18 - Virus&Bacteria Text

Chapter 18
The Genetics of Viruses and Bacteria

PowerPoint Lectures for Biology, Seventh Edition
Neil Campbell and Jane Reece
Lectures by Chris Romero

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
Figure 18.1
0.5 m
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
Recall that bacteria are prokaryotes

With cells much smaller and more simply organized than those of eukaryotes
Viruses
Are smaller and simpler still
Virus
Bacterium Animal cell
0.25 m
Animal cell nucleus
Figure 18.2
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 Tobacco mosaic disease

Stunts the growth of tobacco plants and gives their leaves a mosaic coloration
Figure 18.3
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 Viruses

Are very small infectious particles consisting of nucleic acid enclosed in a protein coat and, in some cases, a membranous envelope
Viral Genomes Viral genomes may consist of

Double- or single-stranded DNA
Double- or single-stranded RNA
Capsids and Envelopes A capsid

Is the protein shell that encloses the viral genome
Can have various structures

Capsomere of capsid RNA Capsomere DNA
Glycoprotein 7090 nm (diameter) 18 250 mm
20 nm Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Figure 18.4a, b (a) Tobacco mosaic virus (b) Adenoviruses
50 nm
Some viruses have envelopes

Which are membranous coverings derived from the membrane of the host cell
Membranous envelope
Capsid RNA
Glycoprotein 80200 nm (diameter)
Figure 18.4c
50 nm (c) Influenza viruses
Bacteriophages, also called phages

Have the most complex capsids found among viruses
Head Tail sheath Tail fiber DNA
80 225 nm
Figure 18.4d
50 nm (d) Bacteriophage T4
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
Viruses use enzymes, ribosomes, and small molecules of host cells

To synthesize progeny viruses
Entry into cell and uncoating of DNA DNA Capsid VIRUS 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
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

Is a phage reproductive cycle that culminates in the death of the host Produces new phages and digests the hosts cell wall, releasing the progeny viruses
The lytic cycle of phage T4, a virulent phage

1 Attachment. The T4 phage uses
its tail fibers to bind to specific receptor 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 into the cell and leaving an empty capsid outside. The cells DNA is hydrolyzed.
5 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.
Phage assembly
4 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. Figure 18.6 Head Tails Tail fibers
3 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.
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
The lytic and lysogenic cycles of phage , a temperate phage

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

Is the basis for the common classification of animal viruses
Classes of animal viruses
Table 18.1
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
The reproductive cycle of an enveloped RNA virus

Capsid RNA Envelope (with glycoproteins)
1 Glycoproteins on the viral envelope bind to specific receptor molecules (not shown) on the host cell, promoting viral entry into the cell. 2 Capsid and viral genome enter cell
HOST CELL
3 The viral genome (red) functions as a template for synthesis of complementary RNA strands (pink) by a viral enzyme.
Viral genome (RNA) Template

5 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).
mRNA
Capsid proteins
ER Glycoproteins Copy of genome (RNA)
4 New copies of viral genome RNA are made using complementary RNA strands as templates.
6 Vesicles transport envelope glycoproteins to the plasma membrane. 8 New virus 7 A capsid assembles
Figure 18.8
around each viral genome molecule.
RNA as Viral Genetic Material The broadest variety of RNA genomes

Is found among the viruses that infect animals
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
Glycoprotein Viral envelope Capsid
Reverse transcriptase
Figure 18.9
RNA (two identical strands)
The reproductive cycle of HIV, a retrovirus

HIV Membrane of white blood cell
1 The virus fuses with the cells plasma membrane. The capsid proteins are removed, releasing the viral proteins and RNA.
2 Reverse transcriptase catalyzes the synthesis of a DNA strand complementary to the viral RNA.
HOST CELL Reverse transcriptase
Viral RNA RNA-DNA hybrid 0.25 m HIV entering a cell DNA
3 Reverse transcriptase catalyzes the synthesis of a second DNA strand complementary to the first. 4 The double-stranded DNA is incorporated as a provirus into the cells DNA.
NUCLEUS Chromosomal DNA RNA genome for the next viral generation
Provirus
mRNA
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.
6 The viral proteins include

capsid proteins and reverse transcriptase (made in the cytosol) and envelope glycoproteins (made in the ER).
Figure 18.10
New HIV leaving a cell
9 New viruses bud off from the host cell.
8 Capsids are assembled around viral genomes and reverse transcriptase molecules.
7 Vesicles transport the glycoproteins from the ER to the cells plasma membrane.
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
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 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
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

Are those that appear suddenly or suddenly come to the attention of medical scientists
Severe acute respiratory syndrome (SARS)

