Overview: Microbial Model Systems

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

• 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


• Bacteria are prokaryotes with cells much smaller and more simply organized than those of eukaryotes

• Viruses are smaller and simpler than bacteria

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Virus

Bacterium

Animalcell

Animal cell nucleus0.25 µm


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

• 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

• 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 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


• 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

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80 225 nm

DNAHead

TailsheathTailfiber

Bacteriophage T450 nm


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

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DNAVIRUS

Capsid

HOST CELL

Viral DNA

Replication

Entry into cell anduncoating of DNA

Transcription

Viral DNA

mRNA

Capsidproteins

Self-assembly ofnew virus particlesand their exit from cell


Reproductive Cycles of Animal Viruses

• Two key variables in classifying viruses that infect animals:

– DNA or RNA?

– Single-stranded or double-stranded?


Class/Family Envelope Examples/Disease

I. Double-stranded DNA (dsDNA)

Adenovirus No Respiratory diseases, animal tumors

Papovavirus No Papillomavirus (warts, cervical cancer): polyomavirus (animal tumors)

Herpesvirus Yes Herpes simplex I and II (cold sores, genital sores); varicella zoster (shingles, chicken pox); Epstein-Barr virus (mononucleosis, Burkitt’s lymphoma)

Poxvirus Yes Smallpox virus, cowpox virus



II. Single-stranded DNA (ssDNA)

Parvovirus No B19 parvovirus (mild rash)

III. Double-stranded RNA (dsRNA)

Reovirus No Rotavirus (diarrhea), Colorado tick fever virus



IV. Single-stranded RNA (ssRNA); serves as mRNA

Picornavirus No Rhinovirus (common cold); poliovirus, hepatitis A virus, and other enteric (intestinal) viruses

Coronavirus Yes Severe acute respiratory syndrome (SARS)

Flavivirus Yes Yellow fever virus, West Nile virus, hepatitis C virus

Togavirus Yes Rubella virus, equine encephalitis viruses



V. ssRNA; template for mRNA synthesis

Filovirus Yes Ebola virus (hemorrhagic fever)

Orthomyxovirus Yes Influenza virus

Paramyxovirus Yes Measles virus; mumps virus

Rhabdovirus Yes Rabies virus

VI. ssRNA; template for DNA synthesis

Retrovirus Yes HIV (AIDS); RNA tumor viruses (leukemia)


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

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RNA

ER

Capsid

HOST CELL

Viral genome (RNA)

mRNA

Capsidproteins

Envelope (withglycoproteins)

Glyco-proteins Copy of

genome (RNA)

Capsid and viral genomeenter cell

New virus

Template


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

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Capsid

Viral envelopeGlycoprotein

Reversetranscriptase

RNA(two identicalstrands)


• 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

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HOST CELL

ReversetranscriptionViral RNA

RNA-DNAhybrid

DNA

NUCLEUS

ChromosomalDNA

Provirus

RNA genomefor thenext viralgeneration

mRNA

New HIV leaving a cell

HIV entering a cell

0.25 µm

HIVMembrane ofwhite blood cell


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

• 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

• 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

• Vaccines can prevent certain viral illnesses


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

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Young ballet students in HongKong wear face masks toprotect themselves from thevirus causing SARS.

The SARS-causing agent is acoronavirus like this one(colorized TEM), so named forthe “corona” of glyco-proteinspikes protruding form theenvelope.


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


• 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 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 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

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Origin ofreplication

Replication fork

Termination of replication


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

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Mutantstrainarg+ trp–

Mutantstrainarg+ trp–

Mixture

Mixture

Nocolonies(control)

Nocolonies(control)

Coloniesgrew

Mutantstrainarg– trp+

Mutantstrainarg– trp+


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

• For example, harmless Streptococcus pneumoniae bacteria can be transformed to pneumonia-causing cells


Transduction

• In the process known as transduction, phages carry bacterial genes from one host cell to another

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A+

Phage DNA

A+

Donorcell

B+

A+

B+

Crossingover

A+

A– B–

Recipientcell

A+ B–

Recombinant cell


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 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

• 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

• 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

• 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


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

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Regulation of enzymeactivity

Regulation of enzymeproduction

Enzyme 1

Regulation of gene expression

Enzyme 2

Enzyme 3

Enzyme 4

Enzyme 5

Gene 2

Gene 1

Gene 3

Gene 4

Gene 5

Tryptophan

Precursor

Feedbackinhibition


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

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Promoter Promoter

DNA trpR

Regulatorygene

RNApolymerase

mRNA

3

5

Protein Inactiverepressor

Tryptophan absent, repressor inactive, operon on

mRNA 5

trpE trpD trpC trpB trpA

OperatorStart codonStop codon

trp operon

Genes of operon

E

Polypeptides that make upenzymes for tryptophan synthesis

D C B A

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DNA

Protein

Tryptophan(corepressor)

Tryptophan present, repressor active, operon off

mRNA

Activerepressor

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DNA

Protein

Tryptophan(corepressor)

Tryptophan present, repressor active, operon off

mRNA

Activerepressor

No RNA made


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

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DNA lacl

Regulatorygene

mRNA

5

3

RNApolymerase

ProteinActiverepressor

NoRNAmade

lacZ

Promoter

Operator

Lactose absent, repressor active, operon off

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DNA lacl

mRNA5

3

lac operon

Lactose present, repressor inactive, operon on

lacZ lacY lacA

RNApolymerase

mRNA 5

Protein

Allolactose(inducer)

Inactiverepressor

-Galactosidase Permease Transacetylase


• 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

• 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

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DNA

cAMP

lacl

CAP-binding site

Promoter

ActiveCAP

InactiveCAP

RNApolymerasecan bindand transcribe

Operator

lacZ

Inactive lacrepressor

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

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DNA lacl

CAP-binding site

Promoter

RNApolymerasecan’t bind

Operator

lacZ

Inactive lacrepressor

InactiveCAP

Lactose present, glucose present (cAMP level low): little lacmRNA synthesized

Overview: Microbial Model Systems

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