Genetics of viruses and bacteria 1

Ch. 18. viral and bacterial genetics 

Virus
 Not



living, nucleic acids and proteins

Viriods and prions
 Viriods:

Single stranded circular Rna
 Prions: only protein


Bacteria
 Living,

prokaryotes
1

Seven characteristics common to life
Cells and organization
 Energy use
 Respond to environmental change
 Regulation and homeostasis
 Growth and development
 Reproduction
 Change over the course of generations


2

Viruses
Over 4,000 different types of viruses
 Virus have their own genomes, but are considered nonliving


 Must

be taken up by a living cell to replicate

3

4

Viral genetics




Tobacco Mosaic Virus
(TMV) first virus discovered in 1883
Yellow fever: first human virus discovered 1900

5

Differences


Host range
 Number



of species and cell types that can be infected

Structural
 All

viruses have a capsid (protein coat) but it varies in shape and complexity
 Some have viral envelope derived from host cell plasma membrane


Genome
 DNA vs.

RNA, Single stranded (ss) vs. Double stranded (ds), linear vs. circular

6

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Helical
capsid

45 nm
(a) Tobacco mosaic virus, a nonenveloped virus with a helical capsid

Protein subunit (capsomer)

Nucleic acid (RNA)

Polyhedral capsid

Capsomer
Nucleic acid (DNA)
25 nm
(b) Adenovirus, a nonenveloped virus with a polyhedral capsid and protein fibers with a knob

Protein fiber with a knob

Polyhedral capsid Viral envelope
Nucleic acid (RNA)
Spike glycoproteins
100 nm
(c) Influenza virus, an enveloped virus with spikes
90 nm

Head
(polyhedral capsid)
Nucleic acid (DNA) inside capsid head Shaft
Tail fiber
Base plate

(d) T4, a bacteriophage a: © Robley C. Williams/Biological Photo Service; b: © Courtesy of R. C. Valentine and H. G. Pereira. Reprinted from Journal of Molecular
Biology, Vol. 13, No. 2, R. C. Valentine and H. G. Pereira, “Antigens and Structure of the Adenovirus,” pages 71-83, 1965, with permission from
Elsevier; c: © Chris Bjornberg/Photo Researchers; d: © mikron/Photo Researchers

7

Reproduction


Viruses are not alive
 Not

cells or composed of cells
 Cannot carry out metabolism on their own


Viral reproductive cycle can be quite different among types of viruses and one virus may have alternative cycles

8

Basic steps
1.
2.
3.
4.
5.
6.

Attachment
Entry
Integration
Synthesis of viral components
Viral assembly
Release
9



http://www.youtube.com/watch?v=Rpj0e mEGShQ 10

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Reverse transcriptase Viral RNA

Spike glycoprotein Cytosol

Reverse transcriptase Receptors
Viral
RNA

RNADNA

DNA

Integrase
Provirus

11

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Capsid proteins

Spike glycoproteins Reverse transcriptase Viral RNA

12

Attachment and Entry


Attachment
 Usually

specific for one kind of cell due to binding to specific molecules on cell surface



Entry
 Bacteriophages

or phage, injects only DNA into

bacteria
 HIV fuses with host membrane and the entire virus enters  One or several viral genes are expressed immediately
 Virus may proceed to synthesis of viral components
OR integrate into host chromosome
13

Integration
Viral gene for integrase
 Integrase cuts host chromosomal DNA and inserts viral genome  Phage in bacterial DNA called prophage


 May



excise later and proceed to synthesis

HIV is an RNA virus
 Uses

viral reverse transcriptase to make complementary DNA strand that will be template for double stranded viral DNA
 Integrates as a provirus

14

Synthesis of viral components
Host cell enzymes such as DNA polymerase make many copies of the phage DNA and transcribe the genes within these copies into mRNA  In the case of HIV, the DNA provirus is not excised from the host chromosome. Instead, it is transcribed in the nucleus to produce many copies of viral RNA


 Translated

to make viral proteins
 Serve as genome for new viral particles
15

Viral assembly
Some viruses self-assemble
 Other are too complicated to selfassemble
 Proteins modify capsid proteins or serve as scaffolding


16

Release
Phages must lyse their host cell to escape
 Enveloped viruses bud from the host cell


17

Latency in bacteriophages
Some viruses can integrate their genomes into a host chromosome
 Prophage or provirus is inactive or latent
 Most viral genes silenced


18



Lysogeny – latency in bacteriophages
 When

host cell replicates, also copies prophage
 Lysogenic cycle
 Lytic cycle –


Temperate phages have a lysogenic cycle
 Environmental

conditions influence integration and length of latency



Virulent phages do not

19

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Bacterial chromosome

Phage DNA

LYTIC
CYCLE

20

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Bacterial chromosome

Phage DNA

LYTIC
CYCLE

LYSOGENIC
CYCLE

or

Prophage

21

Latency in human viruses
2 different ways
1. HIV integrates into host genome and may remain dormant for long periods of time
2. Other viruses can exist as episomes – genetic element that can replicate independently of chromosomal DNA but occasionally integrates into chromosomal DNA


