Download Module 9 – The Viruses

NPTEL – Biotechnology – Microbiology
Module 9 – The Viruses
Lecture 1: Viruses- Introduction and General Characteristics
What are Viruses?
 Infectious acellular agents i.e. devoid of cell components like nucleus, organelles,
cytoplasm, or plasma membrane
 Replicate or multiply only inside living host cell
 Hence, also called obligate intracellular parasites
 Possesses only one type of nucleic acids- either DNA or RNA but never both
(exception is cytomegalovirus)
Fig. 1.Virions of mimivirus, one of the largestvirusesand a parvovirus (arrowed), one of the smallest viruses.
History of Virology
Table 1.1 Selected Milestones in the History of Virology
Date
Discovery
1892 Description of filterable infectious agent (TMV) (Ivanovsky)
1898 Concept of the virus as a contagious living form (TMV) (Beijerinck);
First description of an animal virus (FMDV) (Loeffler, Frosch)
1901 First identification of avian influenza; fowl plague virus (Lode, Gruber)
1901 First description of a human virus (yellow fever virus) (Reed et al.)
1903 Rabies virus identified (Remlinger, Riffat-Bay); Rabies inclusion bodies
described (Negri)
1908 Leukemia-causing virus identified (Ellerman, Bang)
Joint initiative of IITs and IISc – Funded by MHRD
Page 1 of 21
NPTEL – Biotechnology – Microbiology
1909 Poliovirus identified (Landsteiner, Popper)
1911 Discovery of solid tumor virus (RSV) (Rous)
1913 An early example of virus propagation in tissue culture (Steinhardt)
1915 First description of bacterial viruses (bacteriophages) (Twort, d'Herelle)
1931 Virus propagation in embryonated chicken eggs (Woodruff, Goodpasture)
1931 Use of mice as a host for viruses (Furth)
1931 Identification of swine influenza virus (Shope)
1933 Identification of human influenza virus (Smith et al.)
1933 Identification of rabbit papillomavirus (Shope)
1935 Tobacco mosaic virus crystallized (Stanley)
1936 Induction of carcinomas in other species by rabbit papillomavirus (Rous; Beard)
1938 Yellow fever vaccine (Thieler)
1939 One-step growth cycle for phages (Ellis, Delbrück)
1941 Recognition of influenza virus hemagglutination (HA); Discovery of first virusassociated (receptor destroying enzyme, neuraminidase) enzyme (Hirst)
1947 Mutation and DNA repair in bacteriophages (multiplicity reactivation) (Luria)
1948 Poliovirus replication in non-neuronal cell culture (Enders, Weller, Robbins)
1952 Poliovirus plaque assay (Dulbecco)
1952 Bacteriophage genome is nucleic acid (Hershey, Chase)
1954 Polio vaccine developed (Salk)
1957 In vitro assembly of virus (TMV) (Fraenkel-Conrat, Williams)
1958 Bacteriophage lambda regulation paradigm (Pardee, Jacob, Monod)
1961 Discovery of messenger RNA (mRNA) using bacteriophages (Brenner, Jacob,
Meselson)
1961 Elucidation of the triplet code by genetic analysis of bacteriophages (Crick et
al.)