Recently appeared in China
(b) The SARS-causing agent is a coronavirus (a) Young ballet students in Hong Kong like this one (colorized TEM), so named for the wear face masks to protect themselves corona of glycoprotein spikes protruding from from the virus causing SARS. the envelope. Figure 18.11 A, B
Outbreaks of new viral diseases in humans

Are usually caused by existing viruses that expand their host territory
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
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

Are circular RNA molecules that infect plants and disrupt their growth
Prions
Are slow-acting, virtually indestructible infectious proteins that cause brain diseases in mammals Propagate by converting normal proteins into the prion version
Prion Original prion
Many prions Normal protein
New prion
Figure 18.13
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 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
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
Mutation and Genetic Recombination as Sources of Genetic Variation Since bacteria can reproduce rapidly
New mutations can quickly increase a populations genetic diversity
Further genetic diversity

Can arise by recombination of the DNA from two different bacterial cells
Researchers had two mutant strains, one that could make arginine but not tryptophan 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. (arg+ Mixture EXPERIMENT
Mutant strain arg+ trp
Mutant strain arg trp+
Figure 18.15
RESULTS Only the samples from the mixed culture, contained cells that gave rise to colonies on minimal medium, which lacks amino acids.
Mixture
Mutant strain arg+ trp
Mutant strain arg trp+
No colonies (control)
Colonies grew
No colonies (control)
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
Mechanisms of Gene Transfer and Genetic Recombination in Bacteria Three processes bring bacterial DNA from different individuals together
Transformation Transduction Conjugation
Transformation Transformation
Is the alteration of a bacterial cells genotype and phenotype by the uptake of naked, foreign DNA from the surrounding environment
Transduction In the process known as transduction

Phages carry bacterial genes from one host cell to another
Phage DNA 1 Phage infects bacterial cell that has alleles A+ and B+ A+ B+
2 Host DNA (brown) is fragmented, and phage DNA
A+ B+ Donor cell
and proteins are made. This is the donor cell.
3 A bacterial DNA fragment (in this case a fragment with
the A+ allele) may be packaged in a phage capsid. A+

4 Phage with the A+ allele from the donor cell infects
Crossing over A+ A B
a recipient AB cell, and crossing over (recombination) between donor DNA (brown) and recipient DNA (green) occurs at two places (dotted lines).
Recipient cell
5 The genotype of the resulting recombinant cell (A+B)
Figure 18.16
differs from the genotypes of both the donor (A+B+) and the recipient (AB).
A+ B Recombinant cell
Conjugation and Plasmids

Conjugation
Is the direct transfer of genetic material between bacterial cells that are temporarily joined
Figure 18.17
Sex pilus
1 m
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
Conjugation and transfer of an F plasmid from an F+ donor to an F recipient
F Plasmid F+ cell Mating bridge F cell
Bacterial chromosome
F+ cell
Bacterial chromosome 2 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).
F+ cell 3 DNA replication occurs in 4 both donor and recipient cells, using the single parental strands of the F plasmid as templates to synthesize complementary strands.
1 A cell carrying an F plasmid (an F+ cell) can form a mating bridge with an F cell and transfer its F plasmid.
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
Chromosomal genes can be transferred during conjugation When the donor cells 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
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).
The resulting cell is called an Hfr cell (for High frequency of recombination).
Hfr cell
A+
B+
C+
D+
C+ B+
D+ A+ A+ B+ D+ C+ B+ A+ D+ C+ B+ A+
F cell
C A
C A
A+
C D A
B+ A+
C A
Since an Hfr cell has all the F-factor genes, it can form a mating bridge with an F cell and transfer DNA.
4 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
5 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.
The mating bridge usually breaks well before the entire chromosome and the rest of the F factor are transferred.
Temporary partial diploid 7
B+ A+
C A
D A+
B+
C A
Recombinant F bacterium
Two crossovers can result in the exchange of similar (homologous) genes between the transferred chromosome fragment (brown) and the recipient cells chromosome (green).
8 The piece of DNA ending up outside the bacterial chromosome will eventually be degraded by the cells enzymes. The recipient cell now contains a new combination of genes but no F factor; it is a recombinant F cell.
Figure 18.18b
(b) Conjugation and transfer of part of the bacterial chromosome from an Hfr donor to an F recipient, resulting in recombination
R plasmids and Antibiotic Resistance R plasmids

Confer resistance to various antibiotics
Transposition of Genetic Elements Transposable elements

Can move around within a cells genome
Are often called jumping genes

Contribute to genetic shuffling in bacteria
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
Insertion sequence 3 5 A T C C G G T TAG G C CA A C C G G A T TG G C CTA 3 5
Transposase gene Inverted Inverted repeat 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
Transposons Bacterial transposons

