CHAPTER 16 Viral Diversity

Viruses of Prokaryotes RNA Bacteriophages

• A variety of RNA

viruses

that infect bacteria are known. The small RNA genome of these bacterial viruses is translated directly and encodes only a few proteins.

•

Figure 16.2a

shows the genetic map of RNA

bacteriophage

MS2, and

Figure 16.2b

shows the flow of events of MS2 multiplication.

• The small genome encodes only four proteins .

• These are the maturation protein (present in the mature virus particle as a single copy), coat protein , lysis protein (involved in the lysis process that results in release of mature virus particles), and a subunit of

RNA replicase

, the enzyme that brings about replication of the viral RNA.

Icosahedral Single-Stranded DNA Bacteriophages

• M13 and  X174 are ssDNA viruses - ~25 nm •The single-stranded DNA genome (5356nt)of the virus  X174 is so small that

overlapping genes

are required to encode all its essential proteins.

This virus provided the first example of overlapping genes.

• Because cellular DNA always replicates in the double-stranded configuration, the replication process of the single-stranded genome of  X174 is of interest .

• On infection, the plus-sense viral DNA becomes separated from the protein coat. Entrance into the cell is accompanied by the conversion of this single stranded DNA into a double-stranded molecule called the

replicative form

(RF).

•

Figure 16.3a

shows the genetic map of phage  X174, and

Figure 16.3b

shows the flow of events during  X174 replication.

A mRNA is read twice by ribosomes, once for A and second for A *

• The production of progeny viral DNA involves

rolling circle replication

.

Figure 16.4

mechanism in phage  X174.

shows the

A cleaves the plus strand of the RF

Filamentous Single-Stranded DNA Bacteriophages

• Some single-stranded DNA viruses, such as M13, have filamentous

virions

(

Figure 16.5

) related to f1 and fd phages .

•These viruses are very useful tools for DNA sequencing and genetic engineering. They are released without actually killing the host.

•M13 is only 6 nm in diameter but 860 nm long.

•Filamentous phages are released without killing the host cell.

•All phages with protein A (including X174) do not kill host cells.

Release of phages

Double-Stranded DNA Bacteriophages: T7

• The bacteriophage T7 double-stranded DNA genome always enters the host cell in the same orientation.

Figure 16.6

shows the genetic map for T7.

• The late genes in T7 are transcribed by a virus-encoded RNA polymerase . •The replication strategy for the T7 genome employs T7 DNA polymerase and involves terminal repeats and the formation of

concatemers

(

Figure 16.7

).

Formation of concatamers by joining DNA at the unreplicated terminal ends

Production of mature viral DNA

Mu: A Double-Stranded Transposable DNA Bacteriophage

• Bacteriophage Mu is a temperate virus that is also a transposable element . In either the lytic or lysogenic pathway, its genome is integrated into the host chromosome by the activity of a

transposase

.

• Even in the lytic pathway, its genome is replicated as part of a larger DNA molecule. The genome is packaged into the virion in such a way that there are short sequences of host DNA at either end.

•

Figure 16.9

illustrates replication of bacteriophage Mu. Genome – 39 kb (37.2 kb viral DNA and 1.8 kb host DNA) 50-150 bp 1-2 kb Lambda. T4, T7, and Mu have linear dsDNA

Viruses of Eukaryotes Plant Viruses

• Most plant viruses have

positive-strand

RNA genomes. One example is tobacco mosaic virus (TMV), the first virus discovered (

Figure 16.11

).

• The genomes of these viruses can move within the plant through intercellular connections that span the cell walls.

• Other types of plant viruses are also known, including the

Chlorella

viruses , which have very large double-stranded DNA genomes .

Positive-Strand RNA Viruses of Animals: Poliovirus and Coronaviruses

• In small RNA viruses such as poliovirus, the viral RNA is translated directly , causing the production of a long

polyprotein

that is broken down by enzymes into the many small proteins necessary for nucleic acid multiplication and virus assembly (

Figure 16.13

).

Poliovirus

RNA linked 22 a. a. protein serve as a primer

• Coronavirus is a large single-stranded RNA virus that resembles poliovirus in some but not all of its replication features (

Figure 16.14

).

Coronavirus – Flow of information

Negative-Strand RNA Viruses of Animals: Rabies, Influenza, and Related Viruses

• In

negative-strand viruses

, the virus RNA is not the mRNA but is copied into mRNA by an enzyme present in the virion. •

Figure 16.16

illustrates the flow of events during multiplication of a negative-strand RNA virus.

•

Vesicular stomatitis virus (VSV)

• Translation of viral mRNAs leads to the synthesis of viral coat proteins. •Assembly of an

enveloped

virus is considerably more complex than assembly of a naked virion.

• Two kinds of coat proteins are formed,

nucleocapsid

proteins and envelope proteins. The nucleocapsid is formed first by association of the nucleocapsid protein molecules around the viral RNA.

• Important negative-strand viruses include rabies virus and influenza virus (

Figure 6.17

).

influenza virus

Influenza virus

Double-Stranded RNA Viruses: Reoviruses

• Reoviruses contain segmented double stranded RNA genomes. •Like negative-strand RNA viruses, reoviruses contain an RNA-dependent RNA polymerase within the virion.

Replication of Double-Stranded DNA Viruses of Animals

• Most double-stranded DNA animal viruses, such as SV40 , replicate in the nucleus. SV40 has a tiny genome and employs the strategy of overlapping genes to boost its genetic-coding potential. Some of these viruses cause cancer.

•

Figure 16.20

shows the genetic map of polyomavirus SV40.

5.2 kb

•

Figure 16.21

shows the general scheme of molecular events involved in cell transformation by a polyomavirus such as SV40.

• Herpesviruses cause a variety of disease syndromes and can maintain themselves in a latent state in the host indefinitely , initiating viral replication periodically.

Double-Stranded DNA Viruses: Herpesviruses

• Herpesviruses are large, double-stranded DNA viruses. The viral DNA circularizes and is replicated by a rolling circle mechanism .

•

Figure 16.22

illustrates the flow of events in multiplication of herpes simplex virus.

Double-Stranded DNA Viruses: Pox Viruses

• The pox viruses, unlike the other DNA viruses discussed so far, are very large viruses that replicate entirely in the cytoplasm.

These viruses are responsible for several human diseases, but a vaccination campaign has eradicated the smallpox virus in the wild.

Double-Stranded DNA Viruses: Adenoviruses

• Different double-stranded DNA animal viruses have different genome replication strategies.

• The strategy of the adenoviruses involves protein primers and a mode of replication that avoids the synthesis of a lagging strand and occurs within the nucleus (

Figure 16.24

).

Viruses Using Reverse Transcriptase: Retroviruses and Hepadnavirus

• The

retroviruses

contain RNA genomes and use

reverse transcriptase

to make a DNA copy during their life cycle (

Figure 16.25

).

Lys3

•

Figure 16.26

illustrates translation of retrovirus mRNA and processing of the proteins.

• The

hepadnaviruses

contain DNA genomes and use reverse transcriptase to make genomic DNA from an RNA copy .

Figure 16.27

shows the genome of hepatitis B, a hepadnavirus.

Hepadnaviruses (Liver infecting) – Small, irregular, rod shaped

Hepatitis B virus – serious bloodborne pathogen 3-4 kb DNA genome is partially ds Replicated through RNA intermediate

•These viruses have complex patterns of gene expression.