Chapter 18

1. Chapter 18 The Genetics of Viruses and Bacteria

2. Viruses and bacteria are the simplest biological systems • Bacterial cells are much smaller and simpler than those of eukaryotes • Viruses are even smaller and simpler, lacking the structure and metabolic machinery of cells. • Most viruses are an aggregate of nucleic acids and protein—genes in a protein coat.

3. Researchers discovered viruses by studying a plant disease… • In 1883, Adolf Mayer was researching the cause of tobacco mosaic disease, a disease that stunts tobacco plant growth and mottles plant leaves • Mayer concluded that the disease must be caused by an extremely small bacterium

4. Tobacco Mosaic Disease is not caused by a bacterium… • Ten years later, Dimitri Ivanovsky demonstrated that the plant’s sap was still infectious even after passing through a filter designed to remove bacteria

5. But the infectious agent can reproduce… • In 1897, Martinus Beijerinck demonstrated that the infectious agent could reproduce. • The pathogen • could only reproduce within the host • could not be cultivated on nutrient media • was not inactivated by alcohol, generally lethal to bacteria

6. The Tobacco Mosaic Virus is discovered • In 1935, Wendell Stanley crystallized the pathogen, the tobacco mosaic virus (TMV). • This was puzzling because not even the simplest cells can crystallize. • However, viruses are not cells.

7. The genome of viruses • A virus is called a DNA virus or an RNA virus, according to the kind of nucleic acid that makes up its genome. • The viral genome is usually organized as a single linear or circular molecule of nucleic acid. • The smallest viruses have only four genes, while the largest have several hundred.

8. Capsids • The capsid is the protein shell enclosing the viral genome. • Capsids are built of a large number of protein subunits called capsomeres. • The number of different kinds of proteins making up the capsid is usually small.

9. Capsomereof capsid Membranousenvelope RNA Capsomere DNA Head Capsid Tail sheath DNA RNA Tail fiber Glycoprotein Glycoprotein 80  225 nm 18  250 mm 80–200 nm (diameter) 70–90 nm (diameter) 50 nm 20 nm 50 nm 50 nm (d) Bacteriophage T4 (a) Tobacco mosaic virus (b) Adenoviruses (c) Influenza viruses Figure 18.4 Viral structure

10. 0.5 m Complex capsids are found in bacteriophages • The most complex capsids are found in viruses that infect bacteria, called bacteriophages or phages. (right) The T-even phages (T2, T4, T6) that infect E. coli have elongated icosahedral capsid heads that enclose their DNA and a protein tailpiece that attaches the phage to the host and injects the phage DNA inside.

11. Viruses are obligate intracellular parasites. • Viruses can reproduce only within a host cell. • Viruses lack the enzymes for metabolism and the ribosomes for protein synthesis. • An isolated virus is unable to reproduce—or do anything else, except infect an appropriate host.

12. Viruses identify host cells • Viruses identify host cells by a “lock and key” fit between proteins on the outside of the virus and specific receptor molecules on the host’s surface (which evolved for functions that benefit the host).

13. Host Range • Each type of virus can infect and parasitize only a limited range of host cells, called its host range.

14. West Nile Virus has a broad host range • Some viruses can infect several species, while others only infect a single species: • West Nile virus can infect mosquitoes, birds, horses, and humans. • Measles virus can infect only humans.

15. Most viruses of eukaryotes attack specific tissues • Human cold viruses infect only the cells lining the upper respiratory tract. • The AIDS virus binds only to certain white blood cells.

16. Viral infections • A viral infection begins when the genome of the virus enters the host cell. • Once inside, the viral genome reprograms the cell to copy viral nucleic acid and manufacture proteins from the viral genome. • The host provides the nucleotides, ribosomes, tRNAs, amino acids, ATP, etc. for making the viral components dictated by viral genes

17. The viral reproductive cycle • The nucleic acid molecules and capsomeres then self-assemble into viral particles and exit the cell. • The simplest type of viral reproductive cycle ends with the exit of many viruses from the infected host cell, a process that usually damages or destroys the host cell.

18. VIRUS Entry into cell and uncoating of DNA 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 A simplified viral reproductive cycle

19. Phages reproduce using lytic or lysogenic cycles • Research on phages led to the discovery that some double-stranded DNA viruses can reproduce by two alternative mechanisms: the lytic cycle and the lysogenic cycle.

20. The lytic cycle • The lytic cycle culminates in the death of the host. • In the last stage, the bacterium lyses (breaks open) and releases the phages produced within the cell • Each of these phages can infect a healthy cell • Virulent phages use only the lytic cycle

21. Attachment. The T4 phage usesits tail fibers to bind to specificreceptor sites on the outer surface of an E. coli cell. 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. 1 2 4 3 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 Synthesis of viral genomes and proteins. The phage DNAdirects production of phageproteins and copies of the phagegenome by host enzymes, usingcomponents within the cell. 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 Tails Figure 18.6 The lytic cycle of phage T4, a virulent phage

22. The lysogenic cycle • In the lysogenic cycle, the phage genome replicates without destroying the host cell. • Temperate phages, like phage lambda, use both lytic and lysogenic cycles.

