1. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Overview: Microbial Model Systems Viruses called bacteriophages can infect and set in motion a genetic takeover of bacteria, such as Escherichia coli 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

2. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

3. Bacteria are prokaryotes w ith cells much smaller and more simply organized than those of eukaryotes Viruses a re smaller and simpler than bacteria

4. LE 18-2 Virus Bacterium Animal cell Animal cell nucleus 0.25 µm

5. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 18.1: A virus has a genome but can reproduce only within a host cell Scientists detected viruses indirectly long before they could see them The story of how viruses were discovered begins in the late 1800s

6. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Discovery of Viruses: Scientific Inquiry Tobacco mosaic disease stunts growth of tobacco plants and gives their leaves a mosaic coloration In the late 1800s, researchers hypothesized that a particle smaller than bacteria caused the disease In 1935, Wendell Stanley confirmed this hypothesis by crystallizing the infectious particle, now known as tobacco mosaic virus (TMV)

7. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

8. Structure of Viruses Viruses are not cells Viruses are very small infectious particles consisting of nucleic acid enclosed in a protein coat and, in some cases, a membranous envelope

9. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Viral Genomes Viral genomes may consist of – Double- or single-stranded DNA – Double- or single-stranded RNA Depending on its type of nucleic acid, a virus is called a DNA virus or an RNA virus A capsid i s the protein shell that encloses the viral genome A capsid can have various structures

10. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Bacteriophages, also called phages, are viruses that infect bacteria They have the most complex capsids found among viruses Phages have an elongated capsid head that encloses their DNA A protein tailpiece attaches the phage to the host and injects the phage DNA inside

11. LE 18-4d 80  225 nm DNA Head Tail sheath Tail fiber Bacteriophage T4 50 nm

12. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings General Features of Viral Reproductive Cycles Viruses are obligate intracellular parasites, which means they can reproduce only within a host cell Each virus has a host range, a limited number of host cells that it can infect Viruses use enzymes, ribosomes, and small host molecules to synthesize progeny viruses Animation: Simplified Viral Reproductive Cycle Animation: Simplified Viral Reproductive Cycle

13. LE 18-5 DNA VIRUS Capsid HOST CELL Viral DNA Replication Entry into cell and uncoating of DNA Transcription Viral DNA mRNA Capsid proteins Self-assembly of new virus particles and their exit from cell

14. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Reproductive Cycles of Animal Viruses Two key variables in classifying viruses that infect animals: – DNA or RNA? – Single-stranded or double-stranded?

15. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Class/FamilyEnvelopeExamples/Disease I. Double-stranded DNA (dsDNA) AdenovirusNo Respiratory diseases, animal tumors PapovavirusNo Papillomavirus (warts, cervical cancer): polyomavirus (animal tumors) HerpesvirusYes Herpes simplex I and II (cold sores, genital sores); varicella zoster (shingles, chicken pox); Epstein-Barr virus (mononucleosis, Burkitt’s lymphoma) PoxvirusYes Smallpox virus, cowpox virus

16. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Class/FamilyEnvelopeExamples/Disease II. Single-stranded DNA (ssDNA) ParvovirusNoB19 parvovirus (mild rash) III. Double-stranded RNA (dsRNA) ReovirusNoRotavirus (diarrhea), Colorado tick fever virus

17. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Class/FamilyEnvelopeExamples/Disease IV. Single-stranded RNA (ssRNA); serves as mRNA PicornavirusNoRhinovirus (common cold); poliovirus, hepatitis A virus, and other enteric (intestinal) viruses CoronavirusYesSevere acute respiratory syndrome (SARS) FlavivirusYesYellow fever virus, West Nile virus, hepatitis C virus TogavirusYesRubella virus, equine encephalitis viruses

18. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Class/FamilyEnvelopeExamples/Disease V. ssRNA; template for mRNA synthesis FilovirusYes Ebola virus (hemorrhagic fever) OrthomyxovirusYes Influenza virus ParamyxovirusYes Measles virus; mumps virus RhabdovirusYes Rabies virus VI. ssRNA; template for DNA synthesis RetrovirusYes HIV (AIDS); RNA tumor viruses (leukemia)

19. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Viral Envelopes Many viruses that infect animals have a membranous envelope Viral glycoproteins on the envelope bind to specific receptor molecules on the surface of a host cell

