombination contribute to the genetic diversity of bacteria • Bacteria allow researchers • To investigate molecular genetics in the simplest true organisms

28. The Bacterial Genome and Its Replication • The bacterial chromosome • Is usually a circular DNA molecule with few associated proteins • In addition to the chromosome • Many bacteria have plasmids, smaller circular DNA molecules that can replicate independently of the bacterial chromosome

29. Replicationfork Origin of replication Termination of replication Figure 18.14 • Bacterial cells divide by binary fission • Which is preceded by replication of the bacterial chromosome

30. Mutation and Genetic Recombination as Sources of Genetic Variation • Since bacteria can reproduce rapidly • New mutations can quickly increase a population’s genetic diversity

31. EXPERIMENT Researchers had two mutant strains, one that could make arginine but not tryptophan (arg+ trp–) and one that could make tryptophan but not arginine (arg trp+). Each mutant strain and a mixture of both strains were grown in a liquid medium containing all the required amino acids. Samples from each liquid culture were spread on plates containing a solution of glucose and inorganic salts (minimal medium), solidified with agar. Mixture Mutantstrainarg+trp– RESULTS Only the samples from the mixed culture, contained cells that gave rise to colonies on minimal medium, which lacks amino acids. Figure 18.15 • Further genetic diversity • Can arise by recombination of the DNA from two different bacterial cells Mutantstrainargtrp+

32. Mixture Mutantstrainarg+trp– Mutantstrainarg–trp+ No colonies(control) No colonies(control) Coloniesgrew CONCLUSION Because only cells that can make both arginine and tryptophan (arg+ trp+ cells) can grow into colonies on minimal medium, the lack of colonies on the two control plates showed that no further mutations had occurred restoring this ability to cells of the mutant strains. Thus, each cell from the mixture that formed a colony on the minimal medium must have acquired one or more genes from a cell of the other strain by genetic recombination.

33. Mechanisms of Gene Transfer and Genetic Recombination in Bacteria • Three processes bring bacterial DNA from different individuals together • Transformation • Transduction • Conjugation

34. Transformation • Transformation • Is the alteration of a bacterial cell’s genotype and phenotype by the uptake of naked, foreign DNA from the surrounding environment

35. Phage DNA B+ A+ 1 Phage infects bacterial cell that has alleles A+ and B+ Host DNA (brown) is fragmented, and phage DNA and proteins are made. This is the donor cell. A+ 2 B+ Donorcell 3 A bacterial DNA fragment (in this case a fragment withthe A+ allele) may be packaged in a phage capsid. A+ Crossingover Phage with the A+ allele from the donor cell infects a recipient A–B– cell, and crossing over (recombination) between donor DNA (brown) and recipient DNA (green) occurs at two places (dotted lines). 4 A+ A– B– Recipientcell The genotype of the resulting recombinant cell (A+B–) differs from the genotypes of both the donor (A+B+) and the recipient (A–B–). 5 A+ B– Figure 18.16 Recombinant cell Transduction • In the process known as transduction • Phages carry bacterial genes from one host cell to another

36. 1 m Sex pilus Figure 18.17 Conjugation and Plasmids • Conjugation • Is the direct transfer of genetic material between bacterial cells that are temporarily joined

37. The F Plasmid and Conjugation • Cells containing the F plasmid, designated F+ cells • Function as DNA donors during conjugation • Transfer plasmid DNA to an F recipient cell

38. 3 1 2 4 F Plasmid Bacterial chromosome F+ cell F+ cell Mating bridge Bacterial chromosome F+ cell F– cell A cell carrying an F plasmid(an F+ cell) can form amating bridge with an F– celland transfer its F plasmid. A single strand of the F plasmid breaks at a specific point (tip of blue arrowhead) and begins tomove into the recipient cell. As transfer continues, the donor plasmid rotates(red arrow). DNA replication occurs inboth donor and recipientcells, using the single parental strands of the F plasmid as templates to synthesize complementary strands. The plasmid in the recipient cell circularizes. Transfer and replication result in a compete F plasmid in each cell. Thus, both cells are now F+. (a) Conjugation and transfer of an F plasmid from an F+ donor to an F– recipient Figure 18.18a • Conjugation and transfer of an F plasmid from an F+ donor to an F recipient