1961 Genetic definition of nonsense codons as stop signals for translation in
bacteriophages (Campbell, Epstein, Bernstein)
1963 Discovery of hepatitis B virus (Blumberg)
1964 Colinearity of a bacteriophage gene with the polypeptide chain (Sarabhai,
Stretton, Brenner); Discovery of first human tumor virus, EBV (Epstein-Barr)
Joint initiative of IITs and IISc – Funded by MHRD
Page 2 of 21
NPTEL – Biotechnology – Microbiology
1966 Pathways of macromolecular assembly of bacteriophages (Edgar, Wood)
1967 Phage λ repressor isolated (Ptashne)
1967 Description of viroids (Diener)
1970 Discovery of retroviral reverse transcriptase (Temin, Baltimore)
1972 Recombinant DNA technology phage λ and SV40 (Berg)
1973 Discovery that major histocompatibility complex (MHC) presents viral antigens
to lymphocytes (Doherty, Zinkernagel); First restriction enzyme map of a viral
genome, SV40 (Nathans)
1974 Phage lambda viral vectors for recombinant DNA technology (Murray, Davis,
Blattner, Enquist)
1976 Retroviral oncogenes are derived from cells (Bishop, Varmus)
1977 RNA splicing discovered in adenovirus (Roberts, Sharp, Chow, Broker)
1978 First viral genome sequenced (phiX174, Sanger)
1978 Virus crystal structure (TBSV) (Harrison)
1979 Discovery of the p53 tumor suppressor protein bound to the simian vacuolating
virus 40 (SV40) T-antigen (Levine, Lane)
1979 World Health Organization declares smallpox eradicated
1981 Development of infectious recombinant clone for an RNA virus, poliovirus
(Racaniello, Baltimore)
1981 Structure of first viral envelope protein (Wiley, Skehel, Wilson)
1983 Description of human immunodeficiency virus (HIV) as causative agent of
acquired immunodeficiency syndrome (AIDS) (Montagnier, Gallo)
1989 Hepatitis C virus cloned (Houghton et al.)
1990 Human gene therapy with a retrovirus vector
1994 Kaposi's sarcoma herpesvirus discovered (HHV-8) (Chang, Moore)
1997 HAART treatment for AIDS
2003 Severe acute respiratory syndrome (SARS) outbreak and containment; rapid
identification of novel human coronavirus
2005 Hepatitis C virus propagated in tissue culture (Chisari; Rice; Wakita)
2005 1918 influenza virus genome reconstructed and sequenced (Palese, Tumpey,
Taubenberger)
Joint initiative of IITs and IISc – Funded by MHRD
Page 3 of 21
NPTEL – Biotechnology – Microbiology
2006 Vaccine against human papillomavirus
2007 End of vaccination program for rinderpest
2011 Declaration of the eradication of rinderpest
TMV: tobacco mosaic virus; FMDV: foot and mouth disease virus; RSV: respiratory
syncytial virus; TBSV:tomato bushy stunt virus; HAART: highly active anti-retroviral
therapy.
General Characteristics of Viruses
1. Viral structure:Typical viral components are shown in Fig. 2. These components
are a nucleic acid core and a surrounding protein coat called a capsid. In
addition some viruses have a surrounding lipid bilayer membrane called an
envelope.
Fig. 2.The components of helical virus
A. Nucleic acid
 Viral genomes are either DNA or RNA (not both)
 Nucleic acid may be single- or double-stranded
Fig. 3.Types of virus genomes
Joint initiative of IITs and IISc – Funded by MHRD
Page 4 of 21
NPTEL – Biotechnology – Microbiology
B. Capsid
 protein coat
 Protection of Nucleic Acid
 Provides Specificity for Attachment
 Capsomeres are subunits of the capsid
Fig. 4.Capsid structure
C. Envelope
 Outer covering of some viruses
 Envelope is derived from the host cell plasma membrane when the
virus buds out
 Some enveloped viruses have spikes, which are viral glycoproteins
that project from the envelope
 Naked (non-enveloped) viruses are protected by their capsid alone
Fig. 5.Enveloped helical virus
Joint initiative of IITs and IISc – Funded by MHRD
Page 5 of 21
NPTEL – Biotechnology – Microbiology
2. Size of viruses:
 Determined by electron microscopy
 Ranges from 20 to 14000 nm in length
Fig. 6. Size of different viruses
Joint initiative of IITs and IISc – Funded by MHRD
Page 6 of 21
NPTEL – Biotechnology – Microbiology
3. Shape of viruses:
Four basic morphologies
 Icosahedral - efficient means to conserve and enclose space;
formcapsomers (planar faces formed by association of proteins)
 Helical - capsid is shaped like a hollow protein tube
 Enveloped - outer covering derived from the host cell’s nuclear or
plasmamembrane and often possessing spikes or peplomer projections
involved inattachment and entry into a host cell sometimes via their
enzymatic activity
 Complex symmetry - viruses that fit neither of the above categories or
whichmay employ portions in combination, e.g., bacteriophage
Fig. 7.Types of viral symmetry
4. Host Range: The specific types of cells a virus can infect in its host species
represent the host range of the virus.
