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Gene Expression and Replication
in Large DNA Viruses
Herpesviruses
Large cytoplasmic viruses
What unique features of replication
and expression do they posess?
What do these features tell us about
what is important to these viruses?
More autonomous replication,
expression, life style
Much more sophisticated gene
expression strategies
Many interesting genes
Herpesviridae





Genome: ds DNA, linear, 124-235
kbp
Core: genome wrapped around a
cylindrical structure 25-30 nm in
diameter
Capsid: Icosahedron 100-110 nm in
diameter composed of 150
hexamers and 12 pentamers at the
vertices
Tegument: Electron-dense,
assymmetrically distributed
material containing viral regulatory
proteins.
Envelope: derived from cellular
membranes, contains several viral
glycoproteins.
10-200 nm diameter Virion
Three Sub-families of Herpesviridae
Alpha-, Beta- and
Gammaherpesvirinae
Human viruses in
all three
Infect many
species
Human Herpesviruses

HHV-1, Herpes simplex 1: Cold sores, epithelial and neuronal
cells

HHV-2, Herpes simplex 2: STD, epithelial and neuronal cells,
teratogenic, can be fatal in newborns

HHV-3, Varicella-zoster: Chickenpox, shingles epithelial and
neuronal cells
HHV-4, Epstein Barr Virus: Mononucleosis, Burkitt’s lymphoma,
lymphoid tissue restricted

HHV-5, Cytomegalovirus: Salivary gland tropic, teratogenic, can
be fatal in newborns
Human Herpesviruses cont’d
(These viruses were not recognized prior to AIDsrelated research)
• HHV-6 childhood rash; multiple sclerosis (?), tropism for CD4+
lymphocytes
• HHV-7 First isolated in 1990, CD4+ cells, cofactor for HHV-6?
• HHV-8 First isolated in 1995, stimulates angiogenesis and
“causes” Kaposi’s sarcoma
Some Shared Biological Properties Among
Herpesviruses
Synthesis of viral DNAs and assembly of capsids occur in the
nucleus.
Production of infectious progeny virus is accompanied by lysis and
irreversible destruction of the infected cell.
A single virus can cause a number of different diseases.
Herpesviruses infect chordates; teleosts, amphibians,
birds,reptiles & mammals.
Latency
Nucleic acid metabolism enzymes
Diseases Caused by Herpesviruses
Primates
infected by
Herpesviruses:
HSV Genome and Genes
HSV 1: about 150 kbp and 90 “genes”
Expression is Temporally Regulated
Immediate Early or alpha
Early or beta
Middle or gamma-one or leaky late
Late or gamma-two or true late
Protein products within each class
regulate the expression of protein
products in later classes.
CASCADE REGULATION!
LAT RNAs are regulatory RNAs that
control latency.
Host Pol II is polymerase.
Some Types of Infections
Acute-virus eventually
cleared
Persistent-constant level of
production of virus
Latent with reactivation
Aka “cellular latency”
“Slow” infection
Virus production vs. time
Symptoms in red
Brackets-infectious virus
HSV has Latent and Lytic cycles
HSV-1: LAT RNAs and Latency
 -4
•Latency associated transcripts (LATs) do not encode proteins
•LATs are 1.5 to 2.0 kb RNAs that lack poly-A tails. They are
restricted to nucleus.
•40,000 – 100,000 LATs accumulate per latently infected neuron.
•Likely maintain latency by binding to IE RNA promoters to prevent their
transcription and cascade synthesis of viral genes.
• During stress LAT RNAs are destroyed.
Enzymes for Nucleic Acid
Metabolism
 Seven
replication proteins-polymerase,
binding proteins, helicase/primase
 Nucleotide
metabolism: thymidine kinase,
dUTP triphosphatase, uracyl-DNA
glycosylase, alkaline nuclease,
ribonucleotide reductase
Very Large DNA Viruses
What are their unique and intriguing
features?
What does their unique life style have to tell
us about cells and viruses?
Nucleo-Cytoplasmic Large DNA
Viruses (NCLDVs)
Virus Group
Genome Size
Host
Poxviridae
0.1-0.4 Mbp
Various
Iridoviridae
0.3 Mbp
invertebrates
Phycodnaviridae 0.3-0.6 Mbp
algae
Mimiviridae
protozoa
1.2 Mbp
Smallpox Virus
Poxviridae very widely distributedvertebrates and invertebrates
Linear ds DNA
Cytoplasmic life cycle
Transcription, regulation, replication
outside the nucleus
For a long time, poxviridae were
considered the largest and most
complex of viruses
Phycodnaviruses
Ubiquitous
Infect unicellular algae
300-400 genes in at least 300 kbp of DNA-usually more
Methyltransferases and restriction enzymes
Some introns
Enzymes for glycosylating proteins
Plentiful in marine environments
Limiting factor for marine algae?
Do you remember Legionnaire’s
Disease?
Mimivirus
Legionella-like particles observed by light
microscopy in Acanthamoeba polyphaga
Gram positive, unculturable- the “Bradford
coccus”-1992
Reanalyzed-2004
Largest of all viruses-Mimivirus or Microbe
mimic virus
Genome of more than 1 Mbp
Pictures of virus reveal massive size
of about 400 nm or larger
Genomic analysis
Linear ds DNA with terminal repeats
Over 1000 ORFs, about 900 predicted proteins
Noncoding RNAs, tRNAs
About 25% known genes
Some of NCLDV “core” genes
“Metabolic” genes for lipids, amino acids and
carbohydrates
Genes related to protein translation: 4 ARS
enzymes, initiation, elongation, release
factors
Genes related to DNA transactions and repair
Viral genomes can overlap cellular genomes in size
Organism/Code
Genome size (bp)
Date
Mimivirus Y653733
Treponema pallidum NC_000919
Rickettsia prowazekii NC_000963
Chlamydia muridarum NC_002620
Chlamydia trachomatis NC_000117
Mycoplasma pulmonis NC_00277
Tropheryma whipplei NC_004572
Onion yellows phytoplasma NC_005303
Mycoplasma pneumoniae NC_000912
Mycoplasma mobile NC_006908
Ureaplasma parvum NC_002162
Wigglesworthia glossinidia NC_004344
Buchnera aphidicola NC_004545
Mycoplasma genitalium NC_000908
Nanoarchaeum equitans NC_005213
Canarypox virus NC_005309
Ectocarpus siliculosus virus NC_002687
Paramecium bursaria Chlorella virus
1 NC_000852
1.181.404
1.138011
1.111523
1.072950
1.042.519
1 963.879
927.303
860.631
816.394
777.079
751.719
697.724
615.980
580.074
490.885
359.853
335.593
330.743
Nov 2004
Sep 2001
Sep 2001
Oct 2001
Sep 2001
Oct 2001
Feb 2003
Dec 2003
Apr 2001
May 2004
Jan 2000
Jul 2003
Jan 2003
Jan 2001
Feb 2004
Jan 2004
Feb 2001
Feb 1996
Microbe mimic-a virus or a cell?
Reasons it is a cell
Reasons it is a virus
Big as several types of cell
Genome larger than many
cells
It has some of its own
translation apparatus
genes
Extracellular phase may be
thought of as a spore
Does not appear to have
genes for energy
metabolism
Reproduces by selfassembly-not division
Gene homology with viruses
Other Giant Viruses-”Giruses”
 Mamavirus
(2008)
Contact lens isolate
 Sputnik virophage-infects mamavirus
dsDNA, about 18 kbp
 Pithovirus-0.6 Mbp (2014)
permafrost, 30,000 years
still “viable”