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Overview: Microbial Model Systems. Viruses called bacteriophages can infect and set in motion a genetic takeover of bacteria, such as Escherichia coli

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overview microbial model systems
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 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
slide3
Bacteria are prokaryotes with cells much smaller and more simply organized than those of eukaryotes
  • Viruses are smaller and simpler than bacteria
le 18 2

LE 18-2

Virus

Bacterium

Animal

cell

Animal cell nucleus

0.25 µm

concept 18 1 a virus has a genome but can reproduce only within a host cell
Concept 18.1: A virus has a genome but can reproduce only within a host cell
  • Scientists detected viruses indirectly long before they could see them
  • The story of how viruses were discovered begins in the late 1800s
the discovery of viruses scientific inquiry
The Discovery of Viruses: Scientific Inquiry
  • Tobacco mosaic disease stunts growth of tobacco plants and gives their leaves a mosaic coloration
  • In the late 1800s, researchers hypothesized that a particle smaller than bacteria caused the disease
  • In 1935, Wendell Stanley confirmed this hypothesis by crystallizing the infectious particle, now known as tobacco mosaic virus (TMV)
structure of viruses
Structure of Viruses
  • Viruses are not cells
  • 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
  • Viral genomes may consist of
    • Double- or single-stranded DNA
    • Double- or single-stranded RNA
  • Depending on its type of nucleic acid, a virus is called a DNA virus or an RNA virus
  • A capsid is the protein shell that encloses the viral genome
  • A capsid can have various structures
slide10
Bacteriophages, also called phages, are viruses that infect bacteria
  • They have the most complex capsids found among viruses
  • Phages have an elongated capsid head that encloses their DNA
  • A protein tailpiece attaches the phage to the host and injects the phage DNA inside
le 18 4d

LE 18-4d

Head

DNA

Tail

sheath

Tail

fiber

80  225 nm

50 nm

Bacteriophage T4

general features of viral reproductive cycles
General Features of Viral Reproductive Cycles
  • Viruses are obligate intracellular parasites, which means 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 host molecules to synthesize progeny viruses

Animation: Simplified Viral Reproductive Cycle

le 18 5

LE 18-5

VIRUS

Entry into cell and

uncoating of DNA

DNA

Capsid

Transcription

Replication

HOST CELL

Viral DNA

mRNA

Viral DNA

Capsid

proteins

Self-assembly of

new virus particles

and their exit from cell

reproductive cycles of animal viruses
Reproductive Cycles of Animal Viruses
  • Two key variables in classifying viruses that infect animals:
    • DNA or RNA?
    • Single-stranded or double-stranded?
viral envelopes
Viral Envelopes
  • Many viruses that infect animals have a membranous envelope
  • Viral glycoproteins on the envelope bind to specific receptor molecules on the surface of a host cell
le 18 8

LE 18-8

Capsid

Capsid and viral genome

enter cell

RNA

HOST CELL

Envelope (with

glycoproteins)

Viral genome (RNA)

Template

mRNA

Capsid

proteins

ER

Glyco-

proteins

Copy of

genome (RNA)

New virus

rna as viral genetic material
RNA as Viral Genetic Material
  • The broadest variety of RNA genomes is found in viruses that infect animals
  • Retroviruses use reverse transcriptase to copy their RNA genome into DNA
  • HIV is the retrovirus that causes AIDS
le 18 9

LE 18-9

Viral envelope

Glycoprotein

Capsid

RNA

(two identical

strands)

Reverse

transcriptase

slide23
The viral DNA that is integrated into the host genome is called a provirus
  • Unlike a prophage, a provirus remains a permanent resident of the host cell
  • The host’s RNA polymerase transcribes the proviral DNA into RNA molecules
  • The RNA molecules function both as mRNA for synthesis of viral proteins and as genomes for new virus particles released from the cell
le 18 10

