Final- Retroviruses Flashcards
Generals about Retroviridae
A very large family of animal and human viruses
Causative agents of some types of cancer, immunosuppression or
immunodeficiency diseases
May exist as stable components of the host genome
Named “retrovirus” because of an important enzyme they encode “reverse transcriptase” – David Baltimore & Howard Temin
• Retro
• Retro = reverse/backward – reflects the character of the viruses to use the RNA genome to produce DNA intermediates by means of “RNA-dependent DNA polymerase” which is found in the virion of all retroviruses
Reverse transcriptase
• Reverse transcriptase is an RNA-dependent DNA polymerase
Retroviruses of veterinary importance were among the first retroviruses to be recognized e.g.,
• Equine infectious anaemia virus, bovine leucosis virus and jaagsiekte virus of sheep – described in 1800s
- Retroviruses of chicken – detected by Bang and Ellerman in 1908 in Denmark
- Rous sarcoma virus – detected by Rous as early as 1911 in species such as cattle,
cats, primates and mice
• Since 1980 we know that retroviruses cause human diseases too e.g., some lymphomas, leukemia and AIDS
Characteristics of retroviruses
• They are enveloped viruses formed by budding from the cell
membrane
• Have a diploid genome with two copies of single stranded, positive
sense RNA
• All replicate with use of the reverse transcriptase, an enzyme encoded by the virus
Positive sense RNA means:
RNA serves as mRNA from which protein translation can directly begin
What is special about Retroviruses?
They integrate into the genome of the host by means of an enzyme called integrase
IMPLICATION: they may alter or acquire host genome sequences, may activate or inactivate particular host genes located near the integration site
What is the taxonomy of Retroviridae?
Morphology of retroviridae
Virions are spherical
Surrounded by an envelope consisting of a lipid membrane bilayer
The surface is studded by projections of envelope glycoprotein
A spherical layer of protein (matrix)
beneath the envelope
An internal capsid protein which encloses the viral RNA = nucleocapsid
• Inside the nucleocapsid - two single strand viral RNA, reverse transcriptase, integrase and protease
Virion properties
- Diameter 80-100 nm
- Each RNA genome is between 7 and 11 kb and has a 3’
polyadenylated tail and a 5’ cap
• Because virions are enveloped, they are easily inactivated by lipid
solvents or detergents and by heating
• Virions are resistant to ultraviolet or X-rays
What is required for replication of these viruses?
- At least 30 molecules of reverse transcriptase (RT) are included in the virion
- RT is required for replication
- RT serves as:
- RNA-dependent DNA polymerase
- DNA-dependent DNA polymerase • Rnase
- Virion has at least 3-4 important genes
What are the different genes that in the viruses?
gag, pol, env,, pro
The gag gene encodes
- The gag gene encodes the viruses core proteins
- Capsid (CA)
- Nucleocapsid (NC)
- Matrix (MA)
The pol gene encodes:
The pol gene encodes:
• Reverse transcriptase (RT)
• Integrase (IN)
The env gene encodes:
The env gene encodes:
• Virion envelope proteins, surface (SU) and transmembrane (TM)
The pro gene encodes
The pro gene encodes the protease
In lentiviruses
• the tat gene encodes a transactivator that enhances the efficiency of
cellular RNA polymerase
• the rev gene encodes a protein that facilitates transport of non-
spliced viral RNA from the nucleus to the cytoplasm
- the nef gene encodes Nef protein that:
- is essential for replication in target hosts but not in cell culture in vitro
- may downregulate expression of the CD4 molecule or alter the activation status of target cells
- the vif gene encodes a protein Vif which enhances replication in lymphocytes
Alpharetroviruses - characteristics
- Referred to as simple retroviruses
- Have a type C virion morphology
- Represented by avian leucosis and sarcoma virus (ALSV)
- The genome contains gag, pro, pol and env genes
- The pro gene is at the 3’ end of gag in the same reading frame • Mostly endogenous and exogenous viruses of chicken
Exogenous retroviruses
Exogenous retroviruses are those viruses transmitted horizontally and are rarely transmitted via in-utero or germline infection
Endogenous retroviruses
Endogenous retroviruses (retroviral elements) are those viruses included in the genome of most if not all animals
• Are transmitted vertically as part of the host genome • Are passed on from generation to generation
Betaretroviruses
• Simple retroviruses
Have type B morphology with round eccentric core or type D with cylindrical core
Exemplified by mouse mammary tumor virus (MMTV) and Mason-Pfizer monkey virus (M-PMV)
Virions are assembled in the cytoplasm via A type intermediate
The genomes contain gag, pro, pol and env genes
gag, pro and pol are all in different reading frames
MMTV additionally has the sag gene which encodes the superantigen
The genus contains both endogenous and exogenous retroviruses
Gammaretroviruses
Simple retroviruses with a C type morphology
Has the largest number of members e.g., murine leukemia virus, feline leukemia virus etc.
