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Chapter 18. The Genetics of Viruses and Bacteria. 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. E. coli and its viruses

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chapter 18

Chapter 18

The Genetics of Virusesand Bacteria

slide2

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
slide3
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
slide4

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
slide5
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
the discovery of viruses scientific inquiry

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
slide7
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)
structure of viruses
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
  • Viral genomes may consist of
    • Double- or single-stranded DNA
    • Double- or single-stranded RNA
capsids and envelopes

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
slide10

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
    • How then do you think

the virus entered the host?

slide11

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
general features of viral reproductive cycles
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
    • Very specific! Typically will not cross species barrier.
slide13

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
reproductive cycles of phages
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
the lytic cycle
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
slide16

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
the lysogenic cycle
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
slide18

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
reproductive cycles of animal viruses

Table 18.1

Reproductive Cycles of Animal Viruses
  • The nature of the genome
    • Is the basis for the common

classification of animal viruses

viral envelopes
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
slide21

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
rna as viral genetic material
RNA as Viral Genetic Material
  • The broadest variety of RNA genomes
    • Is found among the viruses that infect animals
slide23

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
slide24

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
evolution of viruses
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
slide26
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
viral diseases in animals
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
slide28
Vaccines
    • Are harmless derivatives of pathogenic microbes that stimulate the immune system to mount defenses against the actual pathogen
    • Can prevent certain viral illnesses
emerging viruses
Emerging Viruses
  • Emerging viruses (campbell video)
    • Are those that appear suddenly or suddenly come to the attention of medical scientists
slide30

(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.

(a) Young ballet students in Hong Kong wear face masks to protect themselves from the virus causing SARS.

Figure 18.11 A, B

  • Severe acute respiratory syndrome (SARS)
    • Recently appeared in China
slide31
Outbreaks of “new” viral diseases in humans
    • Are usually caused by existing viruses that expand their host territory
viral diseases in plants

Figure 18.12

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
slide33
Plant viruses spread disease in two major modes
    • Horizontal transmission, entering through damaged cell walls
    • Vertical transmission, inheriting the virus from a parent
viroids and prions the simplest infectious agents
Viroids and Prions: The Simplest Infectious Agents
  • Viroids
    • Are circular RNA molecules that infect plants and disrupt their growth
slide35

Originalprion

Prion

Many prions

Normalprotein

Newprion

Figure 18.13

  • Prions
    • Are slow-acting, virtually indestructible infectious proteins that cause brain diseases in mammals
    • Propagate by converting normal proteins into the prion version
slide36
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
the bacterial genome and its replication
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
slide38

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
mutation and genetic recombination as sources of genetic variation
Mutation and Genetic Recombination as Sources of Genetic Variation
  • Since bacteria can reproduce rapidly
    • New mutations can quickly increase a population’s genetic diversity
slide40

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+

slide41

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.

mechanisms of gene transfer and genetic recombination in bacteria
Mechanisms of Gene Transfer and Genetic Recombination in Bacteria
  • Three processes bring bacterial DNA from different individuals together
    • Transformation
    • Transduction
    • Conjugation
transformation
Transformation
  • Transformation
    • Is the alteration of a bacterial cell’s genotype and phenotype by the uptake of naked, foreign DNA from the surrounding environment
transduction

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
conjugation and plasmids

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
the f plasmid and conjugation
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

The Fertility factor (also known as F factor or sex factor) is a bacterial DNA sequence that allows a bacterium to produce a sex pillus necessary for conjugation. It contains 20 tra (for "transfer") genes and a number of other genetic sequences responsible for incompatibility, replication, and other functions.

episome
Episome
  • An episome is a plasmid that can integrate itself into the chromosomal DNA of the host organism.
slide48

1

2

3

4

F Plasmid

Bacterial chromosome

F+ cell

F+ cell

Mating bridge

Bacterial chromosome

F+ cell

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.

Conjugation and transfer of an F plasmid from an F+ donor to an F– recipient

(a)

Figure 18.18a

  • Conjugation and transfer of an F plasmid from an F+ donor to an F recipient
slide49
Chromosomal genes can be transferred during conjugation
    • When the donor cell’s F factor (plasmid) 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
slide50

2

1

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+

B+

D+

A+

C+

B+

A+

A+

D+

C+

B+

B+

C–

C–

C–

F– cell

B–

D–

D–

A+

B–

D–

B–

A–

A–

A–

C–

B+

D–

B–

A–

3

4

6

Since an Hfr cell has all the F-factor genes, it can form a mating bridge with an F– cell and transfer DNA.