 Herpes

simplex type I and II, varicella zoster

22

AIDS and HIV










Human immunodeficiency virus (HIV) is the causative agent of acquired immune deficiency syndrome (AIDS)
AIDS is primarily spread by sexual contact between infected and uninfected individuals
Can also be spread by the transfusion of HIV-infected blood, by the sharing of needles among drug users, and from infected mother to unborn child Total number of AIDS deaths between 1981 and the end of 2006 was over
25 million; more than 0.5 million of these deaths occurred in the U.S.
During 2008, around 3 million adults and children became infected with
HIV. Worldwide, nearly 1 in every 100 adults between 15 and 49 is infected In the U.S. about 55,000 new HIV infections occur each year
70% of these new infections are in men and 30% in women

23





Devastating effects of AIDS result from viral destruction of a type of white blood cell termed a helper T cell, which plays an essential role in the immune system of mammals
When large numbers of T cells are destroyed by
HIV, the function of the immune system is seriously compromised and the individual becomes highly susceptible to opportunistic infections  Would

not normally occur in a healthy person

24

25

HIV


Reverse transcriptase lacks a proofreading function  Makes

more errors and tends to create mutant strains of HIV
 Makes it difficult to create vaccine


In U.S., estimated annual number of AIDSrelated deaths fell 14% from 1998 to 2002 due in part to the use of new antiviral drugs
26

Origin of viruses


Many biologists argue that cells evolved before viruses
 Viruses

evolved from macromolecules inside living cells (maybe plasmids)

Others argue for regressive evolution
 Another theory is that viruses did not evolve from cells but evolved in parallel with cellular organisms 

27

Viriods
Composed solely of a single-stranded circular
RNA molecule a few hundred nucleotides in length  Infect plant cells
 Some replicate in host cell nucleus, others in chloroplast  RNA genome does not code for proteins
 Disease mechanism not well understood


28

29

Prions








Composed entirely of protein
Proteinaceous infectious agent
Disease causing conformation PrPSc
Normal conformation PrPC
Normal protein expressed at low levels on surface of nerve cells
Prion converts normal proteins to abnormal conformation
Several types of neurodegenerative diseases of human and livestock
 Group

of diseases called transmissible spongiform encephalopathies (TSE)

30

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

PrPSC
PrPC

Original
PrPSc
molecule
PrPSc
converted from PrPC

Fibril

40 nm
© Eye of Science/Photo Researchers

31

Affected animal(s) sheep, goat cattle Disease
Scrapie[39]
Bovine spongiform encephalopathy (BSE), mad cow disease[39]

mink[39]

Transmissible mink encephalopathy (TME)

white-tailed deer, elk, mule deer, moose[39]

Chronic wasting disease (CWD)

cat[39]

Feline spongiform encephalopathy (FSE)

nyala, oryx, greater kudu[39]

Exotic ungulate encephalopathy (EUE)
Spongiform encephalopathy
(Has not been shown to be transmissible.)
Creutzfeldt–Jakob disease (CJD)[39]

ostrich[40]

Iatrogenic Creutzfeldt–Jakob disease (iCJD)
Variant Creutzfeldt–Jakob disease (vCJD)
Familial Creutzfeldt–Jakob disease (fCJD) human Sporadic Creutzfeldt–Jakob disease (sCJD)
Gerstmann–Sträussler–Scheinker
syndrome (GSS)[39]
Fatal familial insomnia (FFI)[41]
Kuru[39]

32

Genetic properties of bacteria








Genes of bacteria are found in bacterial chromosomes
Usually a single type of chromosome
May have more than one copy of that chromosome
Number of copies depends on the bacterial species and on growth conditions
Typically 1-4 identical chromosomes
Nucleoid – region where tightly packed bacterial chromosome found

33

Molecules of double-stranded DNA
 Usually circular
 Tend to be shorter
 Contains a few thousand unique genes
 Mostly structural genes
 Single origin of replication


34

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Origin of replication Genes
Intergenic
regions

Key features
• Most, but not all, bacterial species contain circular chromosomal DNA.

• Several thousand different genes are interspersed throughout the chromosome.

• A typical chromosome is a few million base pairs in length. • One origin of replication is required to initiate DN A replication. • Most bacterial species contain a single type of chromosome, but it may be present in multiple copies.
35

Compaction
Typical bacterial chromosome must be compacted about 1,000-fold
 Bacterial DNA is not wound around histone proteins to form nucleosomes
 Proteins important in forming loop domains


 Compacts



DNA about 10-fold

DNA supercoiling
 Topoisomerases

supercoiling

twist the DNA and control degree of

36

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Loop domains
Proteins anchoring loops Circular chromosomal DNA