 Animal virus
 Plant virus
 Bacterial virus (bacteriophage)
Host range is determined by attachment sites (receptors)
Joint initiative of IITs and IISc – Funded by MHRD
Page 7 of 21
NPTEL – Biotechnology – Microbiology
Important points to remember:
•
VIRION – a complete single viral particle
•
Obligatory intracellular parasites
•
Contain DNA or RNA
•
Do not undergo binary fission
•
Sensitive to interferon
•
Contain a protein coat
•
Some are enclosed by an envelope
•
Some viruses have spikes
•
Most viruses infect only specific types of cells in one host
•
Host range is determined by specific host attachment sites and cellular factors
(receptors)
•
Viruses replicate through replication of their nucleic acid and synthesis of the
viral protein.
•
Viruses do not multiply in chemically defined media
•
All ss-RNA viruses with negative polarity have the enzyme transcriptase (RNA
dependent RNA polymerase) inside virions.
•
Retroviruses and hepatitis B virus contain the enzyme reverse transcriptase.
Joint initiative of IITs and IISc – Funded by MHRD
Page 8 of 21
NPTEL – Biotechnology – Microbiology
REFERENCES:
Text Books:
1. Jeffery C. Pommerville. Alcamo’s Fundamentals of Microbiology (Tenth Edition).
Jones and Bartlett Student edition.
2. Gerard J. Tortora, Berdell R. Funke, Christine L. Case. Pearson - Microbiology: An
Introduction. Benjamin Cummings.
Reference Books:
1. Lansing M. Prescott, John P. Harley and Donald A. Klein. Microbiology. Mc Graw
Hill companies.
2. Biology, Raven and Jhonson, 6th edition (2001)
3. Microbiology, Pelczar. M.J , Chan E.C.S, Kreig N.R, 5th edition (2007)
Joint initiative of IITs and IISc – Funded by MHRD
Page 9 of 21
NPTEL – Biotechnology – Microbiology
Module 9 – The Viruses
Lecture 2 - The Bacteriophages
What are Bacteriophages?
Bacteriophages are obligate intracellular parasite on bacteria that uses bacterial
machinery system for its own multiplication and development. These are commonly
referred as “phage”. Bacteriophages were jointly discovered by Frederick Twort (1915)
in England and by Felix d'Herelle (1917) at the Pasteur Institute in France.
“Bacteriophage” term was coined by Felix d'Herelle. Some of the examples of
bacteriophages are, Spherical phages such as φX174 (ssDNA), Filamentous phages such
as M13(ssDNA), T-even phages such as T2, T4 and T6 that infect E.coli, Temperate
phages such as λ and μ.
Fig. 8. Basic structure of Bacteriophages
Composition:
All bacteriophages contain nucleic acid as genetic material and protein.
Depending upon the phage, the genetic material may be either DNA or RNA. Certain
unusual modified bases are present in the genetic material of phages which protect the
phage genetic material from nucleases during infection. Protein surrounds the genetic
materials and protects to the surrounding environment.
Joint initiative of IITs and IISc – Funded by MHRD
Page 10 of 21
NPTEL – Biotechnology – Microbiology
Structure:
The basic structural features of T4 bacteriophages are illustrated in Figure 2. It is
approximately 200 nm long and 80-100 nm wide. Size of other phages is of 20 – 200nm
in length. All bacteriophages contain head and tail part. Head part is also termed ad
capsid which composed of one or different types of proteins. Genetic materials are
present inside and protected by capsid. Tails are attached to the capsid in most of the
phages. These are hollow tube like structure through which viruses inject their genetic
material inside the host during infection. Tail part is more complex structure in phages. In
T4 phage, tail part is surrounded by a contractile sheath and basal plate like structure
present at the end of tail from which certain tail fibres are attached. Tail fibres help in
attachment phages to bacteria and contractile sheath helps in contraction during infection.
Some of the phagesdo not contain tail fibres at the end. Certain other structures are
involved in these phages for binding to the bacterium during infection.
