Genetics of Viruses & Bacteria

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

PowerPoint Lectures for Biology, Seventh Edition

Neil Campbell and Jane Reece

Lectures by Chris Romero

Chapter 18

The Genetics of Virusesand Bacteria


• 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

Figure 18.20.25 m

Virus

Animalcell

Bacterium

Animal cell nucleus


• 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


Figure 18.4a, b

18 250 mm 70–90 nm (diameter)

20 nm 50 nm(a) Tobacco mosaic virus (b) Adenoviruses

RNADNACapsomere

Glycoprotein

Capsomereof capsid

Capsids and Envelopes

• A capsid

– Is the protein shell that encloses the viral genome

– Can have various structures


• 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

Membranousenvelope

Capsid


• 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


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 virusesVIRUS

Capsid proteins

mRNA

Viral DNA

HOST CELL

Viral DNA

DNACapsid

Figure 18.5

Entry into cell anduncoating of DNA

ReplicationTranscription

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


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 host’s cell wall, releasing the progeny viruses


• The lytic cycle of phage T4, a virulent phage

Phage assembly

Head Tails Tail fibersFigure 18.6

Attachment. The T4 phage usesits tail fibers to bind to specificreceptor sites on the outer surface of an E. coli cell.

1Entry 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.

2

Synthesis of viral genomes and proteins. The phage DNAdirects production of phageproteins and copies of the phagegenome by host enzymes, usingcomponents within the cell.

3Assembly. 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.

4

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.

5


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

Many cell divisions produce a large population of bacteria infected with the prophage.

The bacterium reproducesnormally, copying the prophageand 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 factorsdetermine whether

The phage attaches to ahost cell and injects its DNA.

Phage DNAcircularizes

The cell lyses, releasing phages.Lytic cycleis induced

Lysogenic cycleis entered

Lysogenic cycleLytic cycle

or Prophage

Bacterialchromosome

Phage

PhageDNA

Figure 18.7


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


RNA

Capsid

Envelope (withglycoproteins)

HOST CELL

Viral genome (RNA)

Template

Capsidproteins

Glyco-proteins

mRNA

Copy ofgenome (RNA)

ER

Figure 18.8

• The reproductive cycle of an enveloped RNA virus 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 genomeenter cell2

The viral genome (red)functions as a template forsynthesis of complementary RNA strands (pink) by a viral enzyme.

3

New copies of viralgenome RNA are madeusing complementary RNAstrands as templates.

4

Complementary RNAstrands also function as mRNA,

which is translated into bothcapsid proteins (in the cytosol)and glycoproteins for the viral

envelope (in the ER).

5

Vesicles transportenvelope glycoproteins to

the plasma membrane.

6

A capsid assemblesaround each viral

genome molecule.

7New virus8


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

Figure 18.9

Reversetranscriptase

Viral envelope

Capsid

Glycoprotein

RNA(two identicalstrands)


• The reproductive cycle of HIV, a retrovirus

Figure 18.10

mRNA

RNA genomefor the nextviral generation

Viral RNA

RNA-DNAhybrid

DNA

ChromosomalDNA

NUCLEUSProvirus

HOST CELL

Reverse transcriptase

New HIV leaving a cell

HIV entering a cell0.25 µm

HIV Membrane of white blood cell

The virus fuses with thecell’s plasma membrane.The capsid proteins areremoved, releasing the viral proteins and RNA.

1 Reverse transcriptasecatalyzes the synthesis of aDNA strand complementaryto the viral RNA.

2

Reverse transcriptasecatalyzes the synthesis ofa second DNA strandcomplementary to the first.

3

The double-stranded DNA is incorporatedas 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 theglycoproteins from the ER tothe cell’s plasma membrane.

7 Capsids areassembled aroundviral genomes and reverse transcriptase molecules.

8

New viruses budoff from the host cell.9


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

Figure 18.11 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.


• 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

Figure 18.13

Prion

Normalprotein

Originalprion

Newprion

Many prions


• 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

Replicationfork

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 population’s genetic diversity


• Further genetic diversity

– Can arise by recombination of the DNA from two different bacterial cells

Mutantstrain

arg trp+

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.

Mutantstrain

arg+ trp–

Mixture


Coloniesgrew

Mutantstrain

arg+ trp–

Mutantstrain

arg– trp+

No colonies(control)

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


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 cell’s 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

1

Figure 18.16

Donorcell

Recipientcell

A+ B+

A+

A+ B–

A– B–

A+

Recombinant cell

Crossingover

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 withthe 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

A+ B+


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

Figure 18.18a

A cell carrying an F plasmid(an F+ cell) can form amating bridge with an F– celland transfer its F plasmid.

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).

2 DNA replication occurs inboth donor and recipientcells, 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

F+ cell

F+ cell

Mating bridge

1

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

(a)

F– cell


• 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


• 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 factorThe circular F plasmid in an F+ cellcan be integrated into the circularchromosome by a single crossoverevent (dotted line).

1The 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 factorbreaks 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 bridgeusually breaks well before the entire chromosome andthe 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 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.

8

Temporarypartialdiploid

Recombinant F–

bacterium

A+B+ C+

D+

F– cell A–B–

C–

D–

A–B–

C–

D– D–

A–

C–B–

A+

B+C+D+A+B+

D+C+

A+

A+

B+

A–B–

C–

D–

A–B+

C–

D–

A+

B+ B–

A+

Hfr cell

D–

A–

C–

B–

A+

B+C+D+

A+

B+

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

(b)

Figure 18.18b


R plasmids and Antibiotic Resistance

• R plasmids

– Confer resistance to various antibiotics


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


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 geneInvertedrepeat

Invertedrepeat

3

5

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 …

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

• 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

Insertion sequence

Antibioticresistance gene

Transposon

5

3

5

3


• 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

Figure 18.20a, b

(a) Regulation of enzyme activity

Enzyme 1

Enzyme 2

Enzyme 3

Enzyme 4

Enzyme 5

Regulationof geneexpression

Feedbackinhibition

Tryptophan

Precursor

(b) Regulation of enzyme production

Gene 2

Gene 1

Gene 3

Gene 4

Gene 5

–

–


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

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

Inactiverepressor

Protein

Operator

Polypeptides that make upenzymes for tryptophan synthesis

Promoter

Regulatorygene

RNA polymerase

Start codon Stop codon

Promoter

trp operon

5

3mRNA 5

trpDtrpE trpC trpB trpAtrpRDNA

mRNA

E D C B A


DNA

mRNA

Protein

Tryptophan(corepressor)

Active repressor

No RNA made

Tryptophan present, repressor active, operon off. As tryptophanaccumulates, it inhibits its own production by activating the repressor protein.

(b)

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

Figure 18.22a

DNA

mRNA

ProteinActiverepressor

RNApolymerase

NoRNAmade

lacZlacl

Regulatorygene

Operator

Promoter

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.

(a)

5

3


mRNA 5'

DNA

mRNA

Protein

Allolactose(inducer)

Inactiverepressor

lacl lacz lacY lacA

RNApolymerase

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


• 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)


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 OperatorRNApolymerasecan bindand transcribe

InactiveCAP

ActiveCAPcAMP

DNA

Inactive lacrepressor

lacl lacZ

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)


• 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 lacrepressor

InactiveCAP

DNA

RNApolymerasecan’t bind

Operator

lacl lacZ

CAP-binding site

Promoter

Genetics of Viruses & Bacteria

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