39. Chromosomal genes can be transferred during conjugation • When the donor cell’s F factor is integrated into the chromosome • A cell with the F factor built into its chromosome • Is called an Hfr cell • The F factor of an Hfr cell • Brings some chromosomal DNA along with it when it is transferred to an F– cell

40. R plasmids and Antibiotic Resistance • R plasmids • Confer resistance to various antibiotics

41. Transposition of Genetic Elements • Transposable elements • Can move around within a cell’s genome • Are often called “jumping genes” • Contribute to genetic shuffling in bacteria

42. Insertion sequence 3 5 3 5 A T C C G G T… A C C G G A T… T A G G C C A … T G G C C T A … Transposase gene Inverted repeat Inverted repeat (a) Insertion sequences, the simplest transposable elements in bacteria, contain a single gene that encodes transposase, which catalyzes movement within the genome. The inverted repeats are backward, upside-down versions of each other; only a portion is shown. The inverted repeat sequence varies from one type of insertion sequence to another. Figure 18.19a Insertion Sequences • An insertion sequence contains a single gene for transposase • An enzyme that catalyzes movement of the insertion sequence from one site to another within the genome

43. Transposon Antibioticresistance gene Insertion sequence Insertion sequence 5 3 5 3 Inverted repeats Transposase gene (b) Transposons contain one or more genes in addition to the transposase gene. In the transposon shown here, a gene for resistance to an antibiotic is located between twin insertion sequences. The gene for antibiotic resistance is carried along as part of the transposon when the transposon is inserted at a new site in the genome. Figure 18.19b Transposons • Bacterial transposons • Also move about within the bacterial genome • Have additional genes, such as those for antibiotic resistance

44. Concept 18.4: Individual bacteria respond to environmental change by regulating their gene expression • E. coli, a type of bacteria that lives in the human colon • Can tune its metabolism to the changing environment and food sources

45. (a) Regulation of enzyme activity (b) Regulation of enzyme production Precursor Feedback inhibition Enzyme 1 Gene 1 Regulation of gene expression Enzyme 2 Gene 2 Gene 3 Enzyme 3 – Gene 4 Enzyme 4 – Gene 5 Enzyme 5 Tryptophan Figure 18.20a, b • This metabolic control occurs on two levels • Adjusting the activity of metabolic enzymes already present • Regulating the genes encoding the metabolic enzymes

46. Operons: The Basic Concept • In bacteria, genes are often clustered into operons, composed of • An operator, an “on-off” switch • A promoter • Genes for metabolic enzymes

47. An operon • Is usually turned “on” • Can be switched off by a protein called a repressor

48. trp operon Promoter Promoter Genes of operon RNA polymerase Start codon Stop codon trpR trpD trpC trpB trpE trpA DNA Operator Regulatory gene 3 mRNA 5 mRNA 5 C E D B A Polypeptides that make up enzymes for tryptophan synthesis Inactiverepressor Protein (a) Tryptophan absent, repressor inactive, operon on. RNA polymerase attaches to the DNA at the promoter and transcribes the operon’s genes. Figure 18.21a • The trp operon: regulated synthesis of repressible enzymes

49. DNA No RNA made mRNA Active repressor Protein Tryptophan (corepressor) (b) Tryptophan present, repressor active, operon off. As tryptophan accumulates, it inhibits its own production by activating the repressor protein. Figure 18.21b

50. Repressible and Inducible Operons: Two Types of Negative Gene Regulation • In a repressible operon • Binding of a specific repressor protein to the operator shuts off transcription • In an inducible operon • Binding of an inducer to an innately inactive repressor inactivates the repressor and turns on transcription