Looped chromosomal DNA with associated proteins

Supercoiled and looped DNA

37

Plasmids






Small, circular pieces of DNA that exist independently of the bacterial chromosome
Occur naturally in many strains of bacteria and in a few types of eukaryotic cells, such as yeast
Own origin of replication that allows it to be replicated independently of the bacterial chromosome
Not usually necessary for survival but can provide growth advantages
Episome – plasmid that can integrate into bacterial chromosome 38

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Bacterial chromosome Plasmids

80 µm

© Stanley Cohen/Photo Researchers

39

5 types of plasmids


Resistance plasmids (R factors)
 Contain

genes that confer resistance against antibiotics and other types of toxins



Degradative plasmids
 Carry

genes that enable the bacterium to digest and utilize an unusual substance 

Col-plasmids
 Contain

bacteria



Virulence plasmids
 carry



genes that encode colicines, which are proteins that kill other

genes that turn a bacterium into a pathogenic strain

Fertility plasmids (F factors)
 Allow

bacteria to mate with each other

40

Reproduction








Cells of some species, such as E. coli, can divide every
20–30 minutes
Single cell can form a bacterial colony in less than a day
Reproduce by binary fission – NOT mitosis
Except when a mutation occurs, each daughter cell contains an identical copy of the mother cell’s genetic material Does not involve genetic contributions from two different parents Plasmids may replicate independently of the bacterial chromosome 41

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Mother cell
Plasma membrane

Cell wall

Chromosome

Two daughter cells

42

Genetic diversity in bacteria


2 sources
1.
2.

Mutations can occur that alter the bacterial genome and affect the traits of bacterial cells
Genetic transfer – genetic material is transferred from one bacterial cell to another

43

Genetic transfer
1.

Conjugation
 Direct

physical interaction transfers genetic material from donor to recipient cell

2.

Transformation
 DNA released

from a dead bacterium into the environment is taken up by another bacteria

3.

Transduction
 A virus

transfers genetic information from one bacterium to another
44

Lederberg and Tatum’s Work with E. coli
Demonstrated Genetic Transfer Between Bacteria and Led to the Discovery of Conjugation




Studying strains of E. coli that had different nutritional requirements for growth
Differences in nutritional requirements correspond to allelic differences between the strains
When 2 strains were mixed, found new genotypes









Not mutation

Hypothesized that some genetic material was transferred between the two strains when they were mixed
Either genetic material was released from one strain and taken up by the other, or cells of the two different strains made contact with each other and directly transferred genetic material
U-tube allows pieces of DNA to transfer but not cells to touch
Without physical contact, genetic material could not be transferred

Conjugation
Only about 5% of E. coli strains found in nature can act as donor strains
 Donor strains contain a fertility factor (F factor) that can be transferred to recipient strains 

 Some

donor strains are Hfr (for High frequency of recombination)

46

F factors








Carry several genes that are required for conjugation and also may carry genes that confer a growth advantage for the bacterium
F+ has an F factor, F- does not
Sex pili are made by F+ cells that bind specifically to F- cells
Once contact is made, the pili shorten, drawing the donor and recipient cells closer together
One strand of F factor is transferred, other strand stays in donor Both replicate so that donor and recipient now have complete double stranded F factor

47

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

1.3 µm

Sex pilus (a) Micrograph of conjugating cells
Donor cell Recipient cell
Bacterial
chromosome
F factor
Sex pilus
Origin of transfer F+

F+

F–

F+

(b) Transfer of an F factor a: © Dr. L. Caro/SPL/Photo Researcher

48

Transformation






Does not require direct contact between bacterial cells
Living bacterial cell imports a strand of DNA that another bacterium released into the environment when it died
Only competent cells with competence factors can do this Facilitate the binding of DNA fragments to the bacterial cell surface, the uptake of DNA into the cytoplasm, and the incorporation of the imported DNA into the bacterial chromosome

49

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Receptor

tetR

50

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Receptor tetR tetR

51

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Receptor

tetR

tetR

DNA uptake system tetR 52

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Receptor

tetR

tetR

DNA uptake system

tetR

tetR

Transformed cell that is resistant to the antibiotic tetracycline

53

Transduction
Viruses that infect bacteria transfer bacterial genes from one bacterium to another  Usually an error in a phage lytic cycle
 Newly assembled phages incorporate piece of host DNA instead


54

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Phage DNA

Bacterial chromosome his+
Donor
cell
(his+)

55

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Phage DNA

Bacterial chromosome his+
Donor
cell
(his+)

his+

56

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Phage DNA

Bacterial chromosome his+

Donor cell (his+)

his+

Transducing phage with host DN A
Crossing over

his+ his+ Recipient cell
(his–)
Recombinant bacterium his1

The recombinant bacterium has a genotype (his+) that is different from the original recipient bacterial cell (his–).

57

Horizontal Gene Transfer Is the Transfer of
Genes Between Different Species
Vertical gene transfer that occurs when genes are passed from one generation to the next among individuals of the same species
 Roughly 17% of the genes of E. coli and of
Salmonella typhimurium have been acquired by horizontal transfer during the past 100 million years
 Medical relevance of horizontal gene transfer is profound – acquired antibiotic resistance
