1. The Genetics of Viruses and Bacteria
Chapter 18
The Genetics of Viruses and Bacteria

2. E. coli and its viruses (bacteriophages)
Are model systems
Beyond their value as model systems
Viruses and bacteria have unique genetic mechanisms that are interesting in their own right
Figure 18.1
0.5 m

3. 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

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

5. In the late 1800s In 1935, Wendell Stanley
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)

6. Viral genomes may consist of
Structure of Viruses
Viruses
nucleic acid in a protein coat and, in some cases, a membranous envelope
Viral genomes may consist of
Double- or single-stranded DNA
Double- or single-stranded RNA

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

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

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

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

11. Reproductive Cycles of Viruses
*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
*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

12. The lytic cycle of phage T4, a virulent phage
Phage assembly
Head
Tails
Tail fibers
Figure 18.6
Attachment. The T4 phage uses its tail fibers to bind to specific receptor sites on the outer surface of an E. coli cell. 1
Entry of phage DNA and degradation of host DNA. The sheath of the tail contracts, injecting the phage DNA into the cell and leaving an empty capsid outside. The cell’s DNA is hydrolyzed. 2
Release. The phage directs production of an enzyme that damages the bacterial cell wall, allowing fluid to enter. The cell swells and finally bursts, releasing 100 to 200 phage particles. 5
Assembly. Three separate sets of proteins self-assemble to form phage heads, tails, and tail fibers. The phage genome is packaged inside the capsid as the head forms. 4
Synthesis of viral genomes and proteins. The phage DNA directs production of phage proteins and copies of the phage genome by host enzymes, using components within the cell. 3

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

14. Viral glycoproteins on the envelope
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

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

16. 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
Figure 18.9
Reverse transcriptase
Viral envelope
Capsid
Glycoprotein
RNA (two identical strands)

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

18. 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

19. Vaccines
Are harmless derivatives of pathogenic microbes that stimulate the immune system to mount defenses against the actual pathogen
Can prevent certain viral illnesses

20. Emerging Viruses Emerging viruses
Are those that appear suddenly or suddenly come to the attention of medical scientists

21. Severe acute respiratory syndrome (SARS)
Recently appeared in China
Figure A, B
(a) Young ballet students in Hong Kong wear face masks to protect themselves from the virus causing SARS.
(b) The SARS-causing agent is a coronavirus like this one (colorized TEM), so named for the “corona” of glycoprotein spikes protruding from the envelope.

22. Outbreaks of “new” viral diseases in humans
Are usually caused by existing viruses that expand their host territory

23. Viral Diseases in Plants
More than 2,000 types of viral diseases of plants are known
Common symptoms of viral infection include
Spots on leaves and fruits, stunted growth, and damaged flowers or roots
Figure 18.12

24. Plant viruses spread disease in two major modes
Horizontal transmission, entering through damaged cell walls
Vertical transmission, inheriting the virus from a parent

25. Viroids and Prions: The Simplest Infectious Agents
Are circular RNA molecules that infect plants and disrupt their growth

26. Prions
Are slow-acting, virtually indestructible infectious proteins that cause brain diseases in mammals
Propagate by converting normal proteins into the prion version
Figure 18.13
Prion
Normal protein
Original prion
New prion
Many prions

27. Bacteria allow researchers
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. Bacterial cells divide by binary fission
Which is preceded by replication of the bacterial chromosome
Replication fork
Origin of replication
Termination of replication
Figure 18.14

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. Further genetic diversity
Can arise by recombination of the DNA from two different bacterial cells
EXPERIMENT
Figure 18.15
Only the samples from the mixed culture, contained cells that gave rise to colonies on minimal medium, which lacks amino acids.
RESULTS
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.
Mutant strain arg+ trp–
Mixture
Mutant strain arg trp+

32. Mutant strain arg+ trp– Mutant strain arg– trp+
Colonies grew
Mutant strain arg+ trp–
Mutant strain arg– trp+
No colonies (control)
Mixture
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.
CONCLUSION

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 infects bacterial cell that has alleles A+ and B+
Transduction
In the process known as transduction
Phages carry bacterial genes from one host cell to another 1
Figure 18.16
Donor cell
Recipient cell A+ B+ B– A–
Recombinant cell
Crossing over
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 bacterial DNA fragment (in this case a fragment with the A+ allele) may be packaged in a phage capsid.
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).
The genotype of the resulting recombinant cell (A+B–) differs from the genotypes of both the donor (A+B+) and the recipient (A–B–). 2 3 4 5
Phage DNA