5

The mating bridgeusually breaks well before the entire chromosome andthe rest of the F factor are transferred.

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.

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

Temporary

partial

diploid

Recombinant F–

bacterium

C–

C–

B+

B–

D–

D–

B+

B–

A–

A–

A+

A+

7

Two crossovers can result in the exchange of similar (homologous) genes between the transferred chromosome fragment (brown) and the recipient cell’s chromosome (green).

8

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.

(b)

Conjugation and transfer of part of the bacterial chromosome from an Hfr donor to an F– recipient, resulting in recombination

  • Conjugation and transfer of part of the bacterial chromosome from an Hfr donor to an F– recipient, resulting in recombination

Figure 18.18b

r plasmids and antibiotic resistance
R plasmids and Antibiotic Resistance
  • R plasmids
    • Confer resistance to various antibiotics
    • We’ll see the transformation of an R plasmid in our lab
transposition of genetic elements
Transposition of Genetic Elements
  • Transposons are sequences of DNA that can move around to different positions within the genome of a cell (Transposition)
    • (jumping genes)
    • Contribute to genetic shuffling in bacteria
insertion sequences

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
transposons

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
slide55
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
slide56

(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
operons the basic concept
Operons: The Basic Concept
  • In bacteria, genes are often clustered into operons, composed of
    • An operator, (“on-off” switch)
    • A promoter
    • Genes for metabolic enzymes
  • Most prokaryotes lack introns, so genes occur together for one purpose/pathway.
    • Thus regulation of the operator can stop/enhance production of the entire operon
slide58
An operon
    • Is usually turned “on” (left in on position)
    • Can be switched off by a protein called a repressor
slide59

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
slide60

DNA

No RNA made

mRNA

Active

repressor

Protein

Tryptophan

(corepressor)

Tryptophan present, repressor active, operon off. As tryptophan

accumulates, it inhibits its own production by activating the repressor protein. (negative feedback)

(b)

Figure 18.21b

repressible and inducible operons two types of negative gene regulation
Repressible and Inducible Operons: Two Types of Negative Gene Regulation
  • In a repressible operon (typically an anabolic pathway)
    • Binding of a specific repressor protein (tryptophan in previous example) to the operator shuts off transcription
  • In an inducible operon (typically an catabolic pathway)
    • Binding of an inducer to an innately active repressor inactivates the repressor and turns on transcription
slide62

Promoter

Regulatorygene

Operator

DNA

lacl

lacZ

NoRNAmade

3

RNApolymerase

mRNA

5

Activerepressor

Protein

(a)

Lactose absent, repressor active, operon off. The lac repressor is innately active, and inthe absence of lactose it switches off the operon by binding to the operator.

Figure 18.22a

  • The lac operon: regulated synthesis of inducible enzymes
slide63

lac operon

DNA

lacl

lacz

lacY

lacA

RNApolymerase

3

mRNA 5

mRNA 5'

mRNA

5

-Galactosidase

Permease

Transacetylase

Protein

Inactiverepressor

Allolactose(inducer)

(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.

Figure 18.22b

slide64
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
positive gene regulation
Positive Gene Regulation
  • Some operons are also subject to positive control
    • Via a stimulatory activator protein, such as catabolite activator protein (CAP)
    • Controls RATE of expression, not overall expression itself
slide66

Operator

RNA

polymerase

can bindand transcribe

Promoter

DNA

lacl

lacZ

CAP-binding site

ActiveCAP

cAMP

Inactive lac

repressor

InactiveCAP

(a)

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.

Figure 18.23a

  • 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)
slide67

Promoter

Operator

DNA

lacl

lacZ

CAP-binding site

RNA

polymerase

can’t bind

InactiveCAP

Inactive lac

repressor

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.

(b)

Figure 18.23b

  • When glucose levels in an E. coli cell increase
    • CAP detaches from the lac operon, slowing down transcription of the lac operon.

Play operon activity campbell