LE 18-10

Membrane of

white blood cell

HIV

HOST CELL

Reverse

transcription

Viral RNA

RNA-DNA

hybrid

0.25 µm

HIV entering a cell

DNA

NUCLEUS

Provirus

Chromosomal

DNA

RNA genome

for the

next viral

generation

mRNA

New HIV leaving a cell

evolution of viruses
Evolution of Viruses
  • Viruses do not fit our definition of living organisms
  • Since viruses can reproduce only within cells, they probably evolved as bits of cellular nucleic acid
concept 18 2 viruses viroids and prions are formidable pathogens in animals and plants
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
  • Smaller, less complex entities called viroids and prions also cause disease in plants and animals
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
  • Vaccines can prevent certain viral illnesses
emerging viruses
Emerging Viruses
  • Emerging viruses are those that appear suddenly or suddenly come to the attention of scientists
  • Severe acute respiratory syndrome (SARS) recently appeared in China
  • Outbreaks of “new” viral diseases in humans are usually caused by existing viruses that expand their host territory
le 18 11

LE 18-11

The SARS-causing agent is a

coronavirus like this one

(colorized TEM), so named for

the “corona” of glyco-protein

spikes protruding form the

envelope.

Young ballet students in Hong

Kong wear face masks to

protect themselves from the

virus causing SARS.

viral diseases in plants
Viral Diseases in Plants
  • More than 2,000 types of viral diseases of plants are known
  • Some symptoms are spots on leaves and fruits, stunted growth, and damaged flowers or roots
slide32
Plant viruses spread disease in two major modes:
    • Horizontal transmission, entering through damaged cell walls
    • Vertical transmission, inheriting the virus from a parent
bacteria
Bacteria
  • Bacteria allow researchers to investigate molecular genetics in the simplest true organisms
  • The well-studied intestinal bacterium Escherichia coli(E. coli) is “the laboratory rat of molecular biology”
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
  • Many bacteria also have plasmids, smaller circular DNA molecules that can replicate independently of the chromosome
  • Bacterial cells divide by binary fission, which is preceded by replication of the chromosome
le 18 14

LE 18-14

Replication fork

Origin of

replication

Termination

of replication

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 quickly increase genetic diversity
  • More genetic diversity arises by recombination of DNA from two different bacterial cells
le 18 15

LE 18-15

Mixture

Mutant

strain

arg+trp–

Mutant

strain

arg–trp+

Mixture

Mutant

strain

arg+trp–

Mutant

strain

arg–trp+

No

colonies

(control)

No

colonies

(control)

Colonies

grew

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
  • For example, harmless Streptococcus pneumoniae bacteria can be transformed to pneumonia-causing cells
transduction
Transduction
  • In the process known as transduction, phages carry bacterial genes from one host cell to another
le 18 16

LE 18-16

Phage DNA

A+

B+

A+

B+

Donor

cell

A+

Crossing

over

A+

A–

B–

Recipient

cell

A+

B–

Recombinant cell

conjugation and plasmids
Conjugation and Plasmids
  • Conjugation is the direct transfer of genetic material between bacterial cells that are temporarily joined
  • The transfer is one-way: One cell (“male”) donates DNA, and its “mate” (“female”) receives the genes
r plasmids and antibiotic resistance
R plasmids and Antibiotic Resistance
  • R plasmids confer resistance to various antibiotics
  • When a bacterial population is exposed to an antibiotic, individuals with the R plasmid will survive and increase in the overall population
transposition of genetic elements
Transposition of Genetic Elements
  • The DNA of a cell can also undergo recombination due to movement of transposable elements within the cell’s genome
  • Transposable elements, often called “jumping genes,” contribute to genetic shuffling in bacteria
insertion sequences
Insertion Sequences
  • The simplest transposable elements, called insertion sequences, exist only in bacteria
  • An insertion sequence has a single gene for transposase, an enzyme catalyzing movement of the insertion sequence from one site to another within the genome
transposons
Transposons
  • Transposable elements called transposons are longer and more complex than insertion sequences
  • In addition to DNA required for transposition, transposons have extra genes that “go along for the ride,” such as genes for antibiotic resistance
slide47
Concept 18.4: Individual bacteria respond to environmental change by regulating their gene expression
  • A bacterium can tune its metabolism to the changing environment and food sources
  • This metabolic control occurs on two levels:
    • Adjusting activity of metabolic enzymes
    • Regulating genes that encode metabolic enzymes
le 18 20