The genome contains gag, pro, pol and env
The gag, pro, pol are in the same reading frame
They contain both endogenous and exogenous retroviruses of mammals and reptiles
Deltaretroviruses
- Complex retroviruses with a C-type morphology
- The famous examples are: human T-lymphotropic virus (HTLV), bovine leukemia virus
- The genome contains gag, pro, pol, env and regulatory genes rex and tax
- The gag, prol and pol are presented in 3 different reading frames
- Expression of Gag-Pro-Pol requires 2 successive frame shifts
- Rex and Tax are expressed from an alternatively spliced mRNA • Rex and Tax control synthesis and processing of viral RNA
- There are no known endogenous deltaretroviruses
- Exogenous retroviruses are found only in a few mammals
Epsilonretroviruses
Complex retroviruses with a type C morphology
Prototype is the Walleye dermal sarcoma virus
Contain gag, pro, pol and env with gag, pro and pol in the same reading
frame
Additionally, 3 more genes termed ORF A, B, and C are present
The ORFa is a viral homologue of the host cyclin D and may regulate host cell cycle
Only endogenous retroviruses are found in fish and reptiles
Lentiviruses
- Complex viruses with a cylindrical or conical shaped core
- The most important members are the human immunodeficiency virus (HIV) and non-primate viruses such as caprine arthritis-encephalitis virus and visna virus
- The genome contains gag, pro, pol and env
- gag is in a separate reading frame while pro and pol are in the same reading frame
- A single frame shift is used to express Gag-Pro-Pol
What are the acessory genes in Lentiviruses?
- Accessory genes such as vif, vpr, vpo, tat, rev and nef are present
- Accessory genes control transcription, RNA processing, virion assembly, host gene expression and other replication functions
- Exogenous retroviruses are found in many mammals
Lentiviruses have extra genes
In lentiviruses
The tat gene encodes a transactivator that enhances the efficiency of the cellular RNA polymerase
The rev gene encodes a protein that facilitates transport of non-spliced viral RNA from the nucleus to the cytoplasm
The nef gene encodes NEF protein that:
is essential for replication in target hosts but not in cell culture in vitro
may downregulate expression of the CD4 molecule or alter the activation status of target cells
The vif gene encodes a protein VIF which enhances replication in lymphocytes
Spumaviruses
- Complex viruses with a unique virion morphology containing spikes on the surface, a central but uncondensed core
- Exemplified by human foamy virus
Virions are assembled in the cytoplasm and budded into endoplasmic reticulum (ER) and plasma membrane
The genome contains gag, pro, pol and env
Accessory genes, tas/bel-1 and bet are present
The tas gene encodes a transcriptional activator
Exogenous viruses are found in diverse mammals
Replication of retroviruses
Receptor binding and membrane fusion
Internalization and uncoating
Reverse transcription of the RNA genome to form linear dsDNA
Nuclear entry of DNA
Integration of linear DNA into the host genome to form a provirus
Transcription of the provirus to form viral RNA
Splicing and nuclear export of RNA to the cytoplasm
Translation of the RNA to form precursor proteins
Assembly of virions and packaging of viral RNA genome
- Budding and release of the virions
- Proteolytic processing of the precursors and maturation of the virions
Receptors - binding
To enter a cell and initiate infection, retroviruses require interaction between a cell
surface molecule (receptor) and the envelope proteins on the virion surface
Alpharetroviruses Receptor binding
a membrane anchored glycoprotein with a sequence similar
to ligand-binding repeat of the low-density lipoprotein receptor (LDLR)
Betaretroviruses receptor binding
(MMTV) transferrin receptor tfr-1
Gammaretroviruses receptor binding
Gammaretroviruses – several receptors, mCat-1 for mouse viruses; GLVR1 for cat, dog and primate viruses; FeLIX and Pit for FeLV
Deltaretroviruses Receptor binding
a protein similar to AP-3 complex for BLV
Lentiviruses receptor binding
Lentiviruses – CD4 on T helper cells, also expressed on macrophages and dendritic cells; CCR5 and CXCR4 expressed on lymphoid cells
Penetration and uncoating
Upon binding to the receptor the virion fuses with the host cell membrane
Mostly, entry is pH-independent (no endosomal acidification is required). Some retrovirus may require endosomal passage.