Also move about within the bacterial genome
Have additional genes, such as those for antibiotic resistance

Transposon Insertion sequence Antibiotic resistance gene 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
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
This metabolic control occurs on two levels

Adjusting the activity of metabolic enzymes already present Regulating the genes encoding the metabolic enzymes
(a) Regulation of enzyme activity Precursor (b) Regulation of enzyme production Feedback inhibition Enzyme 1 Gene 1 Enzyme 2 Gene 2
Regulation of gene expression
Enzyme 3 Gene 3
Enzyme 4 Gene 4
Enzyme 5 Gene 5
Tryptophan
Figure 18.20a, b
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
Is usually turned on
Can be switched off by a protein called a repressor
The trp operon: regulated synthesis of repressible enzymes

trp operon Promoter Promoter Genes of operon trpD trpC trpE trpB trpA
DNA Regulatory gene mRNA 5 Protein
trpR
Operator
3 RNA polymerase Start codon mRNA 5 E Inactive repressor D C B A Stop codon
Polypeptides that make up enzymes for tryptophan synthesis
(a) Tryptophan absent, repressor inactive, operon on. RNA polymerase attaches to the DNA at the promoter and transcribes the operons genes. Figure 18.21a
DNA No RNA made
mRNA
Protein
Active repressor
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
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
The lac operon: regulated synthesis of inducible enzymes Promoter

Regulatory gene
Operator
DNA
lacl
lacZ No RNA made
3 mRNA 5
RNA polymerase
Protein
Active repressor
(a) 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. Figure 18.22a
lac operon
DNA
lacl
RNA polymerase mRNA 5' 5 mRNA
lacz
lacY
lacA
3 mRNA
Protein Allolactose (inducer) Inactive repressor
-Galactosidase
Permease
Transacetylase
(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
Inducible enzymes
Usually function in catabolic pathways
Repressible enzymes
Usually function in anabolic pathways
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 Some operons are also subject to positive control
Via a stimulatory activator protein, such as catabolite activator protein (CAP)
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 Promoter (CAP)
DNA lacl CAP-binding site
lacZ
RNA Operator polymerase can bind Active and transcribe CAP
cAMP
Inactive CAP
Inactive lac repressor
(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 Figure 18.23a large amounts of mRNA for the lactose pathway.
When glucose levels in an E. coli cell increase

CAP detaches from the lac operon, turning it off
Promoter DNA
lacl
CAP-binding site RNA polymerase cant bind
lacZ
Operator
Inactive CAP
Inactive lac repressor
(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. Figure 18.23b

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Chapter 18

The Genetics of Viruses and Bacteria

Lectures by Chris Romero

Overview: Microbial Model Systems Viruses called bacteriophages

E. coli and its viruses

Beyond their value as model systems

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Recall that bacteria are prokaryotes

Bacterium Animal cell

Animal cell nucleus

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

The Discovery of Viruses: Scientific Inquiry Tobacco mosaic disease

In the late 1800s

In 1935, Wendell Stanley

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Structure of Viruses Viruses

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Viral Genomes Viral genomes may consist of

Double- or single-stranded RNA

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Capsids and Envelopes A capsid

Can have various structures

Glycoprotein 7090 nm (diameter) 18 250 mm

20 nm Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Figure 18.4a, b (a) Tobacco mosaic virus (b) Adenoviruses

Some viruses have envelopes

Glycoprotein 80200 nm (diameter)

50 nm (c) Influenza viruses

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Bacteriophages, also called phages

Each virus has a host range

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Viruses use enzymes, ribosomes, and small molecules of host cells

Self-assembly of new virus particles and their exit from cell

Reproductive Cycles of Phages Phages

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

The Lytic Cycle The lytic cycle

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

The lytic cycle of phage T4, a virulent phage

2 Entry of phage DNA

5 Release. The phage directs production

4 Assembly. Three separate sets of proteins

3 Synthesis of viral genomes

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

The Lysogenic Cycle The lysogenic cycle

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

The lytic and lysogenic cycles of phage , a temperate phage

Lysogenic cycle is entered

Phage DNA integrates into the bacterial chromosome, becoming a prophage.

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Reproductive Cycles of Animal Viruses The nature of the genome

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Classes of animal viruses

Viral Envelopes Many animal viruses

Viral glycoproteins on the envelope

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

The reproductive cycle of an enveloped RNA virus

Viral genome (RNA) Template

around each viral genome molecule.

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

RNA as Viral Genetic Material The broadest variety of RNA genomes

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Retroviruses, such as HIV, use the enzyme reverse transcriptase