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

Beyond their value as model systems 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 18.2 0.25 m Virus Animal cell Bacterium Animal cell nucleus

Scientists were able to detect viruses indirectly 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 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)

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

(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

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

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 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

Reproductive Cycles of 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 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

The Lysogenic Cycle The lysogenic cycle Temperate phages 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 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

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 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

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

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 Reverse transcriptase Viral envelope Capsid Glycoprotein RNA (two identical strands)

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

Viruses do not really fit our definition of living organisms 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

Diseases caused by viral infections 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 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 Normal protein Original prion New prion Many prions

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

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 population’s genetic diversity

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+

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

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

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

Conjugation and Plasmids 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 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

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 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

R plasmids and Antibiotic Resistance 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

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 …

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

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

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 –

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 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

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

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

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

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

Inducible enzymes Repressible 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 (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

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