Entry may require major rearrangements in the virion envelope proteins e.g., exchange of sulphide bonds between TM and SU
The virion core is released into the cytoplasm of the infected cell
Uncoating is not well studied
Reverse transcription
• A dsDNA copy of the retroviral sRNA is made by the reverse
transcriptase associated with virion
In this process, about 300-1300 bp are added to each end of the
genomic RNA molecule called LTR
Host cell-derived transfer RNA (tRNA) (specific for each retrovirus)
binds viral 5’ LTR sequence and primes the RT reaction
During the copying of cDNA from the viral RNA, the RNase H degrades the RNA leaving only the sDNA
- The sDNA then hybridizes with the genomic viral RNA to complete synthesis of the first strand followed by dsDNA
- Linear dsDNA intermediate is then transported to the nucleus
Integration
Takes place in the nucleus
• Most retroviruses (except lentiviruses) require cell
division in order to integrate into the host genome
- First the 3’ prime ends of viral dsDNA are processed by the integrase (IN) to prepare for insertion
- The strand is then transferred into the host DNA
Is integration site specific?
Integration is not site specific, however sites such as DNA bendings, open chromosomal structures that are transcriptionally active are preferred
provirus
After integration into the host cell chromosome has completed, the viral DNA is now called “a provirus”
Basically proviruses are templates for transcription
• The provirus may remain latent (“silent”, i.e., transcriptionally innate)
or may be transcriptionally active
Transcription
• Transcription is performed by host cellular RNA polymerase to generate viral RNA
• the upstream LTR directs transcription
• Once the viral RNA is produced it is spliced and transported to the cytoplasm, spliced or non-spliced
There are two pools of viral mRNA found in the cytoplasm of an infected cell
- _Full-length genomic RNA t_hat is later packaged into virions as viral RNA
- Spliced mRNA used to express structural proteins such as Gag, Pol and Env
In cells infected with retroviruses, viral protein synthesis occurs in the
In cells infected with retroviruses, viral protein synthesis occurs in the cytoplasm and is regulated similarly to host proteins
what are the spliced and non-spliced RNA are used for?
- Spliced* forms mRNA are used to translate envelop and accessory proteins
- Full-length, non-spliced is packaged into the virion
Splicing
Removal of introns from pre-messenger RNA and joining of exons to form mRNA
Assembly and release of virions
- Virion assembly begins once translation of proteins is finished leading to budding of the virion from the cell membrane
- Almost all retroviruses replicate in dividing cells
- No overt pathology or change in cell metabolism is observed
• Lentivirus cause cell death by formation of cell syncytium and apoptosis
Depending on the presence of the key transforming genes in the viral genome, infection with retrovirus may lead to
• Depending on the presence of the key transforming genes in the viral genome, infection with retrovirus may lead to
- Acute transformation
- Chronic transformation
• Retroviruses that can lead to acute transformation
• Retroviruses that can lead to acute transformation contain viral oncogenes (v-onc)
Retroviruses that cause chronic transformation do so by
Retroviruses that cause chronic transformation do so by insertion/mutation through random integration into the genome of the host
Cellular oncogenes are required for
Cellular oncogenes are required for normal cell growth and differentiation
How do retroviruses cause onocogeneisis?
Retroviruses acquire cellular oncogenes (c-onc) during replication
These acquired c-onc become viral oncogenes (v-onc)
Viral oncogenes undergo mutations which usually removes the regulatory mechanisms
What do viral oncogenese lead to?
• Such a viral oncogene may lead to transformation of infected cells by acting as growth factors, receptors, intracellular signal transducers or intranuclear transcription factors