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

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. Conjugation and transfer of an F plasmid from an F+ donor to an F recipient
Figure 18.18a
A cell carrying an F plasmid (an F+ cell) can form a mating bridge with an F– cell and transfer its F plasmid.
A single strand of the F plasmid breaks at a specific point (tip of blue arrowhead) and begins to move into the recipient cell. As transfer continues, the donor plasmid rotates (red arrow). 2
DNA replication occurs in both donor and recipient cells, using the single parental strands of the F plasmid as templates to synthesize complementary strands. 3
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+. 4
F Plasmid
Bacterial chromosome
Bacterial chromosome
F+ cell
Mating bridge 1
Conjugation and transfer of an F plasmid from an F+ donor to an F– recipient
(a)
F– cell

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. Conjugation and transfer of part of the bacterial chromosome from an Hfr donor to an F– recipient, resulting in recombination
F+ cell
Hfr cell
F factor
The circular F plasmid in an F+ cell can be integrated into the circular chromosome by a single crossover event (dotted line). 1
The resulting cell is called an Hfr cell
(for High frequency of recombination). 2
Since an Hfr cell has all the F-factor genes, it can form a mating bridge with an F– cell and transfer DNA. 3
A single strand of the F factor breaks and begins to move through the bridge. DNA replication occurs in both donor and recipient cells, resulting in double-stranded DNA 4
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. 5
The mating bridge usually breaks well before the entire chromosome and the rest of the F factor are transferred. 6
Two crossovers can result in the exchange of similar (homologous) genes between the transferred chromosome fragment (brown) and the recipient cell’s chromosome (green). 7
The piece of DNA ending up outside the bacterial 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. 8
Temporary
partial
diploid
Recombinant F–
bacterium A+ B+ C+ D+
F– cell A– B– C– D–
Conjugation and transfer of part of the bacterial chromosome from an Hfr donor to an F– recipient, resulting in recombination
(b)
Figure 18.18b

41. R plasmids and Antibiotic Resistance
Confer resistance to various antibiotics

42. 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

43. An insertion sequence contains a single gene for transposase
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
Figure 18.19a
(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.
Insertion sequence
Transposase gene
Inverted
repeat 3 5
A T C C G G T…
T A G G C C A …
A C C G G A T…
T G G C C T A …

44. Bacterial transposons
Also move about within the bacterial genome
Have additional genes, such as those for antibiotic resistance
Figure 18.19b
(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.
Inverted repeats
Transposase gene
Insertion sequence
Antibiotic resistance gene
Transposon 5 3

45. E. coli, a type of bacteria that lives in the human colon
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

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

47. 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

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

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

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

51. In a repressible operon
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

52. The lac operon: regulated synthesis of inducible enzymes
Figure 18.22a
DNA
mRNA
Protein
Active repressor
RNA polymerase
No RNA made
lacZ
lacl
Regulatory gene
Operator
Promoter
Lactose absent, repressor active, operon off. The lac repressor is innately active, and in the absence of lactose it switches off the operon by binding to the operator.
(a) 5 3

53. lacl mRNA 5' DNA mRNA Protein Allolactose (inducer) Inactive repressor
lacz
lacY
lacA
RNA polymerase
Permease
Transacetylase
-Galactosidase 5 3
(b)
Lactose present, repressor inactive, operon on. Allolactose, an isomer of lactose, derepresses the operon by inactivating the repressor. In this way, the enzymes for lactose utilization are induced.
mRNA 5
lac operon
Figure 18.22b

54. Inducible enzymes Repressible enzymes
Usually function in catabolic pathways
Repressible enzymes
Usually function in anabolic pathways

55. Regulation of both the trp and lac operons
Involves the negative control of genes, because the operons are switched off by the active form of the repressor protein

56. Positive Gene Regulation
Some operons are also subject to positive control
Via a stimulatory activator protein, such as catabolite activator protein (CAP)

57. In E. coli, when glucose, a preferred food source, is scarce
The lac operon is activated by the binding of a regulatory protein, catabolite activator protein (CAP)
Promoter
Lactose present, glucose scarce (cAMP level high): abundant lac mRNA synthesized. If glucose is scarce, the high level of cAMP activates CAP, and the lac operon produces large amounts of mRNA for the lactose pathway.
(a)
CAP-binding site
Operator
RNA
polymerase
can bind and transcribe
Inactive CAP
Active CAP
cAMP
DNA
Inactive lac
repressor
lacl
lacZ
Figure 18.23a

58. When glucose levels in an E. coli cell increase
CAP detaches from the lac operon, turning it off
Figure 18.23b
(b)
Lactose present, glucose present (cAMP level low): little lac mRNA synthesized. When glucose is present, cAMP is scarce, and CAP is unable to stimulate transcription.
Inactive lac
repressor
Inactive CAP
DNA
RNA
polymerase
can’t bind
Operator
lacl
lacZ
CAP-binding site
Promoter