# ENA

:::info
> [name=Elif Nur Akın]
:::

**1. POLYOMA VIRUSES-SV40**

* Polyoma word derived from "many" poly and "oma" tumor
* SV40 is an abbreviation for simian vacuolating


| **genome type** | circular dsDNA |
| ----------------- | ---------------------- |
| **genome length** | 5,5 kbp |
| **diameter** | 45 nm |
| **diseases** | malignant tumors,. |
| **Shape** |Non-envelope icosahedral|
|**Polarity**|minus|
|**Hosts**|narrow host species|
|**Family**|Polyomaviridae|

---

**Examples of polyomaviruses:**
> -- Merkel cell polyomavirus (MCPyV),
> -- Trichodysplasia spinulosa polyomavirus (TSPyV),
> -- John Cunningham Polyomavirus (JCPyV)
> -- BK polyomavirus (BKPyV)

## Classification of Human Polyomaviruses

---
:::info
### Info Box
#### Merkel Cell Polyomavirus (MCV)
MCV was discovered in 2008 from Merkel cell carcinoma, a rare but aggressive form of skin cancer. Merkel cells are oval receptor cells found in the dermis of the skin that is associated with the sense of light touch discrimination. MCV is suspected to cause the majority of cases of Merkel cell carcinoma.
Most MCV viruses found in MCC tumors have at least two mutations that render the virus nontransmissible:
(1) The virus is integrated into the host genome in a monoclonal fashion and
(2) The viral T-antigen has truncation mutations that make T-antigen defective in initiating DNA replication.
Importantly, the integration into the host chromosome precedes the viral oncogenesis, a feature that is not obligatory in the virus life cycle.
:::
---

# Structure

- VP1 pentamers constitute the vertices of icosahedron, in which one molecule of VP2/VP3 underlies.
- VP2 is modified by *myristate* to facilitate interaction with host cell membrane.
- minichromosome: Nucleosome-like structures where inside the capsid. Viral DNA.
! The nucleosome-like structure of the SV40 genome is one of the features that makes SV40 suitable for a model for eukaryotic DNA replication.

:::success
myristate: fatty acid with 14 carbons
:::

---
* *regulatory region* consists of All regulatory elements, including the replication origin5 (Ori), promoter of early genes, and promoter of late genes, are clustered.
* The viral mRNAs are transcribed from both strands of the DNA genome, as two promoters lie in the opposite direction
:::success
**Figure**: Early and late genes are transcribed from respective promoters embedded into “regulatory region” in opposite direction. The origin of replication (Ori) is also positioned in the regulatory region. The ORFs for early genes (ie, small and large T-antigens) and late genes (ie, VP1, VP2, and VP3) are depicted by arrowed boxes. Polyadenylation sites for early and late mRNAs are denoted by A with an arrow, respectively.***
:::

---

---

# Life Cycle

---

# Attachment and Entry
* receptor for sv40 is GM1 **GANGLIOSIDE (GM1)**
* sv40 binds to GM1 via the galactose and sialic acid residues.
* caveolin/lipid raft-mediated endocytosis
* Membrane fusion: The lower pH inside the endosome induces conformational change of VP2 such that the now exposed N-terminus of VP2 attaches to the membrane via the modified myristate.

# Transcription
**1. Early Phase**
- Cellular RNA polymerase II
- Early mRNAs are translated into two early proteins: small T-antigen and large T-antigen.

---

**2. Switching to Late Phase**
- T-antigen binds to the T-antigen binding sites I to III. So switch from early to late phase is triggered.
- Late mRNAs are translated into three capsids proteins, VP1, VP2, and VP3.
- *T-antigen* regulates its own expression
- Finally transvaction starts.
:::success

#### Transvaction
It is the process that the engagement of T-antigen to the binding site III activates transcription from the late promoter,
:::

---

Graph: Shows the amount of RNA and DNA according to the phase. (T antigen is important)

---

**3. Late Phase**
- It begins with the initiation of viral DNA replication.
- late mRNAs are translated into three capsids proteins, VP1, VP2, and VP3

:::info
### T-antigen
It is sufficient to orchestrate the viral genome replication in infected cells. As a matter of fact, the diverse biochemical activities of T-antigen contribute to DNA synthesis:
(1) DNA helicase
(2) ATPase
(3) DNA polymerase
binding activity
Figure: Functional domains of large T-antigen
Figure: Initiation of Replication with T-antigen

:::

:::warning
## Question??
Intriguingly, although SV40 heavily relies on host DNA machinery, SV40 overrides the re-replication block so that it induces multiple rounds of cellular DNA synthesis, giving rise to polyploid cells. How does the T-antigen override the re-replication block?
:::

# Assembly and Release
The capsids of the virus are assembled in the nucleus and subsequently released extracellularly by cell lysis. The mechanism that causes cell lysis is still unknown.
VP4, a new viral capsid protein, was recently discovered. It shares the C-terminus with VP2 and VP3 and is translated from the third AUG codon of the VP2 ORF.Importantly, VP4 was shown to exert “viroporin” function, which induces pore formation in the membrane. It is VP4 that triggers cell lysis by disrupting the cell membrane.

---
:::info
## info box
###
Polyomaviruses have served as a model for molecular oncology as well as eukaryotic molecular biology. A payoff was the discovery of p53 and Rb protein as tumor suppressor gene products, in which their tumor suppressor functions are suppressed by T-antigen via a protein—protein interaction. Until recent discoveries of human polyomaviruses, such as BK virus and JC virus, the research on polyomaviruses served as a model, and seemed to be unrelated to human diseases. More recently, quite a few human polyomaviruses, including MCV, were discovered by the advent of new sequencing technology termed next generation sequencing. In particular, MCV has drawn a lot of attention, as it is clearly found to be associated with MCC, an aggressive form of skin cancer. Knowledge accumulated from studies on animal polyomaviruses during the 1970s and 1980s now serves as a keystone for the investigation of human polyomaviruses.
:::

---
# Conclusion
* Polyomavirus: Polyomavirus possess a small circular DNA genome (B5.3 kb in size).
* SV40 genome: SV40, the prototype of polyomavirus, infects lytically permissive monkey cells but transforms nonpermissive rodent cells.
* Human polyomavirus: MCV is found associated with MCC, an aggressive form of skin cancer.
* Virion structure: Nonenveloped capsid structure, inside which the viral DNA genome is found in association with histone molecules.
* Genome replication: The viral replication heavily relies on host DNA replication machinery. T-antigen is the only viral protein essential for viral genome replication.
* Host effect: SV40 infection leads to tumor formation in rodent cells. The binding ability of T-antigen to p53 and Rb protein is critical for tumorigenesis.
# Further Readings

**[1]** Liu, Wei; You, Jianxin (2020). Molecular Mechanisms of Merkel Cell Polyomavirus Transformation and Replication. Annual Review of Virology, 7(1), annurev-virology-011720-121757–. doi:10.1146/annurev-virology-011720-121757
**[2]** Harms, Paul W.; Harms, Kelly L.; Moore, Patrick S.; DeCaprio, James A.; Nghiem, Paul; Wong, Michael K. K.; Brownell, Isaac (2018). The biology and treatment of Merkel cell carcinoma: current understanding and research priorities. Nature Reviews Clinical Oncology, (), –. doi:10.1038/s41571-018-0103-2
**[3]** Prado, JC; Monezi, TA; Amorim, AT; Lino, V; Paladino, A; Boccardo, E (2018). Human polyomaviruses and cancer: an overview. Clinics, 73(Suppl 1), –. doi:10.6061/clinics/2018/e558s