Fig. 9. Structure of T4 Bacteriophage
Infection of Host Cells:
The first step in the infections is binding of phage to bacterium which is mediated
by tail fibres are some other structures on those phages that lack tail fibres. Binding of
phage tail fibre to bacterium is through adsorption process and it is reversible. There are
specific receptors are present on bacterial cell surface through which phages bind on it by
its tail fibre. These receptors are proteins, lipopolysaccharides, pili and lipoproteins of
Joint initiative of IITs and IISc – Funded by MHRD
Page 11 of 21
NPTEL – Biotechnology – Microbiology
bacterium. Some phages lacking basal plate and tail fibre bind tightly to bacterial cell
surface and it is reversible.
After binding of phage to bacterium, there is contraction in tail by contractile
sheath and phages inject their genetic material through hollow tube like tail. Some phages
also contain certain enzymes that digest the bacterial cell surface. Phages that don’t
contain tail fibre and contractile sheath, uses different mechanism for inject its own
genetic material inside the host. Only genetic material of phages enters inside the
bacterium and the remainder of phages (ex. capsid) remain outside of bacterium.
Life Cycle:
There are two different types of life cycle present in phages: (i) Lytic cycle and
(ii) Lysogenic cycle. Lytic (virulent) cycle kill the host cell that they infect, while
lysogenic (temperate) cycle establishes a persistent infection without killing the host cell.
(A.) Lytic Cycle:
These are also known as virulent cycle because phages multiply inside the host
and lyse the cell at the end of its life cycle.After attachment of tail fibre to host, genetic
materials are injected inside the host. The time period between the entry of genetic
material inside the host and release of mature phage after end of life cycle is termed as
eclipse period. Synthesis of phage components and its packaging into mature phages
takes place in this period. After infection, the genetic material of phages uses host
biosynthetic machinery for replication, transcription and translation. Structural proteins
of phages (capsid, tail etc.) are also synthesized inside the host using host biosynthetic
machinery. After synthesis, genetic materials are packed inside the capsid and tail is
attached on it. This process is called as maturation of phages. In lytic phage, phages also
synthesized lysis protein. Bacterial cells are lysed due to accumulation of phage lysis
protein and mature phages are released into the medium. Around 10-1000 phages are
released from the bacterial cell. The average yield of phages per infected bacterial cell is
known as burst size.
Joint initiative of IITs and IISc – Funded by MHRD
Page 12 of 21
NPTEL – Biotechnology – Microbiology
Fig. 10. Lytic cycle of bacteriophage infection
(B.) Lysogenic cycle:
These are also known as temperate phage because phages multiply via the lytic
cycle or may enter a dormant state inside the cell. After entry of genetic material into the
host cell, the phage DNA integrates into the host chromosome and starts replication along
with it and passed to the daughter cells of host. Integration of phage DNA to host
chromosome is termed as prophage and bacteria is termed as lysogenic bacteria. Due to
integration of phage DNA to host chromosome, extra genes carried by phage get
expressed in the host cell and it may change the properties of bacterial cell. This process
is termed as lysogenisc or phage conversion.
Due to exposure to UV rays, ionizing radiations, mutagenic chemicals etc, DNA of phage
is released from host chromosome and separated phage DNA initiates lytic cycle
resulting in the lysis of cell and release of phages into the medium.
Joint initiative of IITs and IISc – Funded by MHRD
Page 13 of 21
NPTEL – Biotechnology – Microbiology
Significance of bacteriophages:
 New characteristics are acquired using lysogenic conversion
 Insertional mutation can be induced in bacterial chromosome by random insertion
of genes or nucleotides.
 Latent infection in mammalian cells by retroviruses can be studied using Lambda
phage as model system.
 In genetic engineering, phages are used extensively where they serve as cloning
vectors.
 Phages are used to maintain libraries of genes and monoclonal antibodies
 Natural removal of bacteria from water bodies can be done using bacteriophages
REFERENCES:
Text Books:
1. Jeffery C. Pommerville. Alcamo’s Fundamentals of Microbiology (Tenth Edition).
Jones and Bartlett Student edition.
2. Gerard J. Tortora, Berdell R. Funke, Christine L. Case. Pearson - Microbiology: An
Introduction. Benjamin Cummings.
Reference Books:
1. Lansing M. Prescott, John P. Harley and Donald A. Klein. Microbiology. Mc Graw
Hill companies.
