Genetics of Viruses and Bacteria

Virus Size Bacteria are

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

Viruses are smaller and simpler than bacteria

Virus Bacterium

Animalcell

Animal cell nucleus0.25 µm

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)

Viruses: “Non-living” Entities Small packages of nucleic acids in a

protein coat Are NOT cells—no cytoplasm and do

not perform metabolic reactions Obligate intracellular parasites—

dependent upon other cells for replication

Types of Viruses DNA viruses

Genome is DNA RNA viruses

Genome is RNA Smaller than DNA viruses Lack of proofreading—leads to

evolution rate

Viruses have a Specific Host Range Recognition by complementary fit

between external viral protein and specific cell surface receptor sites

http://pathmicro.med.sc.edu/mhunt/rep1.jpg

Bacteriophages

Viruses that infect bacteria

Set in motion a genetic takeover of bacteria, such as Escherichia coli

Viruses Replicate Inside Living Cells

Obligate intracellular parasites Viruses lack enzymes needed for

metabolism and have no structures to make proteins

Use cells own machinery to replicate viruses

Pathogen: agent that causes disease Viruses damage cells during replication

Reproductive Cycles of Phages Phages are the

best understood of all viruses

Phages have two reproductive mechanisms: the lytic cycle and the lysogenic cycle

Lytic Cycle Lysogenic Cycle

Results in the death of the host cellVirulent phageBacterial defenses—restriction enzymes cut up certain phage DNA

Replicates without destroying the hostTemperate virusThe viral DNA incorporated into the host DNA (prophage)

Lytic Cycle

Virulent Viruses-reproduce only by lytic cycle

Temperate Viruses-reproduces by lytic cycle or lysogenic cycle

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

Class/Family Envelope

Examples/Disease

II. Single-stranded DNA (ssDNA)

Parvovirus No B19 parvovirus (mild rash)

III. Double-stranded RNA (dsRNA)

Reovirus No Rotavirus (diarrhea), Colorado tick fever virus

Class/Family Envelope Examples/Disease

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

Class/Family Envelope Examples/Disease

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)

Animal Viruses1. Glycoproteins on viral envelope

recognize/bind specific receptors on host cell

2. Viral envelope fises with cell’s plasma membrane, and the capsid and viral genome enter the cell

3. Cellular enzymes remove capsid4. Viral genome serves as template

for replication of RNA strandsa. Templates for new RNAb. Serve as mRNA for protein

synthesis5. Vesicles transport glycoproteins

to cell’s plasma membrane6. Capsid forms around viral

genome7. Virus buds from the cell

After entering the cell, viral DNA uses host nucleotides and enzymes to replicate itself

It uses host materials and machinery to produce capsid proteins

Viral DNA and capsid proteins assemble into new virus particles, which leave the cell

Plant Viruses Plant viruses are

serious agricultural pests Most plant viruses

• Have RNA genomes• Enter their hosts via

wounds in the plant’s outer layers

• Injuries, insects feeding, contaminated farming tools

• Once infected, virus spreads through plasmodesmata

Protein RNA

Figure 10.19

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

•Genetic flow : RNA DNA

•2 identical strands of RNA•Infects white blood cells

HIV virus

Vaccinations Antibiotics don’t work—no metabolic

reactions to interfere with Vaccines—harmless derivatives of

pathogenic microbes that stimulate the immune system to mount defenses against the actual pathogen Parts of viruses, modified or killed viruses

are injected into the body Allows immune system to make antibodies

against specific markers on the viral coat• HIV mutates too fast for immune system to keep

up with

Influenza Vaccine Influenza, also known as the

flu, is a contagious disease that is caused by the influenza virus.  It attacks the respiratory tract in humans (nose, throat, and lungs).  The flu is different from a cold.  Influenza usually comes on suddenly and may include these symptoms: Fever Headache Tiredness (can be

extreme) Dry cough Sore throat Nasal congestion Body aches

                                                                                                                       

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

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.

