Term
| Describe the SV40 promoter |
|
Definition
1. +TATA -initiation site
2. 2 72 bp enhancers which are position and orientation independent.
3. Enhancers bound by co-activators, which is bound by the mediator complex, which is bound by TRXN factors. |
|
|
Term
| What are 3 ways viruses ensure good transcription of their genome? |
|
Definition
1. Strong promoters.
2. High genome copy number.
3. Viral encoded transcriptional activators. |
|
|
Term
| What are 2 ways in which high viral genome copy number increase transcription efficiency? |
|
Definition
1. Increased substrate of transcription, and increased substrate=increased rate.
2. Increased ratio of genomes:repressor proteins "dilutes" out repressors. |
|
|
Term
| 3 basic modules of a transcriptional activator |
|
Definition
1. DNA binding domain
2. Dimerization domain (Leu zipper for example).
3. Activation domain associates with co-activators and mediators. |
|
|
Term
| How does HSV VP16 work to preferentially increase viral transcription? How about Adenovirus E1a? |
|
Definition
HSV VP16: Binds to viral DNA and recruits TFIIb.
Ad E1a : Binds viral DNA and recruits TFIId. |
|
|
Term
| What is the structure of the EBV Zta protein and what is its function? |
|
Definition
| Zta is a transcription factor with the following domains from C to N terminus: transactivation domain, DNA binding domain, coiled coil domain, basic leucine zipper domain. |
|
|
Term
| How does HSV VP16 increase transcription of viral genes? |
|
Definition
| Oct-1 is bound to viral DNA. VP16 binds to Hcf (host cell factor) and changes conformation. This complex binds to Oct-1 on the DNA. |
|
|
Term
| What are 3 models for the means by which VP16 activates transcription? |
|
Definition
1. Conformational activation of TFIID.
2. Formation of PIC.
3. Releaves nucleosomal repression and facilitates binding of TFIID to viral DNA. |
|
|
Term
| What are 2 ways in which Adenovirus L-E1A increase transcription? |
|
Definition
1. Initiation: TFIID targeted to viral promoter.
2. Elongation: SEC targeted to transcription elongation complex. |
|
|
Term
| How does the HIV-1 Tat protein increase transcription? |
|
Definition
1. Tat binds to TAR elements on nascent RNA. Tat recruits pTEFb. pTEFb phosphorylates NELF and DSIF. NELF falls off elongation complex and DSIF is changed from a neg elongation factor to a pos elongation factor by this phosphorylation.
2. Recruitment of SEC.
3. Recruits chromatin remodeling complex p300/Cbp to relieve nucleosomal repression. |
|
|
Term
| How do RNA viruses differ from DNA viruses in terms of transcription? |
|
Definition
| RNA viruses code for own polymerase and initiation factors. |
|
|
Term
| How are tRNAs loaded with amino acids? |
|
Definition
| 5'-CCA-3' at 3' end of tRNA is loaded with amino acid by appropriate tRNA synthetase. |
|
|
Term
| What are the 4 components of the PIC? (One component is a ternary complex of 3 molecules) |
|
Definition
| 1. 40S ribosomal subunit, eIF1A, eIF3, and the ternary complex of met-tRNA, eIF2, and GTP. |
|
|
Term
| Describe eukaryotic translation initiation (4 steps)? |
|
Definition
1. eIF4E binds 5' cap structure (7-meG linked to mRNA in 5'-5' linkage).
2. eIF3 of PIC binds eIF4E and brings PIC to mRNA.
3. At the cost of ATP, the PIC scans the transcript until an AUG is encountered.
4. Upon encountering of AUG, PIC hydrolyzes GTP and sheds many of its component proteins. |
|
|
Term
| What does the poly-A binding protein 1 do (Pab1p)? |
|
Definition
| Binds to eIF4 (which is on cap) and poly-A tail. This ensures only intact mRNA is translated. |
|
|
Term
| What does the Bunyavirus N protein do? |
|
Definition
| Functions as surrogate eIF4F (no need for eIF4A, G, or E). |
|
|
Term
| Do some viruses use non-Met initiation codons? |
|
Definition
|
|
Term
| How is translation initiated in HCV? |
|
Definition
| There is a tertiary RNA structure in the viral genome called the IRES, or internal ribosome entry site. PIC binds to this structure. |
|
|
Term
| Do all viral proteins begin with Met like eukaryotic proteins? |
|
Definition
| No, some viral proteins begin with Glu, Pro, or Ala. |
|
|
Term
| How is it possible that some viral translation begins without an initiator tRNA (and thus forms proteins with non Met starting AAs)? |
|
Definition
| Viral mRNA may contain tRNA like structures. |
|
|
Term
| How do HAV, HCV, and Polioviruses initiate translation at their IRES? |
|
Definition
Hep A: requires only a limited number of initiation factors.
Hep C: 40S Rib binds directly to IRES
Poliovirus: PIC binds IRES via eIF4G which it cleaves. |
|
|
Term
| What is an example of a virus that uses high genome copy number to increase transcription? |
|
Definition
| SV40's late genes are not transcribed early in infection. The "late promoter" has 3 binding sites for the Initiator Binding Protein, which is a host protein. Early in infection, transcription of late genes is repressed, because genome copy number is low, and IBP is occupying all 3 binding sites on every copy of the genome. Late in infection, when replication ramps up and genome copy number increases, there becomes too many genomes for the cellular supply of IBP to bind all of them, and late genes are transcribed. |
|
|