23. 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

24. Glycoprotein Viral envelope Capsid RNA(two identicalstrands) Reversetranscriptase Retroviruses have the most complicated life cycles • Human immunodeficiency virus (HIV), the virus that causes AIDS (acquired immunodeficiency syndrome) is a retrovirus • Retroviruses carry an enzyme called reverse transcriptase that transcribes DNA from an RNA template. • RNA  DNA information flow.

25. The virus fuses with the cell’s plasma membrane. The capsid proteins are removed, releasing the viral proteins and RNA. 1 HIV Membrane of white blood cell 2 Reverse transcriptase catalyzes the synthesis of a DNA strand complementary to the viral RNA. HOST CELL 3 Reverse transcriptase catalyzes the synthesis ofa second DNA strand complementary to the first. Reverse transcriptase Viral RNA RNA-DNAhybrid 4 The double-stranded DNA is incorporated as a provirus into the cell’s DNA. 0.25 µm HIV entering a cell DNA NUCLEUS Provirus ChromosomalDNA RNA genomefor the nextviral generation 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. 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. 8 Vesicles transport the glycoproteins from the ER to the cell’s plasma membrane. 9 New viruses bud off from the host cell. New HIV leaving a cell Figure 18.10 The reproductive cycle of HIV, a retrovirus

26. Evolution of Viruses • Because viruses depend on cells for their own propagation • They most likely evolved after the first cells appeared • They may have originated from fragments of cellular nucleic acids that could move from one cell to another

27. Candidates for the original sources of viral genomes • Candidates for the original sources of viral genomes include plasmids and transposable elements. • Plasmids are small, circular DNA molecules that are separate from chromosomes. • found in bacteria and in eukaryote yeast • can replicate independently of the cell • are occasionally transferred between cells. • Transposable elements are DNA segments that can move from one location to another within a cell’s genome.

28. Vaccines • Vaccines are harmless variants or derivatives of pathogenic microbes that stimulate the immune system to mount defenses against the actual pathogen. • Vaccination has eradicated smallpox. • Effective vaccines are available against polio, measles, rubella, mumps, hepatitis B, and a number of other viral diseases.

29. Antibiotics • Medical technology can do little to cure viral diseases once they occur. • Antibiotics kill bacteria by inhibiting enzymes or processes specific to bacteria • Antibiotics are powerless against viruses, which have few or no enzymes of their own. • Most antiviral drugs interfere with viral nucleic acid synthesis.

30. New viral diseases are emerging • In recent years, several emerging viruses have risen to prominence: • HIV - the AIDS virus, seemed to appear suddenly in the early 1980s. • Influenza - Each year new strains of the virus cause millions to miss work or class, and deaths are not uncommon. • Ebola – this deadly virus has caused hemorrhagic fevers in central Africa since 1976. • West Nile virus - appeared for the first time in North America in 1999. • SARS (severe acute respiratory syndrome) first appeared in southern China in 2002.

31. Emergence of new viral diseases • The emergence of these new viral diseases is due to three processes: • mutation • spread of existing viruses from one species to another • dissemination of a viral disease from a small, isolated population.

32. Viroids and prions • Viroids and prions are the simplest infectious agents • Viroids are even smaller and simpler than viruses, consisting of tiny molecules of naked circular RNA that infect plants. • Prions are infectious proteins that spread disease, likely a misfolded form of a normal brain protein

33. The Genetics of Bacteria • The major component of the bacterial genome is one double-stranded, circular DNA molecule associated with a small amount of protein. • The region of DNA, called the nucleoid, is not bound by a membrane. • Many bacteria also have plasmids, smaller circles of DNA. • Each plasmid has only a small number of genes

34. Bacterial cells can reproduce rapidly • Bacterial cells reproduce by binary fission, preceded by replication of the bacterial chromosome. • Bacteria proliferate very rapidly in a favorable environment. • New mutations can have a significant impact on genetic diversity because of short generation spans.

35. Genetic recombination generates diversity • In addition to mutation, genetic recombination generates diversity within bacterial populations • Here, recombination is defined as the combining of DNA from two individuals into a single genome. • Genetic recombination produces new bacterial strains

36. Bacterial recombination occurs by three processes • Bacterial recombination occurs through three processes: • Transformation • Transduction • Conjugation

37. Transformation • Transformation is the uptake of naked DNA from the surroundings • (Fig 18.15)

38. Transduction • Transduction occurs when a phage carries bacterial genes from one host cell to another. • (Fig 18.16)

39. 1 m Sex pilus Conjugation • Conjugation transfers genetic material between two bacterial cells that are temporarily joined. • (Fig 18.17) • The transfer is one-way. One cell (“male”) donates DNA and its “mate” (“female”) receives the genes.