Emerging Viruses RNA viruses have unusually high

mutation rate Spread of virus from one host

species to another Dissemination of a virus from a

small, isolated populations to widespread epidemics

Global View of HIV epidemicas of 2008

http://www.who.int/hiv/facts/en/hiv_global2003sm.jpg

Viruses and Cancer Tumor viruses can transform cells

into cancerous cellsViral Group Examples/

DiseasesCancer Types

Retrovirus HTLV-1/adult leukemia

Leukemia

Herpesvirus Epstein-Barr/ infectious mononucleosis

Burkitt’s lymphoma

Hepatitis B virus Chronic Hepatitis Liver cancer

Viruses and Cancer Virus inserts viral nucleic acids into host

cell DNA Insertion is permanent-provirus never excises Insertion for DNA tumor viruses

straightforward Oncogenes-genes found in viruses or as

part of normal eukaryotic genome; trigger transformation of a cell to a cancerous state Usually more than one must be activated to

transform a cell

Viroids Smaller and simpler than viruses Small, naked, circular RNA molecules that

do not code for proteins Disrupt normal plant metabolism,

development, and growth by causing errors in gene regulation

Affect many commercial plants—tomatoes, potatoes, chrysanthemums

Thought to have originated from escaped introns—sequences similar to self-splicing introns

Chrysanthemum with chrysanthemum chlorotic mottle viroid

Green tomato infected with tomato spotted wilt virus

Prions Pathogens that are proteins Cause several degenerative brain

diseases (Scrapie in sheep, “Mad Cow” disease, Creutzfeldt-Jakob disease)

Prions: Hypothesis for Propagation

               

               INFECTIOUS PRION PROTEINS have a different shape, which they impose on normal prion proteins in a chain reaction that ends in sickness and death.

A hypothesis of how infectious protein particles, or prions, cause disease: PrPSc - an abnormal protein - communicates with its normal twin - PrPc - creating an abnormal form, that will eventually harm neurons. (Adapted by Leigh Coriale Design and Illustration, with permission, Science [July 12], 1996, American Association for the Advancement of Science.)

Normal BrainKuru Infected Brain

It exists only among a single tribe in Papua New Guinea. The afflicted tribe - the Fore Highlanders - describe it as the "laughing death", because it leads to loss of coordination accompanied by dementia.

Kuru Brain

Genetics of Bacteria

The Bacterial Chromosome One double-stranded, circular

molecule of DNA Located in nucleoid region, so

transcription and translation can occur simultaneously

Many also contain extrachromosomal DNA in plasmids

Binary Fission

Genetic Recombination Produces New Bacterial Strain

Transformation Transduction Conjugation

Gene transfer occurs separately from bacterial reproduction

Transformation Alteration of bacterial cell’s

genotype by uptake of naked, foreign DNA from the environment

Transformation Biotech companies use this

technique to artificially introduce foreign genes into bacterial genomes (human insulin, human growth hormone)

Transduction

Gene transfer from one bacterium to another by a bacteriophage

Plasmids Short, circular DNA molecules

outside the chromosome Carry genes that are beneficial but

not essential Replicate independently of

chromosome Episomes—plasmids that can be

incorporated into chromosome

Conjugation Direct transfer of genetic material

between bacterial cells that are temporarily joined (bacterial sex)

Sex pili

“male” “female”

“Maleness” results from presence of F factor—segment of DNA in chromosome or in F plasmid

F+

F-

Conjugation

R Plasmids Contain genes that confer antibiotic

resistance

Medical consequences:resistant strains of pathogens due to overuse of antibiotics

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

Insertion sequence

Transposase gene

53

Invertedrepeat

35

Invertedrepeat

Transposons Transposable elements

called transposons are longer and more complex than insertion sequences Discovered by Barbara

McClintock In addition to DNA required

for transposition, transposons have extra genes that “go along for the ride,” such as genes for antibiotic resistance

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53

35

Transposon

Insertion sequence

Insertion sequence

Antibioticresistance gene

Transposase geneInverted repeat

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

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 Regulatory gene —makes repressor protein that blocks

RNA polymerase Promoter region —DNA sequence that RNA polymerase

binds to start transcription Operator region —an “on-off” switch; can block RNA

polymerase if region is blocked by repressor protein Structural genes —DNA sequences that code for several

related metabolic enzymes that direct production of some end product

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

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

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

LE 18-21a

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

Repressible Operon

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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 Operon

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

Inactive lacrepressor

DNA

cAMP

lacl

CAP-binding site

Promoter

ActiveCAP

InactiveCAP

RNApolymerasecan bindand transcribe

Operator

lacZ

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

LE 18-23b

DNA lacl

CAP-binding site

Promoter

RNApolymerasecan’t bind

Operator

lacZ

Inactive lacrepressor

InactiveCAP

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

                                                                           

Both plates of E.coli are transformed by pGLO plasmid as seen by growth on LB with ampicillin. The upper plate also contains arabinose, the inducer for the green fluorescent protein. This is visualized under UV light. The lower plate does not glow even though it has transformed cells because the media lacks arabinose.