LE 18-20

Regulation of enzyme

production

Regulation of enzyme

activity

Precursor

Feedback

inhibition

Enzyme 1

Gene 1

Gene 2

Enzyme 2

Regulation

of gene

expression

Gene 3

Enzyme 3

Enzyme 4

Gene 4

Gene 5

Enzyme 5

Tryptophan

operons the basic concept
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 can be switched off by a protein called a repressor
  • A corepressor is a small molecule that cooperates with a repressor to switch an operon off
le 18 21a

LE 18-21a

trp operon

Promoter

Promoter

Genes of operon

DNA

trpB

trpA

trpE

trpC

trpD

trpR

Operator

Stop codon

RNA

polymerase

Regulatory

gene

Start codon

mRNA 5¢

mRNA

D

B

E

C

A

Inactive

repressor

Protein

Polypeptides that make up

enzymes for tryptophan synthesis

Tryptophan absent, repressor inactive, operon on

le 18 21b 1

LE 18-21b_1

DNA

mRNA

Active

repressor

Protein

Tryptophan

(corepressor)

Tryptophan present, repressor active, operon off

le 18 21b 2

LE 18-21b_2

DNA

No RNA made

mRNA

Active

repressor

Protein

Tryptophan

(corepressor)

Tryptophan present, repressor active, operon off

repressible and inducible operons two types of negative gene regulation
Repressible and Inducible Operons: Two Types of Negative Gene Regulation
  • A repressible operon is one that is usually on; binding of a repressor to the operator shuts off transcription
  • The trp operon is a repressible operon
  • An inducible operon is one that is usually off; a molecule called an inducer inactivates the repressor and turns on transcription
  • The classic example of an inducible operon is the lac operon, which contains genes coding for enzymes in hydrolysis and metabolism of lactose
le 18 22a

LE 18-22a

Promoter

Regulatory

gene

Operator

lacl

lacZ

DNA

No

RNA

made

mRNA

RNA

polymerase

Active

repressor

Protein

Lactose absent, repressor active, operon off

le 18 22b

LE 18-22b

lac operon

DNA

lacl

lacY

lacA

lacZ

RNA

polymerase

mRNA

mRNA 5¢

Transacetylase

Permease

-Galactosidase

Protein

Inactive

repressor

Allolactose

(inducer)

Lactose present, repressor inactive, operon on

slide56
Inducible enzymes usually function in catabolic pathways
  • Repressible enzymes usually function in anabolic pathways
  • Regulation of the trp and lac operons involves negative control of genes because operons are switched off by the active form of the repressor
positive gene regulation
Positive Gene Regulation
  • Some operons are also subject to positive control through a stimulatory activator protein, such as catabolite activator protein (CAP)
  • When glucose (a preferred food source of E. coli ) is scarce, the lac operon is activated by the binding of CAP
  • When glucose levels increase, CAP detaches from the lac operon, turning it off
le 18 23a

LE 18-23a

Promoter

DNA

lacl

lacZ

RNA

polymerase

can bind

and transcribe

Operator

CAP-binding site

Active

CAP

cAMP

Inactive lac

repressor

Inactive

CAP

Lactose present, glucose scarce (cAMP level high): abundant lac

mRNA synthesized

le 18 23b

LE 18-23b

Promoter

DNA

lacl

lacZ

CAP-binding site

Operator

RNA

polymerase

can’t bind

Inactive

CAP

Inactive lac

repressor

Lactose present, glucose present (cAMP level low): little lac

mRNA synthesized