2. Biology, Raven and Jhonson, 6th edition (2001)
3. Microbiology, Pelczar. M.J , Chan E.C.S, Kreig N.R, 5th edition (2007)
Joint initiative of IITs and IISc – Funded by MHRD
Page 14 of 21
NPTEL – Biotechnology – Microbiology
Module 9 – The Viruses
Lecture 3 -The Viruses of Eukaryotes
1. Characteristics of Eukaryotic Viruses
 Obligate intracellular parasites
 Infect and reproduce only within the living eukaryotic cells
 Viruses contain single or double stranded DNA or RNA as their genomes (Fig. 1)
 ssRNA able to function as mRNA is referred to as positive (+) sense or plus
strand RNA and if it is the equivalent to antisense RNA it said to be as minus
strand or negative (-) sense RNA
 In certain cases, the genome encodes mRNAs which are of either sense
 Processes that are found both in eukaryotes and their viruses- Glycosylation, RNA
processing and protein modification (proteolytic cleavage)
Fig. 11. General structure of enveloped Eukaryotic Virus
2. Structure of Eukaryotic viruses
 The viral genome is enclosed by a protein coat known as capsid.
 Capsid composed of protein subunits known as capsomeres
 The nucleic acid genome along with the protective protein coat is called the
nucleocapsid.
 Nucleocapsid can be of following symmetry:
 Icosahedral,
 Helical or
 Enveloped symmetry
Joint initiative of IITs and IISc – Funded by MHRD
Page 15 of 21
NPTEL – Biotechnology – Microbiology
 Majority of viruses have helical or icosahedral symmetry
(a.) Icosahedral symmetry
 Icosahedral is regular polyhedran with 20 equivalent triangular faces 12 vertices.
 In the icosahedral structure, the individual polypeptide molecules form a
geometrical structure that surrounds the nucleic acid
For example:Adenovirus has icosahedral structure (Fig. 2)
Fig. 12. Structure of Adenovirus
Joint initiative of IITs and IISc – Funded by MHRD
Page 16 of 21
NPTEL – Biotechnology – Microbiology
(b.) Helical symmetry
 In viruses with helical symmetry, the polypeptide units are arranged as a helix
and form a rod like structure surrounding the nucleic acid genome
For example: TMV (Tobacco Mosaic Virus) has helical symmetry (Fig. 3)
Fig. 13. Structure of Tobacco Mosaic Virus
(c.) Enveloped symmetry
 In envelope viruses,nucleocapsid is surrounded by a lipid bilayer and
glycoprotein derived from the modified host cell membrane called envelope.
 Enveloped viruses are readily infectious agents if the envelope remains intact.
For example: Influenzavirus has enveloped symmetry
Fig. 14. Structure of Influenzavirus
Joint initiative of IITs and IISc – Funded by MHRD
Page 17 of 21
NPTEL – Biotechnology – Microbiology
4. Classification of Eukaryotic Viruses on the basis of Nucleic Acid
Major groups of viruses are distinguished on the basis of their nucleic acid content as:
 DNA Viruses
 RNA Viruses
Subsequent subdivisions are based largely on other properties of nucleic acids. The RNA
viruses can be ssRNA or dsRNA, although most are ssRNA.