40. F factor • “Maleness” results from an F (for fertility) factor as a section of the bacterial chromosome or as a plasmid. • Cells with either the F factor or the F plasmid are called F+ and they pass this condition to their offspring. • Cells lacking either form of the F factor, are called F−, and they function as DNA recipients.

41. F Plasmid Bacterial chromosome F+ cell F+ cell Mating bridge F+ cell Bacterial chromosome F– cell 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 cell carrying an F plasmid(an F+ cell) can form amating bridge with an F– celland transfer its F plasmid. 5 3 2 3 7 8 1 4 2 1 6 4 (a) Conjugation and transfer of an F plasmid from an F+ donor to an F– recipient Hfr cell F+ cell F factor The circular F plasmid in an F+ cellcan be integrated into the circularchromosome by a single crossoverevent (dotted line). The resulting cell is called an Hfr cell (for High frequency of recombination). B+ D+ C+ C+ Hfr cell A+ D+ A+ A+ B+ D+ D+ A+ C+ C+ B+ B+ A+ B+ C– C– C– C– F– cell B– B+ D– D– D– A+ B– B– D– B– A– A– A– A– A+ The location and orientation of the F factor in the donor chromosome determine the sequence of gene transfer during conjugation. In this example, the transfer sequence for four genes is A-B-C-D. Since an Hfr cell has all the F-factor genes, it can form a mating bridge with an F– cell and transfer DNA. A single strand of the F factorbreaks and begins to move through the bridge. DNA replication occurs in both donor and recipient cells, resulting in double-stranded DNA The mating bridgeusually breaks well before the entire chromosome and the rest of the F factor are transferred. (b) Conjugation and transfer of part of the bacterial chromosome from an Hfr donor to an F– recipient, resulting in recombination Temporary partial diploid Recombinant F– bacterium C– C– B+ B– D– D– B+ B– A– A– A+ A+ The piece of DNA ending up outside thebacterial chromosome will eventually be degraded by the cell’s enzymes. The recipient cell now contains a new combination of genes but no F factor; it is a recombinant F– cell. Two crossovers can result in the exchange of similar (homologous) genes between the transferred chromosome fragment (brown) and the recipient cell’s chromosome (green). Figure 18.18 Conjugation and recombination in E. coli

42. Antibiotic Resistance • The bacterial genes that confer resistance are carried by plasmids, specifically the R plasmid (R for resistance). • When a bacterial population is exposed to an antibiotic, individuals with the R plasmid will survive and increase in the overall population.

43. Bacteria can regulate their gene expression • Individual bacteria respond to environmental change by regulating their gene expression. • First, cells can vary the number of specific enzyme molecules they make by regulating gene expression. • Second, cells can adjust the activity of enzymes already present (for example, by feedback inhibition).

44. Operons: The basic concept • The operon model is the basic mechanism for the control of gene expression in bacteria (proposed by François Jacob and Jacques Monod in 1961). • An operon consists of the operator, the promoter, and the genes they control

45. The operator • Genes coding for a metabolic pathway are often clustered together on the bacterial chromosome • a single “on-off switch” can control a cluster of functionally related genes • The switch is a segment of DNA called an operator.

46. Repressor proteins • If a repressor protein binds to the operator, it can prevent transcription of the operon’s genes. • Each repressor protein recognizes and binds only to the operator of a certain operon. • Repressor proteins are products of regulatory genes which are transcribed continuously at low rates.

47. The trp operon • The trp operon is an example of a repressible operon, one that is inhibited when a specific small molecule binds allosterically to a regulatory protein. • when tryptophan is present in sufficient quantities, the trp operon is turned off

48. The lac operon • The lac operon is an example of an inducible operon, one that is stimulated when a specific small molecule interacts with a regulatory protein. • When lactose is present in sufficient quantities, the lac operon is turned on

49. Repressible and Inducible Enzymes: Negative Gene Regulation • Repressible enzymes generally function in anabolic pathways, synthesizing end products from raw materials. • When the end product is present in sufficient quantities, the cell can allocate its resources to other uses. • Inducible enzymes usually function in catabolic pathways, digesting nutrients to simpler molecules. • By producing the appropriate enzymes only when the nutrient is available, the cell avoids making proteins that have nothing to do.

50. Activator proteins: Positive Gene Regulation • Some regulatory proteins stimulate transcription, and therefore qualify as positive regulation • Positive control of the lac operon is controlled by catabolite activator protein (CAP) • CAP promotes transcription when bound to a site within the promoter.