20. LE 18-8 RNA ER Capsid HOST CELL Viral genome (RNA) mRNA Capsid proteins Envelope (with glycoproteins) Glyco- proteins Copy of genome (RNA) Capsid and viral genome enter cell New virus Template

21. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings RNA as Viral Genetic Material The broadest variety of RNA genomes is found in viruses that infect animals Retroviruses use reverse transcriptase to copy their RNA genome into DNA HIV is the retrovirus that causes AIDS

22. LE 18-9 Capsid Viral envelope Glycoprotein Reverse transcriptase RNA (two identical strands)

23. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The viral DNA that is integrated into the host genome is called a provirus Unlike a prophage, a provirus remains a permanent resident of the host cell The host’s RNA polymerase transcribes the proviral DNA into RNA molecules The RNA molecules function both as mRNA for synthesis of viral proteins and as genomes for new virus particles released from the cell

24. LE 18-10 HOST CELL Reverse transcription Viral RNA RNA-DNA hybrid DNA NUCLEUS Chromosomal DNA Provirus RNA genome for the next viral generation mRNA New HIV leaving a cell HIV entering a cell 0.25 µm HIV Membrane of white blood cell

25. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Evolution of Viruses Viruses do not fit our definition of living organisms Since viruses can reproduce only within cells, they probably evolved as bits of cellular nucleic acid

26. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 18.2: Viruses, viroids, and prions are formidable pathogens in animals and plants Diseases caused by viral infections affect humans, agricultural crops, and livestock worldwide Smaller, less complex entities called viroids and prions also cause disease in plants and animals

27. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Viral Diseases in Animals Viruses may damage or kill cells by causing the release of hydrolytic enzymes from lysosomes Some viruses cause infected cells to produce toxins that lead to disease symptoms

28. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Vaccines are harmless derivatives of pathogenic microbes that stimulate the immune system to mount defenses against the actual pathogen Vaccines can prevent certain viral illnesses

29. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Emerging Viruses Emerging viruses are those that appear suddenly or suddenly come to the attention of scientists Severe acute respiratory syndrome (SARS) recently appeared in China Outbreaks of “new” viral diseases in humans are usually caused by existing viruses that expand their host territory

30. LE 18-11 Young ballet students in Hong Kong wear face masks to protect themselves from the virus causing SARS. The SARS-causing agent is a coronavirus like this one (colorized TEM), so named for the “corona” of glyco-protein spikes protruding form the envelope.

31. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Viral Diseases in Plants More than 2,000 types of viral diseases of plants are known Some symptoms are spots on leaves and fruits, stunted growth, and damaged flowers or roots

32. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Plant viruses spread disease in two major modes: – Horizontal transmission, entering through damaged cell walls – Vertical transmission, inheriting the virus from a parent

33. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Bacteria Bacteria allow researchers to investigate molecular genetics in the simplest true organisms The well-studied intestinal bacterium Escherichia coli (E. coli) is “the laboratory rat of molecular biology”

34. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Bacterial Genome and Its Replication The bacterial chromosome is usually a circular DNA molecule with few associated proteins Many bacteria also have plasmids, smaller circular DNA molecules that can replicate independently of the chromosome Bacterial cells divide by binary fission, which is preceded by replication of the chromosome

35. LE 18-14 Origin of replication Replication fork Termination of replication

36. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Mutation and Genetic Recombination as Sources of Genetic Variation Since bacteria can reproduce rapidly, new mutations quickly increase genetic diversity More genetic diversity arises by recombination of DNA from two different bacterial cells

37. LE 18-15 Mutant strain arg + trp – Mutant strain arg + trp – Mixture No colonies (control) No colonies (control) Colonies grew Mutant strain arg – trp + Mutant strain arg – trp +

38. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Mechanisms of Gene Transfer and Genetic Recombination in Bacteria Three processes bring bacterial DNA from different individuals together: – Transformation – Transduction – Conjugation

39. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Transformation Transformation is the alteration of a bacterial cell’s genotype and phenotype by the uptake of naked, foreign DNA from the surrounding environment For example, harmless Streptococcus pneumoniae bacteria can be transformed to pneumonia-causing cells

40. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Transduction In the process known as transduction, phages carry bacterial genes from one host cell to another

41. LE 18-16 A+A+ Phage DNA A+A+ Donor cell B+B+ A+A+ B+B+ Crossing over A+A+ A–A– B–B– Recipient cell A+A+ B–B– Recombinant cell

42. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Conjugation and Plasmids Conjugation is the direct transfer of genetic material between bacterial cells that are temporarily joined The transfer is one-way: One cell (“male”) donates DNA, and its “mate” (“female”) receives the genes

43. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings R plasmids and Antibiotic Resistance R plasmids confer resistance to various antibiotics When a bacterial population is exposed to an antibiotic, individuals with the R plasmid will survive and increase in the overall population

44. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Transposition of Genetic Elements The DNA of a cell can also undergo recombination due to movement of transposable elements within the cell’s genome Transposable elements, often called “jumping genes,” contribute to genetic shuffling in bacteria

45. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Insertion Sequences The simplest transposable elements, called insertion sequences, exist only in bacteria An insertion sequence has a single gene for transposase, an enzyme catalyzing movement of the insertion sequence from one site to another within the genome

46. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Transposons Transposable elements called transposons are longer and more complex than insertion sequences In addition to DNA required for transposition, transposons have extra genes that “go along for the ride,” such as genes for antibiotic resistance

47. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 18.4: Individual bacteria respond to environmental change by regulating their gene expression A bacterium can tune its metabolism to the changing environment and food sources This metabolic control occurs on two levels: – Adjusting activity of metabolic enzymes – Regulating genes that encode metabolic enzymes

48. LE 18-20 Regulation of enzyme activity Regulation of enzyme production Enzyme 1 Regulation of gene expression Enzyme 2 Enzyme 3 Enzyme 4 Enzyme 5 Gene 2 Gene 1 Gene 3 Gene 4 Gene 5 Tryptophan Precursor Feedback inhibition

49. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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 An operon can be switched off by a protein called a repressor A corepressor is a small molecule that cooperates with a repressor to switch an operon off

50. LE 18-21a Promoter DNA trpR Regulatory gene RNA polymerase mRNA 3 5 Protein Inactive repressor Tryptophan absent, repressor inactive, operon on mRNA 5 trpE trpD trpC trpBtrpA Operator Start codon Stop codon trp operon Genes of operon E Polypeptides that make up enzymes for tryptophan synthesis D C B A

51. LE 18-21b_1 DNA Protein Tryptophan (corepressor) Tryptophan present, repressor active, operon off mRNA Active repressor

52. LE 18-21b_2 DNA Protein Tryptophan (corepressor) Tryptophan present, repressor active, operon off mRNA Active repressor No RNA made

53. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Repressible and Inducible Operons: Two Types of Negative Gene Regulation A repressible operon is one that is usually on; binding of a repressor to the operator shuts off transcription The trp operon is a repressible operon An inducible operon is one that is usually off; a molecule called an inducer inactivates the repressor and turns on transcription The classic example of an inducible operon is the lac operon, which contains genes coding for enzymes in hydrolysis and metabolism of lactose

54. LE 18-22a DNA lacl Regulatory gene mRNA 5 3 RNA polymerase Protein Active repressor No RNA made lacZ Promoter Operator Lactose absent, repressor active, operon off

55. LE 18-22b DNAlacl mRNA 5 3 lac operon Lactose present, repressor inactive, operon on lacZ lacYlacA RNA polymerase mRNA 5 Protein Allolactose (inducer) Inactive repressor  -Galactosidase Permease Transacetylase

56. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Inducible enzymes usually function in catabolic pathways Repressible enzymes usually function in anabolic pathways Regulation of the trp and lac operons involves negative control of genes because operons are switched off by the active form of the repressor

57. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Positive Gene Regulation Some operons are also subject to positive control through a stimulatory activator protein, such as catabolite activator protein (CAP) When glucose (a preferred food source of E. coli ) is scarce, the lac operon is activated by the binding of CAP When glucose levels increase, CAP detaches from the lac operon, turning it off

58. LE 18-23a DNA cAMP lacl CAP-binding site Promoter Active CAP Inactive CAP RNA polymerase can bind and transcribe Operator lacZ Inactive lac repressor Lactose present, glucose scarce (cAMP level high): abundant lac mRNA synthesized

59. LE 18-23b DNA lacl CAP-binding site Promoter RNA polymerase can’t bind Operator lacZ Inactive lac repressor Inactive CAP Lactose present, glucose present (cAMP level low): little lac mRNA synthesized