(A.) DNA Viruses
Important Characteristics:
 DNA as its genetic material
 Replicationoccurs in the nucleus using a DNA-dependent DNA polymerase
 DNA can be ssDNA or dsDNA and may be linear or circular
Important groups of DNA viruses are:
 Adenoviridae
 Herpesviridae
 Poxviridae
 Papovaviridae
 Hepadnaviridae
 Parvoviridae
The dsDNA viruses are further separated in families on the basis of the shape of their
DNA (linear or circular), their capsid shape and the presence or absence of an
envelope. Only one family of viruses has ssDNA (as shown in Table1)
Table 2: Classification of Eukaryotic DNA Viruses
Family
Linear
or
circular
DNA
Enveloped
or naked
Capsid
Shape
Typical
size (nm)
Example
Double-Stranded DNA Viruses
Adenoviridae
Linear
Naked
Polyhedral 75
Herpesviridae
Linear
Enveloped
Polyhedral 120-200
Human
adenoviruses
Simplexvirus
Poxviridae
Linear
Enveloped
Complex
Orthopoxvirus
Papovaviridae
Circular
Naked
Polyhedral 45-55
Joint initiative of IITs and IISc – Funded by MHRD
230×270
Human
Papillomaviruses
Page 18 of 21
NPTEL – Biotechnology – Microbiology
Hepadnaviridae Circular
Enveloped
Polyhedral 40-45
Hepatitis B
virus
Single-Stranded DNA Viruses
Parvoviridae
Linear
Naked
Polyhedral 22
B19
(B.) RNA viruses
Important Characteristics:
 RNA as their genetic material
 Genome may be ssRNA or dsRNA
 ssRNA viruses may be of positive (+) sense or negative (-) sense
 Replicationoccurs in the cytoplasm using a RNA-dependent RNA polymerase
 RNA dependent RNA polymerases are not having proofreading activity and hence
replicate their templates with a higher error rate.
Positive (+) sense viral RNA is similar to mRNA and thus can be immediately translated
by the host cell. Flaviviruses,togaviruses, poliovirus are some examples of (+) sense
RNA viruses.
Negative (-) sense viral RNAis complementary to mRNA and thus must be converted to
positive (+) sense RNA by an RNA dependent RNA polymerase before translation.
Influenza virus, Measles virus, Rabies virus are some examples of negative (-) sense
RNA viruses.
Double-stranded RNA viruses need to package an RNA dependent RNA polymerase to
make their mRNA after infection of the host cell. Examples of dsRNA viruses are
Rotaviruses which belong to family Reoviruses.
Important groups of RNA viruses are:
 Picornaviridae
 Togaviridae
 Flaviviridae
 Retroviridae
 Paramyxoviridae
 Orthomyxoviridae
 Bunyaviridae
 Reoviridae
Joint initiative of IITs and IISc – Funded by MHRD
Page 19 of 21
NPTEL – Biotechnology – Microbiology
The different families of RNA viruses are distinguished from one another by their nucleic
acid content, their capsid shape and presence or absence of an envelope (as shown in
Table 2)
Table 3: Classification of Eukaryotic RNA Viruses
Family
No. of
Copies
Enveloped
or naked
Capsid
Shape
Typical
size
(nm)
Example
(+) Sense RNA Viruses
Picornaviridae
1
Naked
Polyhedral
18-30
Enterovirus
Togaviridae
1
Enveloped
Polyhedral
40-90
Rubella virus
Flaviviridae
1
Enveloped
Polyhedral
40-90
Flavivirus
Retroviridae
2
Enveloped
Spherical
100
HTLV-I
(-) Sense RNA Viruses
Paramyxoviridae
1
Enveloped
Helical
150-200
Morbillivirus
Rhabdoviridae
1
Enveloped
Helical
70-180
Lyssavirus
Orthomyxoviridae 1 copy in Enveloped
8
segments
1
Enveloped
Filoviridae
Helical
100-200
Influenzavirus
Filamentous 80
Filovirus
Bunyaviridae
1 copy in Enveloped Spherical
90-120
3
segments
Double-Stranded RNA Viruses
Hantavirus
Reoviridae
1 copy in Naked
10-12
segments
Rotavirus
Joint initiative of IITs and IISc – Funded by MHRD
Polyhedral
70
Page 20 of 21
NPTEL – Biotechnology – Microbiology
REFERENCES:
Text Books:
1. Jeffery C. Pommerville. Alcamo’s Fundamentals of Microbiology (Tenth Edition).
Jones and Bartlett Student edition.
2. Gerard J. Tortora, Berdell R. Funke, Christine L. Case. Pearson - Microbiology: An
Introduction. Benjamin Cummings.
Reference Books:
1. Lansing M. Prescott, John P. Harley and Donald A. Klein. Microbiology. Mc Graw
Hill companies.
2. Biology, Raven and Jhonson, 6th edition (2001)
3. Microbiology, Pelczar. M.J , Chan E.C.S, Kreig N.R, 5th edition (2007)
Joint initiative of IITs and IISc – Funded by MHRD
Page 21 of 21